[1] "ofn"        "-oTSTAD-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/STAD-TP/15090008/STAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STAD-TP/15197121/transformed.cor.cli.txt"

nPatients in clinical file=438, in cluster file=289, common to both=289
[1] "Reduce the number of clustering variables from 741 to 739."
[1] 739 289
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           137            152 
  TP53 MUTATED TP53 WILD-TYPE 
           137            152 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              90              199 
  ARID1A MUTATED ARID1A WILD-TYPE 
              90              199 
[1] "RNF43 MUTATION ANALYSIS"
[1] 3
  RNF43 MUTATED RNF43 WILD-TYPE 
             49             240 
  RNF43 MUTATED RNF43 WILD-TYPE 
             49             240 
[1] "LARP4B MUTATION ANALYSIS"
[1] 3
  LARP4B MUTATED LARP4B WILD-TYPE 
              27              262 
  LARP4B MUTATED LARP4B WILD-TYPE 
              27              262 
[1] "XYLT2 MUTATION ANALYSIS"
[1] 3
  XYLT2 MUTATED XYLT2 WILD-TYPE 
             32             257 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
             32             257 
[1] "B2M MUTATION ANALYSIS"
[1] 3
  B2M MUTATED B2M WILD-TYPE 
           17           272 
  B2M MUTATED B2M WILD-TYPE 
           17           272 
[1] "BZRAP1 MUTATION ANALYSIS"
[1] 3
  BZRAP1 MUTATED BZRAP1 WILD-TYPE 
              46              243 
  BZRAP1 MUTATED BZRAP1 WILD-TYPE 
              46              243 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            28            261 
  KRAS MUTATED KRAS WILD-TYPE 
            28            261 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            65            224 
  MLL2 MUTATED MLL2 WILD-TYPE 
            65            224 
[1] "GNG12 MUTATION ANALYSIS"
[1] 3
  GNG12 MUTATED GNG12 WILD-TYPE 
             11             278 
  GNG12 MUTATED GNG12 WILD-TYPE 
             11             278 
[1] "LMAN1 MUTATION ANALYSIS"
[1] 3
  LMAN1 MUTATED LMAN1 WILD-TYPE 
             22             267 
  LMAN1 MUTATED LMAN1 WILD-TYPE 
             22             267 
[1] "CDH1 MUTATION ANALYSIS"
[1] 3
  CDH1 MUTATED CDH1 WILD-TYPE 
            29            260 
  CDH1 MUTATED CDH1 WILD-TYPE 
            29            260 
[1] "PLEKHA6 MUTATION ANALYSIS"
[1] 3
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
               20               269 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
               20               269 
[1] "RHOA MUTATION ANALYSIS"
[1] 3
  RHOA MUTATED RHOA WILD-TYPE 
            16            273 
  RHOA MUTATED RHOA WILD-TYPE 
            16            273 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             24             265 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             24             265 
[1] "MTG1 MUTATION ANALYSIS"
[1] 3
  MTG1 MUTATED MTG1 WILD-TYPE 
             9            280 
  MTG1 MUTATED MTG1 WILD-TYPE 
             9            280 
[1] "KLF3 MUTATION ANALYSIS"
[1] 3
  KLF3 MUTATED KLF3 WILD-TYPE 
            19            270 
  KLF3 MUTATED KLF3 WILD-TYPE 
            19            270 
[1] "CTCF MUTATION ANALYSIS"
[1] 3
  CTCF MUTATED CTCF WILD-TYPE 
            18            271 
  CTCF MUTATED CTCF WILD-TYPE 
            18            271 
[1] "ZBTB20 MUTATION ANALYSIS"
[1] 3
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              28              261 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              28              261 
[1] "GAS6 MUTATION ANALYSIS"
[1] 3
  GAS6 MUTATED GAS6 WILD-TYPE 
            16            273 
  GAS6 MUTATED GAS6 WILD-TYPE 
            16            273 
[1] "ATP6V1B1 MUTATION ANALYSIS"
[1] 3
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                20                269 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                20                269 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            23            266 
  PTEN MUTATED PTEN WILD-TYPE 
            23            266 
[1] "HLA-A MUTATION ANALYSIS"
[1] 3
  HLA-A MUTATED HLA-A WILD-TYPE 
             15             274 
  HLA-A MUTATED HLA-A WILD-TYPE 
             15             274 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             27             262 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             27             262 
[1] "MVK MUTATION ANALYSIS"
[1] 3
  MVK MUTATED MVK WILD-TYPE 
           13           276 
  MVK MUTATED MVK WILD-TYPE 
           13           276 
[1] "FRMD4A MUTATION ANALYSIS"
[1] 3
  FRMD4A MUTATED FRMD4A WILD-TYPE 
              18              271 
  FRMD4A MUTATED FRMD4A WILD-TYPE 
              18              271 
[1] "MBD6 MUTATION ANALYSIS"
[1] 3
  MBD6 MUTATED MBD6 WILD-TYPE 
            23            266 
  MBD6 MUTATED MBD6 WILD-TYPE 
            23            266 
[1] "ZBTB7C MUTATION ANALYSIS"
[1] 3
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
              15              274 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
              15              274 
[1] "JARID2 MUTATION ANALYSIS"
[1] 3
  JARID2 MUTATED JARID2 WILD-TYPE 
              28              261 
  JARID2 MUTATED JARID2 WILD-TYPE 
              28              261 
[1] "PAX6 MUTATION ANALYSIS"
[1] 3
  PAX6 MUTATED PAX6 WILD-TYPE 
            18            271 
  PAX6 MUTATED PAX6 WILD-TYPE 
            18            271 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              57              232 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              57              232 
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
           42           247 
  APC MUTATED APC WILD-TYPE 
           42           247 
[1] "NLK MUTATION ANALYSIS"
[1] 3
  NLK MUTATED NLK WILD-TYPE 
           12           277 
  NLK MUTATED NLK WILD-TYPE 
           12           277 
[1] "POLM MUTATION ANALYSIS"
[1] 3
  POLM MUTATED POLM WILD-TYPE 
            10            279 
  POLM MUTATED POLM WILD-TYPE 
            10            279 
[1] "TMEM41A MUTATION ANALYSIS"
[1] 3
  TMEM41A MUTATED TMEM41A WILD-TYPE 
                6               283 
  TMEM41A MUTATED TMEM41A WILD-TYPE 
                6               283 
[1] "WBP1 MUTATION ANALYSIS"
[1] 3
  WBP1 MUTATED WBP1 WILD-TYPE 
             8            281 
  WBP1 MUTATED WBP1 WILD-TYPE 
             8            281 
[1] "KIAA0182 MUTATION ANALYSIS"
[1] 3
  KIAA0182 MUTATED KIAA0182 WILD-TYPE 
                20                269 
  KIAA0182 MUTATED KIAA0182 WILD-TYPE 
                20                269 
[1] "SNAPC2 MUTATION ANALYSIS"
[1] 3
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
              11              278 
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
              11              278 
[1] "C1QTNF5 MUTATION ANALYSIS"
[1] 3
  C1QTNF5 MUTATED C1QTNF5 WILD-TYPE 
                8               281 
  C1QTNF5 MUTATED C1QTNF5 WILD-TYPE 
                8               281 
[1] "AOC3 MUTATION ANALYSIS"
[1] 3
  AOC3 MUTATED AOC3 WILD-TYPE 
            13            276 
  AOC3 MUTATED AOC3 WILD-TYPE 
            13            276 
[1] "CIC MUTATION ANALYSIS"
[1] 3
  CIC MUTATED CIC WILD-TYPE 
           26           263 
  CIC MUTATED CIC WILD-TYPE 
           26           263 
[1] "HLA-B MUTATION ANALYSIS"
[1] 3
  HLA-B MUTATED HLA-B WILD-TYPE 
             14             275 
  HLA-B MUTATED HLA-B WILD-TYPE 
             14             275 
[1] "CD4 MUTATION ANALYSIS"
[1] 3
  CD4 MUTATED CD4 WILD-TYPE 
           15           274 
  CD4 MUTATED CD4 WILD-TYPE 
           15           274 
[1] "ZMYM4 MUTATION ANALYSIS"
[1] 3
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
             17             272 
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
             17             272 
[1] "ZNF43 MUTATION ANALYSIS"
[1] 3
  ZNF43 MUTATED ZNF43 WILD-TYPE 
             34             255 
  ZNF43 MUTATED ZNF43 WILD-TYPE 
             34             255 
[1] "NT5M MUTATION ANALYSIS"
[1] 3
  NT5M MUTATED NT5M WILD-TYPE 
             5            284 
  NT5M MUTATED NT5M WILD-TYPE 
             5            284 
[1] "GBP7 MUTATION ANALYSIS"
[1] 3
  GBP7 MUTATED GBP7 WILD-TYPE 
             9            280 
  GBP7 MUTATED GBP7 WILD-TYPE 
             9            280 
[1] "BCL9L MUTATION ANALYSIS"
[1] 3
  BCL9L MUTATED BCL9L WILD-TYPE 
             24             265 
  BCL9L MUTATED BCL9L WILD-TYPE 
             24             265 
[1] "TBX4 MUTATION ANALYSIS"
[1] 3
  TBX4 MUTATED TBX4 WILD-TYPE 
            11            278 
  TBX4 MUTATED TBX4 WILD-TYPE 
            11            278 
[1] "C7ORF50 MUTATION ANALYSIS"
[1] 3
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
               10               279 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
               10               279 
[1] "DDC MUTATION ANALYSIS"
[1] 3
  DDC MUTATED DDC WILD-TYPE 
            9           280 
  DDC MUTATED DDC WILD-TYPE 
            9           280 
[1] "ADAM28 MUTATION ANALYSIS"
[1] 3
  ADAM28 MUTATED ADAM28 WILD-TYPE 
              14              275 
  ADAM28 MUTATED ADAM28 WILD-TYPE 
              14              275 
[1] "IWS1 MUTATION ANALYSIS"
[1] 3
  IWS1 MUTATED IWS1 WILD-TYPE 
            12            277 
  IWS1 MUTATED IWS1 WILD-TYPE 
            12            277 
[1] "MUC6 MUTATION ANALYSIS"
[1] 3
  MUC6 MUTATED MUC6 WILD-TYPE 
            34            255 
  MUC6 MUTATED MUC6 WILD-TYPE 
            34            255 
[1] "GXYLT1 MUTATION ANALYSIS"
[1] 3
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
              12              277 
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
              12              277 
[1] "HLA-C MUTATION ANALYSIS"
[1] 3
  HLA-C MUTATED HLA-C WILD-TYPE 
             13             276 
  HLA-C MUTATED HLA-C WILD-TYPE 
             13             276 
[1] "PRSS36 MUTATION ANALYSIS"
[1] 3
  PRSS36 MUTATED PRSS36 WILD-TYPE 
              11              278 
  PRSS36 MUTATED PRSS36 WILD-TYPE 
              11              278 
[1] "ZFHX4 MUTATION ANALYSIS"
[1] 3
  ZFHX4 MUTATED ZFHX4 WILD-TYPE 
             53             236 
  ZFHX4 MUTATED ZFHX4 WILD-TYPE 
             53             236 
[1] "C6ORF89 MUTATION ANALYSIS"
[1] 3
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
                9               280 
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
                9               280 
[1] "SLC16A6 MUTATION ANALYSIS"
[1] 3
  SLC16A6 MUTATED SLC16A6 WILD-TYPE 
                7               282 
  SLC16A6 MUTATED SLC16A6 WILD-TYPE 
                7               282 
[1] "PAFAH1B1 MUTATION ANALYSIS"
[1] 3
  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE 
                12                277 
  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE 
                12                277 
[1] "WDR5 MUTATION ANALYSIS"
[1] 3
  WDR5 MUTATED WDR5 WILD-TYPE 
             7            282 
  WDR5 MUTATED WDR5 WILD-TYPE 
             7            282 
[1] "DDX6 MUTATION ANALYSIS"
[1] 3
  DDX6 MUTATED DDX6 WILD-TYPE 
            15            274 
  DDX6 MUTATED DDX6 WILD-TYPE 
            15            274 
[1] "C9ORF131 MUTATION ANALYSIS"
[1] 3
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                13                276 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                13                276 
[1] "PLOD3 MUTATION ANALYSIS"
[1] 3
  PLOD3 MUTATED PLOD3 WILD-TYPE 
             14             275 
  PLOD3 MUTATED PLOD3 WILD-TYPE 
             14             275 
[1] "ZNF878 MUTATION ANALYSIS"
[1] 3
  ZNF878 MUTATED ZNF878 WILD-TYPE 
              12              277 
  ZNF878 MUTATED ZNF878 WILD-TYPE 
              12              277 
[1] "SPG20 MUTATION ANALYSIS"
[1] 3
  SPG20 MUTATED SPG20 WILD-TYPE 
             21             268 
  SPG20 MUTATED SPG20 WILD-TYPE 
             21             268 
[1] "C14ORF43 MUTATION ANALYSIS"
[1] 3
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                20                269 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                20                269 
[1] "FLNB MUTATION ANALYSIS"
[1] 3
  FLNB MUTATED FLNB WILD-TYPE 
            24            265 
  FLNB MUTATED FLNB WILD-TYPE 
            24            265 
[1] "GLI1 MUTATION ANALYSIS"
[1] 3
  GLI1 MUTATED GLI1 WILD-TYPE 
            17            272 
  GLI1 MUTATED GLI1 WILD-TYPE 
            17            272 
[1] "PLAGL2 MUTATION ANALYSIS"
[1] 3
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               7              282 
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               7              282 
[1] "WNT16 MUTATION ANALYSIS"
[1] 3
  WNT16 MUTATED WNT16 WILD-TYPE 
             13             276 
  WNT16 MUTATED WNT16 WILD-TYPE 
             13             276 
[1] "IRF2 MUTATION ANALYSIS"
[1] 3
  IRF2 MUTATED IRF2 WILD-TYPE 
            14            275 
  IRF2 MUTATED IRF2 WILD-TYPE 
            14            275 
[1] "SPTY2D1 MUTATION ANALYSIS"
[1] 3
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
               15               274 
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
               15               274 
[1] "GPSM3 MUTATION ANALYSIS"
[1] 3
  GPSM3 MUTATED GPSM3 WILD-TYPE 
             12             277 
  GPSM3 MUTATED GPSM3 WILD-TYPE 
             12             277 
[1] "STAT2 MUTATION ANALYSIS"
[1] 3
  STAT2 MUTATED STAT2 WILD-TYPE 
             10             279 
  STAT2 MUTATED STAT2 WILD-TYPE 
             10             279 
[1] "PRRG3 MUTATION ANALYSIS"
[1] 3
  PRRG3 MUTATED PRRG3 WILD-TYPE 
              8             281 
  PRRG3 MUTATED PRRG3 WILD-TYPE 
              8             281 
[1] "TP53BP2 MUTATION ANALYSIS"
[1] 3
  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
               14               275 
  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
               14               275 
[1] "BCOR MUTATION ANALYSIS"
[1] 3
  BCOR MUTATED BCOR WILD-TYPE 
            21            268 
  BCOR MUTATED BCOR WILD-TYPE 
            21            268 
[1] "BCORL1 MUTATION ANALYSIS"
[1] 3
  BCORL1 MUTATED BCORL1 WILD-TYPE 
              20              269 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
              20              269 
[1] "RALGAPB MUTATION ANALYSIS"
[1] 3
  RALGAPB MUTATED RALGAPB WILD-TYPE 
               18               271 
  RALGAPB MUTATED RALGAPB WILD-TYPE 
               18               271 
[1] "BAX MUTATION ANALYSIS"
[1] 3
  BAX MUTATED BAX WILD-TYPE 
            6           283 
  BAX MUTATED BAX WILD-TYPE 
            6           283 
[1] "ATP2A1 MUTATION ANALYSIS"
[1] 3
  ATP2A1 MUTATED ATP2A1 WILD-TYPE 
              15              274 
  ATP2A1 MUTATED ATP2A1 WILD-TYPE 
              15              274 
[1] "CCDC88A MUTATION ANALYSIS"
[1] 3
  CCDC88A MUTATED CCDC88A WILD-TYPE 
               20               269 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
               20               269 
[1] "BTBD7 MUTATION ANALYSIS"
[1] 3
  BTBD7 MUTATED BTBD7 WILD-TYPE 
             18             271 
  BTBD7 MUTATED BTBD7 WILD-TYPE 
             18             271 
[1] "ZC3H18 MUTATION ANALYSIS"
[1] 3
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
              18              271 
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
              18              271 
[1] "SLC10A6 MUTATION ANALYSIS"
[1] 3
  SLC10A6 MUTATED SLC10A6 WILD-TYPE 
                8               281 
  SLC10A6 MUTATED SLC10A6 WILD-TYPE 
                8               281 
[1] "CR2 MUTATION ANALYSIS"
[1] 3
  CR2 MUTATED CR2 WILD-TYPE 
           20           269 
  CR2 MUTATED CR2 WILD-TYPE 
           20           269 
[1] "ARHGAP5 MUTATION ANALYSIS"
[1] 3
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
               17               272 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
               17               272 
[1] "RASA1 MUTATION ANALYSIS"
[1] 3
  RASA1 MUTATED RASA1 WILD-TYPE 
             17             272 
  RASA1 MUTATED RASA1 WILD-TYPE 
             17             272 
[1] "ZNF48 MUTATION ANALYSIS"
[1] 3
  ZNF48 MUTATED ZNF48 WILD-TYPE 
             10             279 
  ZNF48 MUTATED ZNF48 WILD-TYPE 
             10             279 
[1] "ADAM30 MUTATION ANALYSIS"
[1] 3
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              14              275 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              14              275 
[1] "SETDB2 MUTATION ANALYSIS"
[1] 3
  SETDB2 MUTATED SETDB2 WILD-TYPE 
              10              279 
  SETDB2 MUTATED SETDB2 WILD-TYPE 
              10              279 
[1] "INPPL1 MUTATION ANALYSIS"
[1] 3
  INPPL1 MUTATED INPPL1 WILD-TYPE 
              22              267 
  INPPL1 MUTATED INPPL1 WILD-TYPE 
              22              267 
[1] "CTNND1 MUTATION ANALYSIS"
[1] 3
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              19              270 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              19              270 
[1] "TFE3 MUTATION ANALYSIS"
[1] 3
  TFE3 MUTATED TFE3 WILD-TYPE 
             8            281 
  TFE3 MUTATED TFE3 WILD-TYPE 
             8            281 
[1] "SERPINI1 MUTATION ANALYSIS"
[1] 3
  SERPINI1 MUTATED SERPINI1 WILD-TYPE 
                 8                281 
  SERPINI1 MUTATED SERPINI1 WILD-TYPE 
                 8                281 
[1] "SOX7 MUTATION ANALYSIS"
[1] 3
  SOX7 MUTATED SOX7 WILD-TYPE 
            15            274 
  SOX7 MUTATED SOX7 WILD-TYPE 
            15            274 
[1] "LEMD1 MUTATION ANALYSIS"
[1] 3
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              4             285 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              4             285 
[1] "ARID1B MUTATION ANALYSIS"
[1] 3
  ARID1B MUTATED ARID1B WILD-TYPE 
              27              262 
  ARID1B MUTATED ARID1B WILD-TYPE 
              27              262 
[1] "PGM5 MUTATION ANALYSIS"
[1] 3
  PGM5 MUTATED PGM5 WILD-TYPE 
            25            264 
  PGM5 MUTATED PGM5 WILD-TYPE 
            25            264 
[1] "FHOD3 MUTATION ANALYSIS"
[1] 3
  FHOD3 MUTATED FHOD3 WILD-TYPE 
             26             263 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
             26             263 
[1] "CABP5 MUTATION ANALYSIS"
[1] 3
  CABP5 MUTATED CABP5 WILD-TYPE 
              5             284 
  CABP5 MUTATED CABP5 WILD-TYPE 
              5             284 
[1] "TTF1 MUTATION ANALYSIS"
[1] 3
  TTF1 MUTATED TTF1 WILD-TYPE 
            14            275 
  TTF1 MUTATED TTF1 WILD-TYPE 
            14            275 
[1] "PHACTR4 MUTATION ANALYSIS"
[1] 3
  PHACTR4 MUTATED PHACTR4 WILD-TYPE 
                8               281 
  PHACTR4 MUTATED PHACTR4 WILD-TYPE 
                8               281 
[1] "RBM43 MUTATION ANALYSIS"
[1] 3
  RBM43 MUTATED RBM43 WILD-TYPE 
              9             280 
  RBM43 MUTATED RBM43 WILD-TYPE 
              9             280 
[1] "CDC25C MUTATION ANALYSIS"
[1] 3
  CDC25C MUTATED CDC25C WILD-TYPE 
              13              276 
  CDC25C MUTATED CDC25C WILD-TYPE 
              13              276 
[1] "GPR161 MUTATION ANALYSIS"
[1] 3
  GPR161 MUTATED GPR161 WILD-TYPE 
              12              277 
  GPR161 MUTATED GPR161 WILD-TYPE 
              12              277 
[1] "SVIL MUTATION ANALYSIS"
[1] 3
  SVIL MUTATED SVIL WILD-TYPE 
            26            263 
  SVIL MUTATED SVIL WILD-TYPE 
            26            263 
[1] "PMEPA1 MUTATION ANALYSIS"
[1] 3
  PMEPA1 MUTATED PMEPA1 WILD-TYPE 
               6              283 
  PMEPA1 MUTATED PMEPA1 WILD-TYPE 
               6              283 
[1] "FILIP1L MUTATION ANALYSIS"
[1] 3
  FILIP1L MUTATED FILIP1L WILD-TYPE 
               17               272 
  FILIP1L MUTATED FILIP1L WILD-TYPE 
               17               272 
[1] "CTSC MUTATION ANALYSIS"
[1] 3
  CTSC MUTATED CTSC WILD-TYPE 
            10            279 
  CTSC MUTATED CTSC WILD-TYPE 
            10            279 
[1] "PAMR1 MUTATION ANALYSIS"
[1] 3
  PAMR1 MUTATED PAMR1 WILD-TYPE 
             17             272 
  PAMR1 MUTATED PAMR1 WILD-TYPE 
             17             272 
[1] "USP21 MUTATION ANALYSIS"
[1] 3
  USP21 MUTATED USP21 WILD-TYPE 
             13             276 
  USP21 MUTATED USP21 WILD-TYPE 
             13             276 
[1] "PAX2 MUTATION ANALYSIS"
[1] 3
  PAX2 MUTATED PAX2 WILD-TYPE 
             8            281 
  PAX2 MUTATED PAX2 WILD-TYPE 
             8            281 
[1] "ZFHX3 MUTATION ANALYSIS"
[1] 3
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             38             251 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             38             251 
[1] "EPHA2 MUTATION ANALYSIS"
[1] 3
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             23             266 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             23             266 
[1] "PREPL MUTATION ANALYSIS"
[1] 3
  PREPL MUTATED PREPL WILD-TYPE 
             22             267 
  PREPL MUTATED PREPL WILD-TYPE 
             22             267 
[1] "RGL2 MUTATION ANALYSIS"
[1] 3
  RGL2 MUTATED RGL2 WILD-TYPE 
            12            277 
  RGL2 MUTATED RGL2 WILD-TYPE 
            12            277 
[1] "ATP6V1C2 MUTATION ANALYSIS"
[1] 3
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
                12                277 
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
                12                277 
[1] "CDC14A MUTATION ANALYSIS"
[1] 3
  CDC14A MUTATED CDC14A WILD-TYPE 
              15              274 
  CDC14A MUTATED CDC14A WILD-TYPE 
              15              274 
[1] "DDX17 MUTATION ANALYSIS"
[1] 3
  DDX17 MUTATED DDX17 WILD-TYPE 
             13             276 
  DDX17 MUTATED DDX17 WILD-TYPE 
             13             276 
[1] "C19ORF40 MUTATION ANALYSIS"
[1] 3
  C19ORF40 MUTATED C19ORF40 WILD-TYPE 
                 6                283 
  C19ORF40 MUTATED C19ORF40 WILD-TYPE 
                 6                283 
[1] "ABCC4 MUTATION ANALYSIS"
[1] 3
  ABCC4 MUTATED ABCC4 WILD-TYPE 
             17             272 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
             17             272 
[1] "ZFC3H1 MUTATION ANALYSIS"
[1] 3
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
              15              274 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
              15              274 
[1] "ZKSCAN5 MUTATION ANALYSIS"
[1] 3
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
                9               280 
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
                9               280 
[1] "RABGAP1 MUTATION ANALYSIS"
[1] 3
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
               20               269 
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
               20               269 
[1] "RNF145 MUTATION ANALYSIS"
[1] 3
  RNF145 MUTATED RNF145 WILD-TYPE 
              18              271 
  RNF145 MUTATED RNF145 WILD-TYPE 
              18              271 
[1] "SNAPC1 MUTATION ANALYSIS"
[1] 3
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
               7              282 
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
               7              282 
[1] "CCDC153 MUTATION ANALYSIS"
[1] 3
  CCDC153 MUTATED CCDC153 WILD-TYPE 
                8               281 
  CCDC153 MUTATED CCDC153 WILD-TYPE 
                8               281 
[1] "OPTN MUTATION ANALYSIS"
[1] 3
  OPTN MUTATED OPTN WILD-TYPE 
             9            280 
  OPTN MUTATED OPTN WILD-TYPE 
             9            280 
[1] "PLEKHA5 MUTATION ANALYSIS"
[1] 3
  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
               15               274 
  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
               15               274 
[1] "SREBF2 MUTATION ANALYSIS"
[1] 3
  SREBF2 MUTATED SREBF2 WILD-TYPE 
              10              279 
  SREBF2 MUTATED SREBF2 WILD-TYPE 
              10              279 
[1] "FASTKD1 MUTATION ANALYSIS"
[1] 3
  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
               11               278 
  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
               11               278 
[1] "MAP7D1 MUTATION ANALYSIS"
[1] 3
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
              12              277 
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
              12              277 
[1] "SLC27A3 MUTATION ANALYSIS"
[1] 3
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
                9               280 
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
                9               280 
[1] "INF2 MUTATION ANALYSIS"
[1] 3
  INF2 MUTATED INF2 WILD-TYPE 
            11            278 
  INF2 MUTATED INF2 WILD-TYPE 
            11            278 
[1] "C13ORF33 MUTATION ANALYSIS"
[1] 3
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
                 7                282 
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
                 7                282 
[1] "AKAP13 MUTATION ANALYSIS"
[1] 3
  AKAP13 MUTATED AKAP13 WILD-TYPE 
              28              261 
  AKAP13 MUTATED AKAP13 WILD-TYPE 
              28              261 
[1] "DYRK4 MUTATION ANALYSIS"
[1] 3
  DYRK4 MUTATED DYRK4 WILD-TYPE 
              9             280 
  DYRK4 MUTATED DYRK4 WILD-TYPE 
              9             280 
[1] "FOXN3 MUTATION ANALYSIS"
[1] 3
  FOXN3 MUTATED FOXN3 WILD-TYPE 
              8             281 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
              8             281 
[1] "SLC16A1 MUTATION ANALYSIS"
[1] 3
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                7               282 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                7               282 
[1] "TNFRSF9 MUTATION ANALYSIS"
[1] 3
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
               10               279 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
               10               279 
[1] "RHOQ MUTATION ANALYSIS"
[1] 3
  RHOQ MUTATED RHOQ WILD-TYPE 
             5            284 
  RHOQ MUTATED RHOQ WILD-TYPE 
             5            284 
[1] "PRPF40B MUTATION ANALYSIS"
[1] 3
  PRPF40B MUTATED PRPF40B WILD-TYPE 
               14               275 
  PRPF40B MUTATED PRPF40B WILD-TYPE 
               14               275 
[1] "STAT5B MUTATION ANALYSIS"
[1] 3
  STAT5B MUTATED STAT5B WILD-TYPE 
              12              277 
  STAT5B MUTATED STAT5B WILD-TYPE 
              12              277 
[1] "CFI MUTATION ANALYSIS"
[1] 3
  CFI MUTATED CFI WILD-TYPE 
           12           277 
  CFI MUTATED CFI WILD-TYPE 
           12           277 
[1] "FERMT2 MUTATION ANALYSIS"
[1] 3
  FERMT2 MUTATED FERMT2 WILD-TYPE 
               7              282 
  FERMT2 MUTATED FERMT2 WILD-TYPE 
               7              282 
[1] "ALDH3A1 MUTATION ANALYSIS"
[1] 3
  ALDH3A1 MUTATED ALDH3A1 WILD-TYPE 
               10               279 
  ALDH3A1 MUTATED ALDH3A1 WILD-TYPE 
               10               279 
[1] "GCC2 MUTATION ANALYSIS"
[1] 3
  GCC2 MUTATED GCC2 WILD-TYPE 
            10            279 
  GCC2 MUTATED GCC2 WILD-TYPE 
            10            279 
[1] "NOX5 MUTATION ANALYSIS"
[1] 3
  NOX5 MUTATED NOX5 WILD-TYPE 
            14            275 
  NOX5 MUTATED NOX5 WILD-TYPE 
            14            275 
[1] "KIF13A MUTATION ANALYSIS"
[1] 3
  KIF13A MUTATED KIF13A WILD-TYPE 
              20              269 
  KIF13A MUTATED KIF13A WILD-TYPE 
              20              269 
[1] "CR1L MUTATION ANALYSIS"
[1] 3
  CR1L MUTATED CR1L WILD-TYPE 
            11            278 
  CR1L MUTATED CR1L WILD-TYPE 
            11            278 
[1] "GALNTL1 MUTATION ANALYSIS"
[1] 3
  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
               10               279 
  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
               10               279 
[1] "SCLT1 MUTATION ANALYSIS"
[1] 3
  SCLT1 MUTATED SCLT1 WILD-TYPE 
             16             273 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
             16             273 
[1] "STAB1 MUTATION ANALYSIS"
[1] 3
  STAB1 MUTATED STAB1 WILD-TYPE 
             28             261 
  STAB1 MUTATED STAB1 WILD-TYPE 
             28             261 
[1] "TP53BP1 MUTATION ANALYSIS"
[1] 3
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
               16               273 
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
               16               273 
[1] "IFRD1 MUTATION ANALYSIS"
[1] 3
  IFRD1 MUTATED IFRD1 WILD-TYPE 
              8             281 
  IFRD1 MUTATED IFRD1 WILD-TYPE 
              8             281 
[1] "SF3B2 MUTATION ANALYSIS"
[1] 3
  SF3B2 MUTATED SF3B2 WILD-TYPE 
             17             272 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
             17             272 
[1] "FAM151A MUTATION ANALYSIS"
[1] 3
  FAM151A MUTATED FAM151A WILD-TYPE 
                9               280 
  FAM151A MUTATED FAM151A WILD-TYPE 
                9               280 
[1] "FHDC1 MUTATION ANALYSIS"
[1] 3
  FHDC1 MUTATED FHDC1 WILD-TYPE 
             15             274 
  FHDC1 MUTATED FHDC1 WILD-TYPE 
             15             274 
[1] "FAM46D MUTATION ANALYSIS"
[1] 3
  FAM46D MUTATED FAM46D WILD-TYPE 
               9              280 
  FAM46D MUTATED FAM46D WILD-TYPE 
               9              280 
[1] "TLE2 MUTATION ANALYSIS"
[1] 3
  TLE2 MUTATED TLE2 WILD-TYPE 
            19            270 
  TLE2 MUTATED TLE2 WILD-TYPE 
            19            270 
[1] "HOXD8 MUTATION ANALYSIS"
[1] 3
  HOXD8 MUTATED HOXD8 WILD-TYPE 
              7             282 
  HOXD8 MUTATED HOXD8 WILD-TYPE 
              7             282 
[1] "ZIM3 MUTATION ANALYSIS"
[1] 3
  ZIM3 MUTATED ZIM3 WILD-TYPE 
            10            279 
  ZIM3 MUTATED ZIM3 WILD-TYPE 
            10            279 
[1] "DDX60 MUTATION ANALYSIS"
[1] 3
  DDX60 MUTATED DDX60 WILD-TYPE 
             10             279 
  DDX60 MUTATED DDX60 WILD-TYPE 
             10             279 
[1] "BEND3 MUTATION ANALYSIS"
[1] 3
  BEND3 MUTATED BEND3 WILD-TYPE 
             12             277 
  BEND3 MUTATED BEND3 WILD-TYPE 
             12             277 
[1] "EIF4G3 MUTATION ANALYSIS"
[1] 3
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
              15              274 
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
              15              274 
[1] "MFRP MUTATION ANALYSIS"
[1] 3
  MFRP MUTATED MFRP WILD-TYPE 
            11            278 
  MFRP MUTATED MFRP WILD-TYPE 
            11            278 
[1] "EIF5B MUTATION ANALYSIS"
[1] 3
  EIF5B MUTATED EIF5B WILD-TYPE 
             18             271 
  EIF5B MUTATED EIF5B WILD-TYPE 
             18             271 
[1] "FANCE MUTATION ANALYSIS"
[1] 3
  FANCE MUTATED FANCE WILD-TYPE 
              7             282 
  FANCE MUTATED FANCE WILD-TYPE 
              7             282 
[1] "PALB2 MUTATION ANALYSIS"
[1] 3
  PALB2 MUTATED PALB2 WILD-TYPE 
              9             280 
  PALB2 MUTATED PALB2 WILD-TYPE 
              9             280 
[1] "ISG20L2 MUTATION ANALYSIS"
[1] 3
  ISG20L2 MUTATED ISG20L2 WILD-TYPE 
                7               282 
  ISG20L2 MUTATED ISG20L2 WILD-TYPE 
                7               282 
[1] "ITGA6 MUTATION ANALYSIS"
[1] 3
  ITGA6 MUTATED ITGA6 WILD-TYPE 
              6             283 
  ITGA6 MUTATED ITGA6 WILD-TYPE 
              6             283 
[1] "SDAD1 MUTATION ANALYSIS"
[1] 3
  SDAD1 MUTATED SDAD1 WILD-TYPE 
              7             282 
  SDAD1 MUTATED SDAD1 WILD-TYPE 
              7             282 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              12              277 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              12              277 
[1] "RTN2 MUTATION ANALYSIS"
[1] 3
  RTN2 MUTATED RTN2 WILD-TYPE 
            11            278 
  RTN2 MUTATED RTN2 WILD-TYPE 
            11            278 
[1] "DNAJC1 MUTATION ANALYSIS"
[1] 3
  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
              11              278 
  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
              11              278 
[1] "TP53RK MUTATION ANALYSIS"
[1] 3
  TP53RK MUTATED TP53RK WILD-TYPE 
               6              283 
  TP53RK MUTATED TP53RK WILD-TYPE 
               6              283 
[1] "CCDC108 MUTATION ANALYSIS"
[1] 3
  CCDC108 MUTATED CCDC108 WILD-TYPE 
               25               264 
  CCDC108 MUTATED CCDC108 WILD-TYPE 
               25               264 
[1] "PYGO2 MUTATION ANALYSIS"
[1] 3
  PYGO2 MUTATED PYGO2 WILD-TYPE 
              7             282 
  PYGO2 MUTATED PYGO2 WILD-TYPE 
              7             282 
[1] "C1R MUTATION ANALYSIS"
[1] 3
  C1R MUTATED C1R WILD-TYPE 
            5           284 
  C1R MUTATED C1R WILD-TYPE 
            5           284 
[1] "FGGY MUTATION ANALYSIS"
[1] 3
  FGGY MUTATED FGGY WILD-TYPE 
             9            280 
  FGGY MUTATED FGGY WILD-TYPE 
             9            280 
[1] "MSH6 MUTATION ANALYSIS"
[1] 3
  MSH6 MUTATED MSH6 WILD-TYPE 
            19            270 
  MSH6 MUTATED MSH6 WILD-TYPE 
            19            270 
[1] "RNF111 MUTATION ANALYSIS"
[1] 3
  RNF111 MUTATED RNF111 WILD-TYPE 
              10              279 
  RNF111 MUTATED RNF111 WILD-TYPE 
              10              279 
[1] "ABCA6 MUTATION ANALYSIS"
[1] 3
  ABCA6 MUTATED ABCA6 WILD-TYPE 
             13             276 
  ABCA6 MUTATED ABCA6 WILD-TYPE 
             13             276 
[1] "WDR7 MUTATION ANALYSIS"
[1] 3
  WDR7 MUTATED WDR7 WILD-TYPE 
            17            272 
  WDR7 MUTATED WDR7 WILD-TYPE 
            17            272 
[1] "ZC3H13 MUTATION ANALYSIS"
[1] 3
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
              29              260 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
              29              260 
[1] "IGFBP7 MUTATION ANALYSIS"
[1] 3
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               4              285 
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               4              285 
[1] "HNF1B MUTATION ANALYSIS"
[1] 3
  HNF1B MUTATED HNF1B WILD-TYPE 
              6             283 
  HNF1B MUTATED HNF1B WILD-TYPE 
              6             283 
[1] "FAM113B MUTATION ANALYSIS"
[1] 3
  FAM113B MUTATED FAM113B WILD-TYPE 
               13               276 
  FAM113B MUTATED FAM113B WILD-TYPE 
               13               276 
[1] "RRS1 MUTATION ANALYSIS"
[1] 3
  RRS1 MUTATED RRS1 WILD-TYPE 
             7            282 
  RRS1 MUTATED RRS1 WILD-TYPE 
             7            282 
[1] "WNK4 MUTATION ANALYSIS"
[1] 3
  WNK4 MUTATED WNK4 WILD-TYPE 
            21            268 
  WNK4 MUTATED WNK4 WILD-TYPE 
            21            268 
[1] "RAD51AP2 MUTATION ANALYSIS"
[1] 3
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                12                277 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                12                277 
[1] "PIGB MUTATION ANALYSIS"
[1] 3
  PIGB MUTATED PIGB WILD-TYPE 
            10            279 
  PIGB MUTATED PIGB WILD-TYPE 
            10            279 
[1] "OGDH MUTATION ANALYSIS"
[1] 3
  OGDH MUTATED OGDH WILD-TYPE 
             9            280 
  OGDH MUTATED OGDH WILD-TYPE 
             9            280 
[1] "SERPINB12 MUTATION ANALYSIS"
[1] 3
  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
                  8                 281 
  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
                  8                 281 
[1] "HEXDC MUTATION ANALYSIS"
[1] 3
  HEXDC MUTATED HEXDC WILD-TYPE 
              5             284 
  HEXDC MUTATED HEXDC WILD-TYPE 
              5             284 
[1] "GATA3 MUTATION ANALYSIS"
[1] 3
  GATA3 MUTATED GATA3 WILD-TYPE 
             16             273 
  GATA3 MUTATED GATA3 WILD-TYPE 
             16             273 
[1] "GPR82 MUTATION ANALYSIS"
[1] 3
  GPR82 MUTATED GPR82 WILD-TYPE 
              9             280 
  GPR82 MUTATED GPR82 WILD-TYPE 
              9             280 
[1] "ELF3 MUTATION ANALYSIS"
[1] 3
  ELF3 MUTATED ELF3 WILD-TYPE 
            11            278 
  ELF3 MUTATED ELF3 WILD-TYPE 
            11            278 
[1] "EPHX1 MUTATION ANALYSIS"
[1] 3
  EPHX1 MUTATED EPHX1 WILD-TYPE 
              9             280 
  EPHX1 MUTATED EPHX1 WILD-TYPE 
              9             280 
[1] "CNBD1 MUTATION ANALYSIS"
[1] 3
  CNBD1 MUTATED CNBD1 WILD-TYPE 
             13             276 
  CNBD1 MUTATED CNBD1 WILD-TYPE 
             13             276 
[1] "SLC26A7 MUTATION ANALYSIS"
[1] 3
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
               14               275 
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
               14               275 
[1] "RCOR3 MUTATION ANALYSIS"
[1] 3
  RCOR3 MUTATED RCOR3 WILD-TYPE 
             12             277 
  RCOR3 MUTATED RCOR3 WILD-TYPE 
             12             277 
[1] "CASC3 MUTATION ANALYSIS"
[1] 3
  CASC3 MUTATED CASC3 WILD-TYPE 
              8             281 
  CASC3 MUTATED CASC3 WILD-TYPE 
              8             281 
[1] "ACVR1B MUTATION ANALYSIS"
[1] 3
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              11              278 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              11              278 
[1] "VPS13A MUTATION ANALYSIS"
[1] 3
  VPS13A MUTATED VPS13A WILD-TYPE 
              32              257 
  VPS13A MUTATED VPS13A WILD-TYPE 
              32              257 
[1] "PLA2G1B MUTATION ANALYSIS"
[1] 3
  PLA2G1B MUTATED PLA2G1B WILD-TYPE 
                4               285 
  PLA2G1B MUTATED PLA2G1B WILD-TYPE 
                4               285 
[1] "ZCCHC6 MUTATION ANALYSIS"
[1] 3
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
              13              276 
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
              13              276 
[1] "ITPR2 MUTATION ANALYSIS"
[1] 3
  ITPR2 MUTATED ITPR2 WILD-TYPE 
             25             264 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
             25             264 
[1] "MLL3 MUTATION ANALYSIS"
[1] 3
  MLL3 MUTATED MLL3 WILD-TYPE 
            45            244 
  MLL3 MUTATED MLL3 WILD-TYPE 
            45            244 
[1] "CDK12 MUTATION ANALYSIS"
[1] 3
  CDK12 MUTATED CDK12 WILD-TYPE 
             19             270 
  CDK12 MUTATED CDK12 WILD-TYPE 
             19             270 
[1] "PODN MUTATION ANALYSIS"
[1] 3
  PODN MUTATED PODN WILD-TYPE 
            13            276 
  PODN MUTATED PODN WILD-TYPE 
            13            276 
[1] "AKNAD1 MUTATION ANALYSIS"
[1] 3
  AKNAD1 MUTATED AKNAD1 WILD-TYPE 
              18              271 
  AKNAD1 MUTATED AKNAD1 WILD-TYPE 
              18              271 
[1] "ERBB3 MUTATION ANALYSIS"
[1] 3
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             31             258 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             31             258 
[1] "RSF1 MUTATION ANALYSIS"
[1] 3
  RSF1 MUTATED RSF1 WILD-TYPE 
            17            272 
  RSF1 MUTATED RSF1 WILD-TYPE 
            17            272 
[1] "KBTBD10 MUTATION ANALYSIS"
[1] 3
  KBTBD10 MUTATED KBTBD10 WILD-TYPE 
                7               282 
  KBTBD10 MUTATED KBTBD10 WILD-TYPE 
                7               282 
[1] "OSBP2 MUTATION ANALYSIS"
[1] 3
  OSBP2 MUTATED OSBP2 WILD-TYPE 
             11             278 
  OSBP2 MUTATED OSBP2 WILD-TYPE 
             11             278 
[1] "EBF3 MUTATION ANALYSIS"
[1] 3
  EBF3 MUTATED EBF3 WILD-TYPE 
            12            277 
  EBF3 MUTATED EBF3 WILD-TYPE 
            12            277 
[1] "LRP1 MUTATION ANALYSIS"
[1] 3
  LRP1 MUTATED LRP1 WILD-TYPE 
            30            259 
  LRP1 MUTATED LRP1 WILD-TYPE 
            30            259 
[1] "PHKB MUTATION ANALYSIS"
[1] 3
  PHKB MUTATED PHKB WILD-TYPE 
             7            282 
  PHKB MUTATED PHKB WILD-TYPE 
             7            282 
[1] "ABCB6 MUTATION ANALYSIS"
[1] 3
  ABCB6 MUTATED ABCB6 WILD-TYPE 
              8             281 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
              8             281 
[1] "DNAJC18 MUTATION ANALYSIS"
[1] 3
  DNAJC18 MUTATED DNAJC18 WILD-TYPE 
               13               276 
  DNAJC18 MUTATED DNAJC18 WILD-TYPE 
               13               276 
[1] "IDH2 MUTATION ANALYSIS"
[1] 3
  IDH2 MUTATED IDH2 WILD-TYPE 
             4            285 
  IDH2 MUTATED IDH2 WILD-TYPE 
             4            285 
[1] "DLGAP3 MUTATION ANALYSIS"
[1] 3
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
              16              273 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
              16              273 
[1] "KIAA0240 MUTATION ANALYSIS"
[1] 3
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                12                277 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                12                277 
[1] "ATXN2L MUTATION ANALYSIS"
[1] 3
  ATXN2L MUTATED ATXN2L WILD-TYPE 
              17              272 
  ATXN2L MUTATED ATXN2L WILD-TYPE 
              17              272 
[1] "ZNF608 MUTATION ANALYSIS"
[1] 3
  ZNF608 MUTATED ZNF608 WILD-TYPE 
              15              274 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
              15              274 
[1] "KIAA0406 MUTATION ANALYSIS"
[1] 3
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                12                277 
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                12                277 
[1] "KIAA1967 MUTATION ANALYSIS"
[1] 3
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
                17                272 
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
                17                272 
[1] "CBLL1 MUTATION ANALYSIS"
[1] 3
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              6             283 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              6             283 
[1] "TENC1 MUTATION ANALYSIS"
[1] 3
  TENC1 MUTATED TENC1 WILD-TYPE 
             11             278 
  TENC1 MUTATED TENC1 WILD-TYPE 
             11             278 
[1] "C1QA MUTATION ANALYSIS"
[1] 3
  C1QA MUTATED C1QA WILD-TYPE 
             5            284 
  C1QA MUTATED C1QA WILD-TYPE 
             5            284 
[1] "PLAU MUTATION ANALYSIS"
[1] 3
  PLAU MUTATED PLAU WILD-TYPE 
             7            282 
  PLAU MUTATED PLAU WILD-TYPE 
             7            282 
[1] "ALG10 MUTATION ANALYSIS"
[1] 3
  ALG10 MUTATED ALG10 WILD-TYPE 
             11             278 
  ALG10 MUTATED ALG10 WILD-TYPE 
             11             278 
[1] "DAO MUTATION ANALYSIS"
[1] 3
  DAO MUTATED DAO WILD-TYPE 
           11           278 
  DAO MUTATED DAO WILD-TYPE 
           11           278 
[1] "CDKL3 MUTATION ANALYSIS"
[1] 3
  CDKL3 MUTATED CDKL3 WILD-TYPE 
              7             282 
  CDKL3 MUTATED CDKL3 WILD-TYPE 
              7             282 
[1] "GLIPR1L2 MUTATION ANALYSIS"
[1] 3
  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE 
                10                279 
  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE 
                10                279 
[1] "FZD3 MUTATION ANALYSIS"
[1] 3
  FZD3 MUTATED FZD3 WILD-TYPE 
            10            279 
  FZD3 MUTATED FZD3 WILD-TYPE 
            10            279 
[1] "CETN3 MUTATION ANALYSIS"
[1] 3
  CETN3 MUTATED CETN3 WILD-TYPE 
              7             282 
  CETN3 MUTATED CETN3 WILD-TYPE 
              7             282 
[1] "PSME4 MUTATION ANALYSIS"
[1] 3
  PSME4 MUTATED PSME4 WILD-TYPE 
             35             254 
  PSME4 MUTATED PSME4 WILD-TYPE 
             35             254 
[1] "GNPNAT1 MUTATION ANALYSIS"
[1] 3
  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE 
                4               285 
  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE 
                4               285 
[1] "ZDHHC7 MUTATION ANALYSIS"
[1] 3
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
               6              283 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
               6              283 
[1] "PANK1 MUTATION ANALYSIS"
[1] 3
  PANK1 MUTATED PANK1 WILD-TYPE 
              8             281 
  PANK1 MUTATED PANK1 WILD-TYPE 
              8             281 
[1] "FAM116A MUTATION ANALYSIS"
[1] 3
  FAM116A MUTATED FAM116A WILD-TYPE 
                6               283 
  FAM116A MUTATED FAM116A WILD-TYPE 
                6               283 
[1] "C11ORF9 MUTATION ANALYSIS"
[1] 3
  C11ORF9 MUTATED C11ORF9 WILD-TYPE 
                8               281 
  C11ORF9 MUTATED C11ORF9 WILD-TYPE 
                8               281 
[1] "KIAA0195 MUTATION ANALYSIS"
[1] 3
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                16                273 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                16                273 
[1] "TRIP10 MUTATION ANALYSIS"
[1] 3
  TRIP10 MUTATED TRIP10 WILD-TYPE 
               8              281 
  TRIP10 MUTATED TRIP10 WILD-TYPE 
               8              281 
[1] "PRKAB1 MUTATION ANALYSIS"
[1] 3
  PRKAB1 MUTATED PRKAB1 WILD-TYPE 
               6              283 
  PRKAB1 MUTATED PRKAB1 WILD-TYPE 
               6              283 
[1] "FAM193A MUTATION ANALYSIS"
[1] 3
  FAM193A MUTATED FAM193A WILD-TYPE 
               15               274 
  FAM193A MUTATED FAM193A WILD-TYPE 
               15               274 
[1] "AXIN2 MUTATION ANALYSIS"
[1] 3
  AXIN2 MUTATED AXIN2 WILD-TYPE 
             15             274 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
             15             274 
[1] "CYP27B1 MUTATION ANALYSIS"
[1] 3
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
                5               284 
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
                5               284 
[1] "C12ORF51 MUTATION ANALYSIS"
[1] 3
  C12ORF51 MUTATED C12ORF51 WILD-TYPE 
                30                259 
  C12ORF51 MUTATED C12ORF51 WILD-TYPE 
                30                259 
[1] "UBQLN2 MUTATION ANALYSIS"
[1] 3
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
               5              284 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
               5              284 
[1] "PHACTR2 MUTATION ANALYSIS"
[1] 3
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
               13               276 
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
               13               276 
[1] "ADNP2 MUTATION ANALYSIS"
[1] 3
  ADNP2 MUTATED ADNP2 WILD-TYPE 
             18             271 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
             18             271 
[1] "VPRBP MUTATION ANALYSIS"
[1] 3
  VPRBP MUTATED VPRBP WILD-TYPE 
             12             277 
  VPRBP MUTATED VPRBP WILD-TYPE 
             12             277 
[1] "PCGF3 MUTATION ANALYSIS"
[1] 3
  PCGF3 MUTATED PCGF3 WILD-TYPE 
              6             283 
  PCGF3 MUTATED PCGF3 WILD-TYPE 
              6             283 
[1] "C20ORF160 MUTATION ANALYSIS"
[1] 3
  C20ORF160 MUTATED C20ORF160 WILD-TYPE 
                  8                 281 
  C20ORF160 MUTATED C20ORF160 WILD-TYPE 
                  8                 281 
[1] "EFHA1 MUTATION ANALYSIS"
[1] 3
  EFHA1 MUTATED EFHA1 WILD-TYPE 
              9             280 
  EFHA1 MUTATED EFHA1 WILD-TYPE 
              9             280 
[1] "ALPK2 MUTATION ANALYSIS"
[1] 3
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             19             270 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             19             270 
[1] "C16ORF7 MUTATION ANALYSIS"
[1] 3
  C16ORF7 MUTATED C16ORF7 WILD-TYPE 
               14               275 
  C16ORF7 MUTATED C16ORF7 WILD-TYPE 
               14               275 
[1] "HIVEP1 MUTATION ANALYSIS"
[1] 3
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
              22              267 
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
              22              267 
[1] "VEZF1 MUTATION ANALYSIS"
[1] 3
  VEZF1 MUTATED VEZF1 WILD-TYPE 
              5             284 
  VEZF1 MUTATED VEZF1 WILD-TYPE 
              5             284 
[1] "SBNO1 MUTATION ANALYSIS"
[1] 3
  SBNO1 MUTATED SBNO1 WILD-TYPE 
             17             272 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
             17             272 
[1] "WASF3 MUTATION ANALYSIS"
[1] 3
  WASF3 MUTATED WASF3 WILD-TYPE 
             11             278 
  WASF3 MUTATED WASF3 WILD-TYPE 
             11             278 
[1] "RAB14 MUTATION ANALYSIS"
[1] 3
  RAB14 MUTATED RAB14 WILD-TYPE 
              8             281 
  RAB14 MUTATED RAB14 WILD-TYPE 
              8             281 
[1] "ZNF124 MUTATION ANALYSIS"
[1] 3
  ZNF124 MUTATED ZNF124 WILD-TYPE 
               9              280 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
               9              280 
[1] "RB1CC1 MUTATION ANALYSIS"
[1] 3
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
              10              279 
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
              10              279 
[1] "HIVEP3 MUTATION ANALYSIS"
[1] 3
  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
              27              262 
  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
              27              262 
[1] "OTX2 MUTATION ANALYSIS"
[1] 3
  OTX2 MUTATED OTX2 WILD-TYPE 
             9            280 
  OTX2 MUTATED OTX2 WILD-TYPE 
             9            280 
[1] "CRYGD MUTATION ANALYSIS"
[1] 3
  CRYGD MUTATED CRYGD WILD-TYPE 
             12             277 
  CRYGD MUTATED CRYGD WILD-TYPE 
             12             277 
[1] "MSL3 MUTATION ANALYSIS"
[1] 3
  MSL3 MUTATED MSL3 WILD-TYPE 
            10            279 
  MSL3 MUTATED MSL3 WILD-TYPE 
            10            279 
[1] "GPR160 MUTATION ANALYSIS"
[1] 3
  GPR160 MUTATED GPR160 WILD-TYPE 
               8              281 
  GPR160 MUTATED GPR160 WILD-TYPE 
               8              281 
[1] "KIN MUTATION ANALYSIS"
[1] 3
  KIN MUTATED KIN WILD-TYPE 
           11           278 
  KIN MUTATED KIN WILD-TYPE 
           11           278 
[1] "SRCIN1 MUTATION ANALYSIS"
[1] 3
  SRCIN1 MUTATED SRCIN1 WILD-TYPE 
              13              276 
  SRCIN1 MUTATED SRCIN1 WILD-TYPE 
              13              276 
[1] "KDELR3 MUTATION ANALYSIS"
[1] 3
  KDELR3 MUTATED KDELR3 WILD-TYPE 
               3              286 
  KDELR3 MUTATED KDELR3 WILD-TYPE 
               3              286 
[1] "FBXO48 MUTATION ANALYSIS"
[1] 3
  FBXO48 MUTATED FBXO48 WILD-TYPE 
               4              285 
  FBXO48 MUTATED FBXO48 WILD-TYPE 
               4              285 
[1] "TBC1D22B MUTATION ANALYSIS"
[1] 3
  TBC1D22B MUTATED TBC1D22B WILD-TYPE 
                 7                282 
  TBC1D22B MUTATED TBC1D22B WILD-TYPE 
                 7                282 
[1] "CDH16 MUTATION ANALYSIS"
[1] 3
  CDH16 MUTATED CDH16 WILD-TYPE 
             13             276 
  CDH16 MUTATED CDH16 WILD-TYPE 
             13             276 
[1] "GLT8D1 MUTATION ANALYSIS"
[1] 3
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               8              281 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               8              281 
[1] "TAS2R42 MUTATION ANALYSIS"
[1] 3
  TAS2R42 MUTATED TAS2R42 WILD-TYPE 
                4               285 
  TAS2R42 MUTATED TAS2R42 WILD-TYPE 
                4               285 
[1] "POP1 MUTATION ANALYSIS"
[1] 3
  POP1 MUTATED POP1 WILD-TYPE 
            19            270 
  POP1 MUTATED POP1 WILD-TYPE 
            19            270 
[1] "PIGO MUTATION ANALYSIS"
[1] 3
  PIGO MUTATED PIGO WILD-TYPE 
            10            279 
  PIGO MUTATED PIGO WILD-TYPE 
            10            279 
[1] "NEXN MUTATION ANALYSIS"
[1] 3
  NEXN MUTATED NEXN WILD-TYPE 
             8            281 
  NEXN MUTATED NEXN WILD-TYPE 
             8            281 
[1] "CLDN6 MUTATION ANALYSIS"
[1] 3
  CLDN6 MUTATED CLDN6 WILD-TYPE 
              7             282 
  CLDN6 MUTATED CLDN6 WILD-TYPE 
              7             282 
[1] "MTIF2 MUTATION ANALYSIS"
[1] 3
  MTIF2 MUTATED MTIF2 WILD-TYPE 
             15             274 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
             15             274 
[1] "HAUS6 MUTATION ANALYSIS"
[1] 3
  HAUS6 MUTATED HAUS6 WILD-TYPE 
             11             278 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
             11             278 
[1] "PLEKHO1 MUTATION ANALYSIS"
[1] 3
  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE 
                7               282 
  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE 
                7               282 
[1] "ASPN MUTATION ANALYSIS"
[1] 3
  ASPN MUTATED ASPN WILD-TYPE 
             6            283 
  ASPN MUTATED ASPN WILD-TYPE 
             6            283 
[1] "HTR1E MUTATION ANALYSIS"
[1] 3
  HTR1E MUTATED HTR1E WILD-TYPE 
              9             280 
  HTR1E MUTATED HTR1E WILD-TYPE 
              9             280 
[1] "KLC2 MUTATION ANALYSIS"
[1] 3
  KLC2 MUTATED KLC2 WILD-TYPE 
            11            278 
  KLC2 MUTATED KLC2 WILD-TYPE 
            11            278 
[1] "BMPR1B MUTATION ANALYSIS"
[1] 3
  BMPR1B MUTATED BMPR1B WILD-TYPE 
               7              282 
  BMPR1B MUTATED BMPR1B WILD-TYPE 
               7              282 
[1] "PAPD4 MUTATION ANALYSIS"
[1] 3
  PAPD4 MUTATED PAPD4 WILD-TYPE 
              8             281 
  PAPD4 MUTATED PAPD4 WILD-TYPE 
              8             281 
[1] "KIAA1009 MUTATION ANALYSIS"
[1] 3
  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
                15                274 
  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
                15                274 
[1] "C5ORF42 MUTATION ANALYSIS"
[1] 3
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
               26               263 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
               26               263 
[1] "YBX2 MUTATION ANALYSIS"
[1] 3
  YBX2 MUTATED YBX2 WILD-TYPE 
             4            285 
  YBX2 MUTATED YBX2 WILD-TYPE 
             4            285 
[1] "SH3KBP1 MUTATION ANALYSIS"
[1] 3
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
               13               276 
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
               13               276 
[1] "USP15 MUTATION ANALYSIS"
[1] 3
  USP15 MUTATED USP15 WILD-TYPE 
              6             283 
  USP15 MUTATED USP15 WILD-TYPE 
              6             283 
[1] "IGF2BP3 MUTATION ANALYSIS"
[1] 3
  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
                5               284 
  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
                5               284 
[1] "PLXNA2 MUTATION ANALYSIS"
[1] 3
  PLXNA2 MUTATED PLXNA2 WILD-TYPE 
              23              266 
  PLXNA2 MUTATED PLXNA2 WILD-TYPE 
              23              266 
[1] "MOCS2 MUTATION ANALYSIS"
[1] 3
  MOCS2 MUTATED MOCS2 WILD-TYPE 
              4             285 
  MOCS2 MUTATED MOCS2 WILD-TYPE 
              4             285 
[1] "PIK3R3 MUTATION ANALYSIS"
[1] 3
  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
               8              281 
  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
               8              281 
[1] "CR1 MUTATION ANALYSIS"
[1] 3
  CR1 MUTATED CR1 WILD-TYPE 
           25           264 
  CR1 MUTATED CR1 WILD-TYPE 
           25           264 
[1] "IL2RG MUTATION ANALYSIS"
[1] 3
  IL2RG MUTATED IL2RG WILD-TYPE 
              6             283 
  IL2RG MUTATED IL2RG WILD-TYPE 
              6             283 
[1] "FAM70B MUTATION ANALYSIS"
[1] 3
  FAM70B MUTATED FAM70B WILD-TYPE 
              13              276 
  FAM70B MUTATED FAM70B WILD-TYPE 
              13              276 
[1] "COL12A1 MUTATION ANALYSIS"
[1] 3
  COL12A1 MUTATED COL12A1 WILD-TYPE 
               46               243 
  COL12A1 MUTATED COL12A1 WILD-TYPE 
               46               243 
[1] "NFE2L1 MUTATION ANALYSIS"
[1] 3
  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
               9              280 
  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
               9              280 
[1] "TCHP MUTATION ANALYSIS"
[1] 3
  TCHP MUTATED TCHP WILD-TYPE 
            10            279 
  TCHP MUTATED TCHP WILD-TYPE 
            10            279 
[1] "WNT1 MUTATION ANALYSIS"
[1] 3
  WNT1 MUTATED WNT1 WILD-TYPE 
             8            281 
  WNT1 MUTATED WNT1 WILD-TYPE 
             8            281 
[1] "UBC MUTATION ANALYSIS"
[1] 3
  UBC MUTATED UBC WILD-TYPE 
            8           281 
  UBC MUTATED UBC WILD-TYPE 
            8           281 
[1] "XK MUTATION ANALYSIS"
[1] 3
  XK MUTATED XK WILD-TYPE 
           5          284 
  XK MUTATED XK WILD-TYPE 
           5          284 
[1] "CTSA MUTATION ANALYSIS"
[1] 3
  CTSA MUTATED CTSA WILD-TYPE 
             4            285 
  CTSA MUTATED CTSA WILD-TYPE 
             4            285 
[1] "TMEM41B MUTATION ANALYSIS"
[1] 3
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                4               285 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                4               285 
[1] "ENTPD2 MUTATION ANALYSIS"
[1] 3
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               4              285 
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               4              285 
[1] "IRS4 MUTATION ANALYSIS"
[1] 3
  IRS4 MUTATED IRS4 WILD-TYPE 
            23            266 
  IRS4 MUTATED IRS4 WILD-TYPE 
            23            266 
[1] "EVL MUTATION ANALYSIS"
[1] 3
  EVL MUTATED EVL WILD-TYPE 
            7           282 
  EVL MUTATED EVL WILD-TYPE 
            7           282 
[1] "OR5M3 MUTATION ANALYSIS"
[1] 3
  OR5M3 MUTATED OR5M3 WILD-TYPE 
             15             274 
  OR5M3 MUTATED OR5M3 WILD-TYPE 
             15             274 
[1] "MYEOV MUTATION ANALYSIS"
[1] 3
  MYEOV MUTATED MYEOV WILD-TYPE 
              8             281 
  MYEOV MUTATED MYEOV WILD-TYPE 
              8             281 
[1] "C15ORF52 MUTATION ANALYSIS"
[1] 3
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                 8                281 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                 8                281 
[1] "PKN2 MUTATION ANALYSIS"
[1] 3
  PKN2 MUTATED PKN2 WILD-TYPE 
            10            279 
  PKN2 MUTATED PKN2 WILD-TYPE 
            10            279 
[1] "IPO11 MUTATION ANALYSIS"
[1] 3
  IPO11 MUTATED IPO11 WILD-TYPE 
             12             277 
  IPO11 MUTATED IPO11 WILD-TYPE 
             12             277 
[1] "INTS12 MUTATION ANALYSIS"
[1] 3
  INTS12 MUTATED INTS12 WILD-TYPE 
               6              283 
  INTS12 MUTATED INTS12 WILD-TYPE 
               6              283 
[1] "PGBD1 MUTATION ANALYSIS"
[1] 3
  PGBD1 MUTATED PGBD1 WILD-TYPE 
             12             277 
  PGBD1 MUTATED PGBD1 WILD-TYPE 
             12             277 
[1] "NCAPH MUTATION ANALYSIS"
[1] 3
  NCAPH MUTATED NCAPH WILD-TYPE 
             10             279 
  NCAPH MUTATED NCAPH WILD-TYPE 
             10             279 
[1] "AQP8 MUTATION ANALYSIS"
[1] 3
  AQP8 MUTATED AQP8 WILD-TYPE 
            11            278 
  AQP8 MUTATED AQP8 WILD-TYPE 
            11            278 
[1] "EXO1 MUTATION ANALYSIS"
[1] 3
  EXO1 MUTATED EXO1 WILD-TYPE 
            16            273 
  EXO1 MUTATED EXO1 WILD-TYPE 
            16            273 
[1] "PRMT8 MUTATION ANALYSIS"
[1] 3
  PRMT8 MUTATED PRMT8 WILD-TYPE 
              8             281 
  PRMT8 MUTATED PRMT8 WILD-TYPE 
              8             281 
[1] "ACP1 MUTATION ANALYSIS"
[1] 3
  ACP1 MUTATED ACP1 WILD-TYPE 
             5            284 
  ACP1 MUTATED ACP1 WILD-TYPE 
             5            284 
[1] "ANKRD40 MUTATION ANALYSIS"
[1] 3
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
                5               284 
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
                5               284 
[1] "RBM6 MUTATION ANALYSIS"
[1] 3
  RBM6 MUTATED RBM6 WILD-TYPE 
            20            269 
  RBM6 MUTATED RBM6 WILD-TYPE 
            20            269 
[1] "SLC12A7 MUTATION ANALYSIS"
[1] 3
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
               18               271 
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
               18               271 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             14             275 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             14             275 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
             18             271 
  CASP8 MUTATED CASP8 WILD-TYPE 
             18             271 
[1] "WHSC1L1 MUTATION ANALYSIS"
[1] 3
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
               16               273 
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
               16               273 
[1] "TBL1XR1 MUTATION ANALYSIS"
[1] 3
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
                5               284 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
                5               284 
[1] "NEK7 MUTATION ANALYSIS"
[1] 3
  NEK7 MUTATED NEK7 WILD-TYPE 
             4            285 
  NEK7 MUTATED NEK7 WILD-TYPE 
             4            285 
[1] "CCDC148 MUTATION ANALYSIS"
[1] 3
  CCDC148 MUTATED CCDC148 WILD-TYPE 
                5               284 
  CCDC148 MUTATED CCDC148 WILD-TYPE 
                5               284 
[1] "ANKRD23 MUTATION ANALYSIS"
[1] 3
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                5               284 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                5               284 
[1] "BTBD11 MUTATION ANALYSIS"
[1] 3
  BTBD11 MUTATED BTBD11 WILD-TYPE 
              20              269 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
              20              269 
[1] "FBXO21 MUTATION ANALYSIS"
[1] 3
  FBXO21 MUTATED FBXO21 WILD-TYPE 
              12              277 
  FBXO21 MUTATED FBXO21 WILD-TYPE 
              12              277 
[1] "C19ORF26 MUTATION ANALYSIS"
[1] 3
  C19ORF26 MUTATED C19ORF26 WILD-TYPE 
                 7                282 
  C19ORF26 MUTATED C19ORF26 WILD-TYPE 
                 7                282 
[1] "NAA25 MUTATION ANALYSIS"
[1] 3
  NAA25 MUTATED NAA25 WILD-TYPE 
             14             275 
  NAA25 MUTATED NAA25 WILD-TYPE 
             14             275 
[1] "MAMSTR MUTATION ANALYSIS"
[1] 3
  MAMSTR MUTATED MAMSTR WILD-TYPE 
               4              285 
  MAMSTR MUTATED MAMSTR WILD-TYPE 
               4              285 
[1] "RING1 MUTATION ANALYSIS"
[1] 3
  RING1 MUTATED RING1 WILD-TYPE 
              8             281 
  RING1 MUTATED RING1 WILD-TYPE 
              8             281 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
           30           259 
  ATM MUTATED ATM WILD-TYPE 
           30           259 
[1] "BRWD1 MUTATION ANALYSIS"
[1] 3
  BRWD1 MUTATED BRWD1 WILD-TYPE 
             21             268 
  BRWD1 MUTATED BRWD1 WILD-TYPE 
             21             268 
[1] "PFKP MUTATION ANALYSIS"
[1] 3
  PFKP MUTATED PFKP WILD-TYPE 
            13            276 
  PFKP MUTATED PFKP WILD-TYPE 
            13            276 
[1] "SAFB MUTATION ANALYSIS"
[1] 3
  SAFB MUTATED SAFB WILD-TYPE 
             9            280 
  SAFB MUTATED SAFB WILD-TYPE 
             9            280 
[1] "KCNH4 MUTATION ANALYSIS"
[1] 3
  KCNH4 MUTATED KCNH4 WILD-TYPE 
              6             283 
  KCNH4 MUTATED KCNH4 WILD-TYPE 
              6             283 
[1] "TMEM63A MUTATION ANALYSIS"
[1] 3
  TMEM63A MUTATED TMEM63A WILD-TYPE 
               11               278 
  TMEM63A MUTATED TMEM63A WILD-TYPE 
               11               278 
[1] "SOAT1 MUTATION ANALYSIS"
[1] 3
  SOAT1 MUTATED SOAT1 WILD-TYPE 
              6             283 
  SOAT1 MUTATED SOAT1 WILD-TYPE 
              6             283 
[1] "CTNNA1 MUTATION ANALYSIS"
[1] 3
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
              13              276 
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
              13              276 
[1] "FAM55C MUTATION ANALYSIS"
[1] 3
  FAM55C MUTATED FAM55C WILD-TYPE 
              13              276 
  FAM55C MUTATED FAM55C WILD-TYPE 
              13              276 
[1] "SLC25A17 MUTATION ANALYSIS"
[1] 3
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 4                285 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 4                285 
[1] "ZNF626 MUTATION ANALYSIS"
[1] 3
  ZNF626 MUTATED ZNF626 WILD-TYPE 
              15              274 
  ZNF626 MUTATED ZNF626 WILD-TYPE 
              15              274 
[1] "OPLAH MUTATION ANALYSIS"
[1] 3
  OPLAH MUTATED OPLAH WILD-TYPE 
             14             275 
  OPLAH MUTATED OPLAH WILD-TYPE 
             14             275 
[1] "MYOCD MUTATION ANALYSIS"
[1] 3
  MYOCD MUTATED MYOCD WILD-TYPE 
             13             276 
  MYOCD MUTATED MYOCD WILD-TYPE 
             13             276 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             4            285 
  NRAS MUTATED NRAS WILD-TYPE 
             4            285 
[1] "SEC24C MUTATION ANALYSIS"
[1] 3
  SEC24C MUTATED SEC24C WILD-TYPE 
              10              279 
  SEC24C MUTATED SEC24C WILD-TYPE 
              10              279 
[1] "CEP57 MUTATION ANALYSIS"
[1] 3
  CEP57 MUTATED CEP57 WILD-TYPE 
              7             282 
  CEP57 MUTATED CEP57 WILD-TYPE 
              7             282 
[1] "TMEM55A MUTATION ANALYSIS"
[1] 3
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                3               286 
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                3               286 
[1] "CASD1 MUTATION ANALYSIS"
[1] 3
  CASD1 MUTATED CASD1 WILD-TYPE 
             11             278 
  CASD1 MUTATED CASD1 WILD-TYPE 
             11             278 
[1] "CADPS2 MUTATION ANALYSIS"
[1] 3
  CADPS2 MUTATED CADPS2 WILD-TYPE 
              11              278 
  CADPS2 MUTATED CADPS2 WILD-TYPE 
              11              278 
[1] "MASTL MUTATION ANALYSIS"
[1] 3
  MASTL MUTATED MASTL WILD-TYPE 
             11             278 
  MASTL MUTATED MASTL WILD-TYPE 
             11             278 
[1] "MRI1 MUTATION ANALYSIS"
[1] 3
  MRI1 MUTATED MRI1 WILD-TYPE 
             4            285 
  MRI1 MUTATED MRI1 WILD-TYPE 
             4            285 
[1] "KBTBD6 MUTATION ANALYSIS"
[1] 3
  KBTBD6 MUTATED KBTBD6 WILD-TYPE 
              13              276 
  KBTBD6 MUTATED KBTBD6 WILD-TYPE 
              13              276 
[1] "PLA2G15 MUTATION ANALYSIS"
[1] 3
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
                9               280 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
                9               280 
[1] "JHDM1D MUTATION ANALYSIS"
[1] 3
  JHDM1D MUTATED JHDM1D WILD-TYPE 
              10              279 
  JHDM1D MUTATED JHDM1D WILD-TYPE 
              10              279 
[1] "NUFIP2 MUTATION ANALYSIS"
[1] 3
  NUFIP2 MUTATED NUFIP2 WILD-TYPE 
               7              282 
  NUFIP2 MUTATED NUFIP2 WILD-TYPE 
               7              282 
[1] "KCNJ10 MUTATION ANALYSIS"
[1] 3
  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
              11              278 
  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
              11              278 
[1] "TRUB1 MUTATION ANALYSIS"
[1] 3
  TRUB1 MUTATED TRUB1 WILD-TYPE 
              9             280 
  TRUB1 MUTATED TRUB1 WILD-TYPE 
              9             280 
[1] "AGBL5 MUTATION ANALYSIS"
[1] 3
  AGBL5 MUTATED AGBL5 WILD-TYPE 
             12             277 
  AGBL5 MUTATED AGBL5 WILD-TYPE 
             12             277 
[1] "PLAG1 MUTATION ANALYSIS"
[1] 3
  PLAG1 MUTATED PLAG1 WILD-TYPE 
             11             278 
  PLAG1 MUTATED PLAG1 WILD-TYPE 
             11             278 
[1] "HEPACAM2 MUTATION ANALYSIS"
[1] 3
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                 8                281 
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                 8                281 
[1] "CSF3R MUTATION ANALYSIS"
[1] 3
  CSF3R MUTATED CSF3R WILD-TYPE 
             12             277 
  CSF3R MUTATED CSF3R WILD-TYPE 
             12             277 
[1] "RPGR MUTATION ANALYSIS"
[1] 3
  RPGR MUTATED RPGR WILD-TYPE 
             8            281 
  RPGR MUTATED RPGR WILD-TYPE 
             8            281 
[1] "EPB49 MUTATION ANALYSIS"
[1] 3
  EPB49 MUTATED EPB49 WILD-TYPE 
              8             281 
  EPB49 MUTATED EPB49 WILD-TYPE 
              8             281 
[1] "LRFN3 MUTATION ANALYSIS"
[1] 3
  LRFN3 MUTATED LRFN3 WILD-TYPE 
             18             271 
  LRFN3 MUTATED LRFN3 WILD-TYPE 
             18             271 
[1] "GRK4 MUTATION ANALYSIS"
[1] 3
  GRK4 MUTATED GRK4 WILD-TYPE 
             4            285 
  GRK4 MUTATED GRK4 WILD-TYPE 
             4            285 
[1] "ZNF23 MUTATION ANALYSIS"
[1] 3
  ZNF23 MUTATED ZNF23 WILD-TYPE 
              3             286 
  ZNF23 MUTATED ZNF23 WILD-TYPE 
              3             286 
[1] "SERPINB8 MUTATION ANALYSIS"
[1] 3
  SERPINB8 MUTATED SERPINB8 WILD-TYPE 
                 8                281 
  SERPINB8 MUTATED SERPINB8 WILD-TYPE 
                 8                281 
[1] "ERBB4 MUTATION ANALYSIS"
[1] 3
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             39             250 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             39             250 
[1] "WDR59 MUTATION ANALYSIS"
[1] 3
  WDR59 MUTATED WDR59 WILD-TYPE 
             11             278 
  WDR59 MUTATED WDR59 WILD-TYPE 
             11             278 
[1] "SPHK2 MUTATION ANALYSIS"
[1] 3
  SPHK2 MUTATED SPHK2 WILD-TYPE 
              3             286 
  SPHK2 MUTATED SPHK2 WILD-TYPE 
              3             286 
[1] "RUSC2 MUTATION ANALYSIS"
[1] 3
  RUSC2 MUTATED RUSC2 WILD-TYPE 
             19             270 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
             19             270 
[1] "CHST15 MUTATION ANALYSIS"
[1] 3
  CHST15 MUTATED CHST15 WILD-TYPE 
              13              276 
  CHST15 MUTATED CHST15 WILD-TYPE 
              13              276 
[1] "TAF1L MUTATION ANALYSIS"
[1] 3
  TAF1L MUTATED TAF1L WILD-TYPE 
             23             266 
  TAF1L MUTATED TAF1L WILD-TYPE 
             23             266 
[1] "USP8 MUTATION ANALYSIS"
[1] 3
  USP8 MUTATED USP8 WILD-TYPE 
             7            282 
  USP8 MUTATED USP8 WILD-TYPE 
             7            282 
[1] "MYB MUTATION ANALYSIS"
[1] 3
  MYB MUTATED MYB WILD-TYPE 
            6           283 
  MYB MUTATED MYB WILD-TYPE 
            6           283 
[1] "CREM MUTATION ANALYSIS"
[1] 3
  CREM MUTATED CREM WILD-TYPE 
             4            285 
  CREM MUTATED CREM WILD-TYPE 
             4            285 
[1] "CD93 MUTATION ANALYSIS"
[1] 3
  CD93 MUTATED CD93 WILD-TYPE 
            11            278 
  CD93 MUTATED CD93 WILD-TYPE 
            11            278 
[1] "B3GNT5 MUTATION ANALYSIS"
[1] 3
  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
              10              279 
  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
              10              279 
[1] "ART1 MUTATION ANALYSIS"
[1] 3
  ART1 MUTATED ART1 WILD-TYPE 
             7            282 
  ART1 MUTATED ART1 WILD-TYPE 
             7            282 
[1] "IKBKE MUTATION ANALYSIS"
[1] 3
  IKBKE MUTATED IKBKE WILD-TYPE 
             12             277 
  IKBKE MUTATED IKBKE WILD-TYPE 
             12             277 
[1] "TIMM44 MUTATION ANALYSIS"
[1] 3
  TIMM44 MUTATED TIMM44 WILD-TYPE 
               5              284 
  TIMM44 MUTATED TIMM44 WILD-TYPE 
               5              284 
[1] "ELOVL2 MUTATION ANALYSIS"
[1] 3
  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
               7              282 
  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
               7              282 
[1] "ALDH2 MUTATION ANALYSIS"
[1] 3
  ALDH2 MUTATED ALDH2 WILD-TYPE 
              9             280 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
              9             280 
[1] "H2AFY2 MUTATION ANALYSIS"
[1] 3
  H2AFY2 MUTATED H2AFY2 WILD-TYPE 
               7              282 
  H2AFY2 MUTATED H2AFY2 WILD-TYPE 
               7              282 
[1] "SOHLH2 MUTATION ANALYSIS"
[1] 3
  SOHLH2 MUTATED SOHLH2 WILD-TYPE 
              14              275 
  SOHLH2 MUTATED SOHLH2 WILD-TYPE 
              14              275 
[1] "CROT MUTATION ANALYSIS"
[1] 3
  CROT MUTATED CROT WILD-TYPE 
            11            278 
  CROT MUTATED CROT WILD-TYPE 
            11            278 
[1] "GON4L MUTATION ANALYSIS"
[1] 3
  GON4L MUTATED GON4L WILD-TYPE 
             10             279 
  GON4L MUTATED GON4L WILD-TYPE 
             10             279 
[1] "CNKSR2 MUTATION ANALYSIS"
[1] 3
  CNKSR2 MUTATED CNKSR2 WILD-TYPE 
              12              277 
  CNKSR2 MUTATED CNKSR2 WILD-TYPE 
              12              277 
[1] "UHRF1BP1 MUTATION ANALYSIS"
[1] 3
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
                15                274 
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
                15                274 
[1] "OR7C1 MUTATION ANALYSIS"
[1] 3
  OR7C1 MUTATED OR7C1 WILD-TYPE 
              6             283 
  OR7C1 MUTATED OR7C1 WILD-TYPE 
              6             283 
[1] "ABLIM2 MUTATION ANALYSIS"
[1] 3
  ABLIM2 MUTATED ABLIM2 WILD-TYPE 
              11              278 
  ABLIM2 MUTATED ABLIM2 WILD-TYPE 
              11              278 
[1] "TPTE2 MUTATION ANALYSIS"
[1] 3
  TPTE2 MUTATED TPTE2 WILD-TYPE 
             10             279 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
             10             279 
[1] "OLFML3 MUTATION ANALYSIS"
[1] 3
  OLFML3 MUTATED OLFML3 WILD-TYPE 
               4              285 
  OLFML3 MUTATED OLFML3 WILD-TYPE 
               4              285 
[1] "RINT1 MUTATION ANALYSIS"
[1] 3
  RINT1 MUTATED RINT1 WILD-TYPE 
              5             284 
  RINT1 MUTATED RINT1 WILD-TYPE 
              5             284 
[1] "CA2 MUTATION ANALYSIS"
[1] 3
  CA2 MUTATED CA2 WILD-TYPE 
            5           284 
  CA2 MUTATED CA2 WILD-TYPE 
            5           284 
[1] "IRS1 MUTATION ANALYSIS"
[1] 3
  IRS1 MUTATED IRS1 WILD-TYPE 
            20            269 
  IRS1 MUTATED IRS1 WILD-TYPE 
            20            269 
[1] "FKBP9 MUTATION ANALYSIS"
[1] 3
  FKBP9 MUTATED FKBP9 WILD-TYPE 
              6             283 
  FKBP9 MUTATED FKBP9 WILD-TYPE 
              6             283 
[1] "LMTK3 MUTATION ANALYSIS"
[1] 3
  LMTK3 MUTATED LMTK3 WILD-TYPE 
              8             281 
  LMTK3 MUTATED LMTK3 WILD-TYPE 
              8             281 
[1] "DNAH5 MUTATION ANALYSIS"
[1] 3
  DNAH5 MUTATED DNAH5 WILD-TYPE 
             56             233 
  DNAH5 MUTATED DNAH5 WILD-TYPE 
             56             233 
[1] "GPATCH2 MUTATION ANALYSIS"
[1] 3
  GPATCH2 MUTATED GPATCH2 WILD-TYPE 
                7               282 
  GPATCH2 MUTATED GPATCH2 WILD-TYPE 
                7               282 
[1] "KCNH2 MUTATION ANALYSIS"
[1] 3
  KCNH2 MUTATED KCNH2 WILD-TYPE 
             13             276 
  KCNH2 MUTATED KCNH2 WILD-TYPE 
             13             276 
[1] "SGOL2 MUTATION ANALYSIS"
[1] 3
  SGOL2 MUTATED SGOL2 WILD-TYPE 
             11             278 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
             11             278 
[1] "ADAMTSL4 MUTATION ANALYSIS"
[1] 3
  ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE 
                15                274 
  ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE 
                15                274 
[1] "CPB2 MUTATION ANALYSIS"
[1] 3
  CPB2 MUTATED CPB2 WILD-TYPE 
             9            280 
  CPB2 MUTATED CPB2 WILD-TYPE 
             9            280 
[1] "THEMIS MUTATION ANALYSIS"
[1] 3
  THEMIS MUTATED THEMIS WILD-TYPE 
               8              281 
  THEMIS MUTATED THEMIS WILD-TYPE 
               8              281 
[1] "KRTAP10-9 MUTATION ANALYSIS"
[1] 3
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
                  9                 280 
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
                  9                 280 
[1] "SGK3 MUTATION ANALYSIS"
[1] 3
  SGK3 MUTATED SGK3 WILD-TYPE 
             5            284 
  SGK3 MUTATED SGK3 WILD-TYPE 
             5            284 
[1] "YIF1A MUTATION ANALYSIS"
[1] 3
  YIF1A MUTATED YIF1A WILD-TYPE 
              3             286 
  YIF1A MUTATED YIF1A WILD-TYPE 
              3             286 
[1] "EGR1 MUTATION ANALYSIS"
[1] 3
  EGR1 MUTATED EGR1 WILD-TYPE 
            10            279 
  EGR1 MUTATED EGR1 WILD-TYPE 
            10            279 
[1] "GTF3C4 MUTATION ANALYSIS"
[1] 3
  GTF3C4 MUTATED GTF3C4 WILD-TYPE 
              12              277 
  GTF3C4 MUTATED GTF3C4 WILD-TYPE 
              12              277 
[1] "ACTL6A MUTATION ANALYSIS"
[1] 3
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               8              281 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               8              281 
[1] "C7ORF49 MUTATION ANALYSIS"
[1] 3
  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
                7               282 
  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
                7               282 
[1] "BEST3 MUTATION ANALYSIS"
[1] 3
  BEST3 MUTATED BEST3 WILD-TYPE 
             11             278 
  BEST3 MUTATED BEST3 WILD-TYPE 
             11             278 
[1] "STX2 MUTATION ANALYSIS"
[1] 3
  STX2 MUTATED STX2 WILD-TYPE 
             6            283 
  STX2 MUTATED STX2 WILD-TYPE 
             6            283 
[1] "ARHGEF5 MUTATION ANALYSIS"
[1] 3
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
                5               284 
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
                5               284 
[1] "FAM92B MUTATION ANALYSIS"
[1] 3
  FAM92B MUTATED FAM92B WILD-TYPE 
               3              286 
  FAM92B MUTATED FAM92B WILD-TYPE 
               3              286 
[1] "BRSK1 MUTATION ANALYSIS"
[1] 3
  BRSK1 MUTATED BRSK1 WILD-TYPE 
             12             277 
  BRSK1 MUTATED BRSK1 WILD-TYPE 
             12             277 
[1] "KIAA1804 MUTATION ANALYSIS"
[1] 3
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 8                281 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 8                281 
[1] "ZNF711 MUTATION ANALYSIS"
[1] 3
  ZNF711 MUTATED ZNF711 WILD-TYPE 
              13              276 
  ZNF711 MUTATED ZNF711 WILD-TYPE 
              13              276 
[1] "HCRTR2 MUTATION ANALYSIS"
[1] 3
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
               9              280 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
               9              280 
[1] "OR51A7 MUTATION ANALYSIS"
[1] 3
  OR51A7 MUTATED OR51A7 WILD-TYPE 
               6              283 
  OR51A7 MUTATED OR51A7 WILD-TYPE 
               6              283 
[1] "C2ORF42 MUTATION ANALYSIS"
[1] 3
  C2ORF42 MUTATED C2ORF42 WILD-TYPE 
               14               275 
  C2ORF42 MUTATED C2ORF42 WILD-TYPE 
               14               275 
[1] "KCTD21 MUTATION ANALYSIS"
[1] 3
  KCTD21 MUTATED KCTD21 WILD-TYPE 
               7              282 
  KCTD21 MUTATED KCTD21 WILD-TYPE 
               7              282 
[1] "SEZ6 MUTATION ANALYSIS"
[1] 3
  SEZ6 MUTATED SEZ6 WILD-TYPE 
            10            279 
  SEZ6 MUTATED SEZ6 WILD-TYPE 
            10            279 
[1] "C7ORF58 MUTATION ANALYSIS"
[1] 3
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               15               274 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               15               274 
[1] "STK38 MUTATION ANALYSIS"
[1] 3
  STK38 MUTATED STK38 WILD-TYPE 
              6             283 
  STK38 MUTATED STK38 WILD-TYPE 
              6             283 
[1] "PTPN4 MUTATION ANALYSIS"
[1] 3
  PTPN4 MUTATED PTPN4 WILD-TYPE 
              9             280 
  PTPN4 MUTATED PTPN4 WILD-TYPE 
              9             280 
[1] "CTSD MUTATION ANALYSIS"
[1] 3
  CTSD MUTATED CTSD WILD-TYPE 
             7            282 
  CTSD MUTATED CTSD WILD-TYPE 
             7            282 
[1] "EOMES MUTATION ANALYSIS"
[1] 3
  EOMES MUTATED EOMES WILD-TYPE 
              8             281 
  EOMES MUTATED EOMES WILD-TYPE 
              8             281 
[1] "AVPR1A MUTATION ANALYSIS"
[1] 3
  AVPR1A MUTATED AVPR1A WILD-TYPE 
              12              277 
  AVPR1A MUTATED AVPR1A WILD-TYPE 
              12              277 
[1] "DDX43 MUTATION ANALYSIS"
[1] 3
  DDX43 MUTATED DDX43 WILD-TYPE 
             10             279 
  DDX43 MUTATED DDX43 WILD-TYPE 
             10             279 
[1] "OR4K5 MUTATION ANALYSIS"
[1] 3
  OR4K5 MUTATED OR4K5 WILD-TYPE 
             12             277 
  OR4K5 MUTATED OR4K5 WILD-TYPE 
             12             277 
[1] "GPR124 MUTATION ANALYSIS"
[1] 3
  GPR124 MUTATED GPR124 WILD-TYPE 
              13              276 
  GPR124 MUTATED GPR124 WILD-TYPE 
              13              276 
[1] "FAAH MUTATION ANALYSIS"
[1] 3
  FAAH MUTATED FAAH WILD-TYPE 
             4            285 
  FAAH MUTATED FAAH WILD-TYPE 
             4            285 
[1] "EYA4 MUTATION ANALYSIS"
[1] 3
  EYA4 MUTATED EYA4 WILD-TYPE 
            15            274 
  EYA4 MUTATED EYA4 WILD-TYPE 
            15            274 
[1] "ZNF701 MUTATION ANALYSIS"
[1] 3
  ZNF701 MUTATED ZNF701 WILD-TYPE 
               8              281 
  ZNF701 MUTATED ZNF701 WILD-TYPE 
               8              281 
[1] "OR2J3 MUTATION ANALYSIS"
[1] 3
  OR2J3 MUTATED OR2J3 WILD-TYPE 
              6             283 
  OR2J3 MUTATED OR2J3 WILD-TYPE 
              6             283 
[1] "MPRIP MUTATION ANALYSIS"
[1] 3
  MPRIP MUTATED MPRIP WILD-TYPE 
             14             275 
  MPRIP MUTATED MPRIP WILD-TYPE 
             14             275 
[1] "SYNJ2 MUTATION ANALYSIS"
[1] 3
  SYNJ2 MUTATED SYNJ2 WILD-TYPE 
             16             273 
  SYNJ2 MUTATED SYNJ2 WILD-TYPE 
             16             273 
[1] "KIAA1324L MUTATION ANALYSIS"
[1] 3
  KIAA1324L MUTATED KIAA1324L WILD-TYPE 
                 21                 268 
  KIAA1324L MUTATED KIAA1324L WILD-TYPE 
                 21                 268 
[1] "GPR141 MUTATION ANALYSIS"
[1] 3
  GPR141 MUTATED GPR141 WILD-TYPE 
               9              280 
  GPR141 MUTATED GPR141 WILD-TYPE 
               9              280 
[1] "TLR4 MUTATION ANALYSIS"
[1] 3
  TLR4 MUTATED TLR4 WILD-TYPE 
            21            268 
  TLR4 MUTATED TLR4 WILD-TYPE 
            21            268 
[1] "LYSMD3 MUTATION ANALYSIS"
[1] 3
  LYSMD3 MUTATED LYSMD3 WILD-TYPE 
              10              279 
  LYSMD3 MUTATED LYSMD3 WILD-TYPE 
              10              279 
[1] "LIAS MUTATION ANALYSIS"
[1] 3
  LIAS MUTATED LIAS WILD-TYPE 
             5            284 
  LIAS MUTATED LIAS WILD-TYPE 
             5            284 
[1] "MAP7D3 MUTATION ANALYSIS"
[1] 3
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
              16              273 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
              16              273 
[1] "ERN2 MUTATION ANALYSIS"
[1] 3
  ERN2 MUTATED ERN2 WILD-TYPE 
            11            278 
  ERN2 MUTATED ERN2 WILD-TYPE 
            11            278 
[1] "DSTN MUTATION ANALYSIS"
[1] 3
  DSTN MUTATED DSTN WILD-TYPE 
             5            284 
  DSTN MUTATED DSTN WILD-TYPE 
             5            284 
[1] "PTPDC1 MUTATION ANALYSIS"
[1] 3
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
               8              281 
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
               8              281 
[1] "FYB MUTATION ANALYSIS"
[1] 3
  FYB MUTATED FYB WILD-TYPE 
           11           278 
  FYB MUTATED FYB WILD-TYPE 
           11           278 
[1] "NDST2 MUTATION ANALYSIS"
[1] 3
  NDST2 MUTATED NDST2 WILD-TYPE 
              8             281 
  NDST2 MUTATED NDST2 WILD-TYPE 
              8             281 
[1] "TAF7L MUTATION ANALYSIS"
[1] 3
  TAF7L MUTATED TAF7L WILD-TYPE 
              7             282 
  TAF7L MUTATED TAF7L WILD-TYPE 
              7             282 
[1] "SAP130 MUTATION ANALYSIS"
[1] 3
  SAP130 MUTATED SAP130 WILD-TYPE 
              11              278 
  SAP130 MUTATED SAP130 WILD-TYPE 
              11              278 
[1] "SMARCB1 MUTATION ANALYSIS"
[1] 3
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
               11               278 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
               11               278 
[1] "EPHA5 MUTATION ANALYSIS"
[1] 3
  EPHA5 MUTATED EPHA5 WILD-TYPE 
             26             263 
  EPHA5 MUTATED EPHA5 WILD-TYPE 
             26             263 
[1] "WAPAL MUTATION ANALYSIS"
[1] 3
  WAPAL MUTATED WAPAL WILD-TYPE 
             13             276 
  WAPAL MUTATED WAPAL WILD-TYPE 
             13             276 
[1] "CEP120 MUTATION ANALYSIS"
[1] 3
  CEP120 MUTATED CEP120 WILD-TYPE 
              10              279 
  CEP120 MUTATED CEP120 WILD-TYPE 
              10              279 
[1] "RDX MUTATION ANALYSIS"
[1] 3
  RDX MUTATED RDX WILD-TYPE 
            7           282 
  RDX MUTATED RDX WILD-TYPE 
            7           282 
[1] "SPATA5L1 MUTATION ANALYSIS"
[1] 3
  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE 
                 7                282 
  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE 
                 7                282 
[1] "TACC2 MUTATION ANALYSIS"
[1] 3
  TACC2 MUTATED TACC2 WILD-TYPE 
             30             259 
  TACC2 MUTATED TACC2 WILD-TYPE 
             30             259 
[1] "CD58 MUTATION ANALYSIS"
[1] 3
  CD58 MUTATED CD58 WILD-TYPE 
             6            283 
  CD58 MUTATED CD58 WILD-TYPE 
             6            283 
[1] "KCTD9 MUTATION ANALYSIS"
[1] 3
  KCTD9 MUTATED KCTD9 WILD-TYPE 
             10             279 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
             10             279 
[1] "KIAA1539 MUTATION ANALYSIS"
[1] 3
  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
                 6                283 
  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
                 6                283 
[1] "ZFP36L2 MUTATION ANALYSIS"
[1] 3
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
                8               281 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
                8               281 
[1] "TNS4 MUTATION ANALYSIS"
[1] 3
  TNS4 MUTATED TNS4 WILD-TYPE 
            12            277 
  TNS4 MUTATED TNS4 WILD-TYPE 
            12            277 
[1] "ZBTB49 MUTATION ANALYSIS"
[1] 3
  ZBTB49 MUTATED ZBTB49 WILD-TYPE 
               7              282 
  ZBTB49 MUTATED ZBTB49 WILD-TYPE 
               7              282 
[1] "CAMTA2 MUTATION ANALYSIS"
[1] 3
  CAMTA2 MUTATED CAMTA2 WILD-TYPE 
              16              273 
  CAMTA2 MUTATED CAMTA2 WILD-TYPE 
              16              273 
[1] "KRT24 MUTATION ANALYSIS"
[1] 3
  KRT24 MUTATED KRT24 WILD-TYPE 
              5             284 
  KRT24 MUTATED KRT24 WILD-TYPE 
              5             284 
[1] "EEF2K MUTATION ANALYSIS"
[1] 3
  EEF2K MUTATED EEF2K WILD-TYPE 
              9             280 
  EEF2K MUTATED EEF2K WILD-TYPE 
              9             280 
[1] "RERE MUTATION ANALYSIS"
[1] 3
  RERE MUTATED RERE WILD-TYPE 
            21            268 
  RERE MUTATED RERE WILD-TYPE 
            21            268 
[1] "TRAM1L1 MUTATION ANALYSIS"
[1] 3
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
               13               276 
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
               13               276 
[1] "EXOSC8 MUTATION ANALYSIS"
[1] 3
  EXOSC8 MUTATED EXOSC8 WILD-TYPE 
               5              284 
  EXOSC8 MUTATED EXOSC8 WILD-TYPE 
               5              284 
[1] "SUCLG2 MUTATION ANALYSIS"
[1] 3
  SUCLG2 MUTATED SUCLG2 WILD-TYPE 
               5              284 
  SUCLG2 MUTATED SUCLG2 WILD-TYPE 
               5              284 
[1] "CNOT6 MUTATION ANALYSIS"
[1] 3
  CNOT6 MUTATED CNOT6 WILD-TYPE 
              7             282 
  CNOT6 MUTATED CNOT6 WILD-TYPE 
              7             282 
[1] "TIGD7 MUTATION ANALYSIS"
[1] 3
  TIGD7 MUTATED TIGD7 WILD-TYPE 
              8             281 
  TIGD7 MUTATED TIGD7 WILD-TYPE 
              8             281 
[1] "ITSN2 MUTATION ANALYSIS"
[1] 3
  ITSN2 MUTATED ITSN2 WILD-TYPE 
             16             273 
  ITSN2 MUTATED ITSN2 WILD-TYPE 
             16             273 
[1] "OGFRL1 MUTATION ANALYSIS"
[1] 3
  OGFRL1 MUTATED OGFRL1 WILD-TYPE 
              10              279 
  OGFRL1 MUTATED OGFRL1 WILD-TYPE 
              10              279 
[1] "KIAA1462 MUTATION ANALYSIS"
[1] 3
  KIAA1462 MUTATED KIAA1462 WILD-TYPE 
                22                267 
  KIAA1462 MUTATED KIAA1462 WILD-TYPE 
                22                267 
[1] "MAP1A MUTATION ANALYSIS"
[1] 3
  MAP1A MUTATED MAP1A WILD-TYPE 
             15             274 
  MAP1A MUTATED MAP1A WILD-TYPE 
             15             274 
[1] "NOB1 MUTATION ANALYSIS"
[1] 3
  NOB1 MUTATED NOB1 WILD-TYPE 
             7            282 
  NOB1 MUTATED NOB1 WILD-TYPE 
             7            282 
[1] "TNK2 MUTATION ANALYSIS"
[1] 3
  TNK2 MUTATED TNK2 WILD-TYPE 
            11            278 
  TNK2 MUTATED TNK2 WILD-TYPE 
            11            278 
[1] "CYP7B1 MUTATION ANALYSIS"
[1] 3
  CYP7B1 MUTATED CYP7B1 WILD-TYPE 
              16              273 
  CYP7B1 MUTATED CYP7B1 WILD-TYPE 
              16              273 
[1] "EDNRB MUTATION ANALYSIS"
[1] 3
  EDNRB MUTATED EDNRB WILD-TYPE 
             25             264 
  EDNRB MUTATED EDNRB WILD-TYPE 
             25             264 
[1] "STAU2 MUTATION ANALYSIS"
[1] 3
  STAU2 MUTATED STAU2 WILD-TYPE 
              8             281 
  STAU2 MUTATED STAU2 WILD-TYPE 
              8             281 
[1] "ARHGEF17 MUTATION ANALYSIS"
[1] 3
  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE 
                17                272 
  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE 
                17                272 
[1] "C10ORF120 MUTATION ANALYSIS"
[1] 3
  C10ORF120 MUTATED C10ORF120 WILD-TYPE 
                  5                 284 
  C10ORF120 MUTATED C10ORF120 WILD-TYPE 
                  5                 284 
[1] "SLC45A4 MUTATION ANALYSIS"
[1] 3
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
               18               271 
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
               18               271 
[1] "CSNK1G3 MUTATION ANALYSIS"
[1] 3
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
                7               282 
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
                7               282 
[1] "SLFN12 MUTATION ANALYSIS"
[1] 3
  SLFN12 MUTATED SLFN12 WILD-TYPE 
               7              282 
  SLFN12 MUTATED SLFN12 WILD-TYPE 
               7              282 
[1] "ARFGEF1 MUTATION ANALYSIS"
[1] 3
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
               24               265 
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
               24               265 
[1] "HDLBP MUTATION ANALYSIS"
[1] 3
  HDLBP MUTATED HDLBP WILD-TYPE 
             24             265 
  HDLBP MUTATED HDLBP WILD-TYPE 
             24             265 
[1] "SYCP2 MUTATION ANALYSIS"
[1] 3
  SYCP2 MUTATED SYCP2 WILD-TYPE 
             17             272 
  SYCP2 MUTATED SYCP2 WILD-TYPE 
             17             272 
[1] "TUBE1 MUTATION ANALYSIS"
[1] 3
  TUBE1 MUTATED TUBE1 WILD-TYPE 
              7             282 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
              7             282 
[1] "PTPRJ MUTATION ANALYSIS"
[1] 3
  PTPRJ MUTATED PTPRJ WILD-TYPE 
             24             265 
  PTPRJ MUTATED PTPRJ WILD-TYPE 
             24             265 
[1] "MDM2 MUTATION ANALYSIS"
[1] 3
  MDM2 MUTATED MDM2 WILD-TYPE 
             5            284 
  MDM2 MUTATED MDM2 WILD-TYPE 
             5            284 
[1] "MZF1 MUTATION ANALYSIS"
[1] 3
  MZF1 MUTATED MZF1 WILD-TYPE 
            10            279 
  MZF1 MUTATED MZF1 WILD-TYPE 
            10            279 
[1] "SIK1 MUTATION ANALYSIS"
[1] 3
  SIK1 MUTATED SIK1 WILD-TYPE 
             5            284 
  SIK1 MUTATED SIK1 WILD-TYPE 
             5            284 
[1] "PIGT MUTATION ANALYSIS"
[1] 3
  PIGT MUTATED PIGT WILD-TYPE 
             8            281 
  PIGT MUTATED PIGT WILD-TYPE 
             8            281 
[1] "NUPL2 MUTATION ANALYSIS"
[1] 3
  NUPL2 MUTATED NUPL2 WILD-TYPE 
              7             282 
  NUPL2 MUTATED NUPL2 WILD-TYPE 
              7             282 
[1] "NOS3 MUTATION ANALYSIS"
[1] 3
  NOS3 MUTATED NOS3 WILD-TYPE 
            10            279 
  NOS3 MUTATED NOS3 WILD-TYPE 
            10            279 
[1] "LUC7L3 MUTATION ANALYSIS"
[1] 3
  LUC7L3 MUTATED LUC7L3 WILD-TYPE 
               6              283 
  LUC7L3 MUTATED LUC7L3 WILD-TYPE 
               6              283 
[1] "LINGO4 MUTATION ANALYSIS"
[1] 3
  LINGO4 MUTATED LINGO4 WILD-TYPE 
              10              279 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
              10              279 
[1] "CHRNB3 MUTATION ANALYSIS"
[1] 3
  CHRNB3 MUTATED CHRNB3 WILD-TYPE 
              11              278 
  CHRNB3 MUTATED CHRNB3 WILD-TYPE 
              11              278 
[1] "NARG2 MUTATION ANALYSIS"
[1] 3
  NARG2 MUTATED NARG2 WILD-TYPE 
             11             278 
  NARG2 MUTATED NARG2 WILD-TYPE 
             11             278 
[1] "FLG MUTATION ANALYSIS"
[1] 3
  FLG MUTATED FLG WILD-TYPE 
           62           227 
  FLG MUTATED FLG WILD-TYPE 
           62           227 
[1] "PCBP2 MUTATION ANALYSIS"
[1] 3
  PCBP2 MUTATED PCBP2 WILD-TYPE 
              4             285 
  PCBP2 MUTATED PCBP2 WILD-TYPE 
              4             285 
[1] "PIAS3 MUTATION ANALYSIS"
[1] 3
  PIAS3 MUTATED PIAS3 WILD-TYPE 
              5             284 
  PIAS3 MUTATED PIAS3 WILD-TYPE 
              5             284 
[1] "SERPINA1 MUTATION ANALYSIS"
[1] 3
  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
                 7                282 
  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
                 7                282 
[1] "PIWIL2 MUTATION ANALYSIS"
[1] 3
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
               6              283 
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
               6              283 
[1] "TMEM79 MUTATION ANALYSIS"
[1] 3
  TMEM79 MUTATED TMEM79 WILD-TYPE 
               6              283 
  TMEM79 MUTATED TMEM79 WILD-TYPE 
               6              283 
[1] "HIST1H1B MUTATION ANALYSIS"
[1] 3
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 9                280 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 9                280 
[1] "FGF13 MUTATION ANALYSIS"
[1] 3
  FGF13 MUTATED FGF13 WILD-TYPE 
              9             280 
  FGF13 MUTATED FGF13 WILD-TYPE 
              9             280 
[1] "SCAMP2 MUTATION ANALYSIS"
[1] 3
  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
               6              283 
  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
               6              283 
[1] "SLC22A16 MUTATION ANALYSIS"
[1] 3
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                11                278 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                11                278 
[1] "GLYR1 MUTATION ANALYSIS"
[1] 3
  GLYR1 MUTATED GLYR1 WILD-TYPE 
             13             276 
  GLYR1 MUTATED GLYR1 WILD-TYPE 
             13             276 
[1] "LRRC43 MUTATION ANALYSIS"
[1] 3
  LRRC43 MUTATED LRRC43 WILD-TYPE 
              10              279 
  LRRC43 MUTATED LRRC43 WILD-TYPE 
              10              279 
[1] "NLRC5 MUTATION ANALYSIS"
[1] 3
  NLRC5 MUTATED NLRC5 WILD-TYPE 
             19             270 
  NLRC5 MUTATED NLRC5 WILD-TYPE 
             19             270 
[1] "EAF2 MUTATION ANALYSIS"
[1] 3
  EAF2 MUTATED EAF2 WILD-TYPE 
             7            282 
  EAF2 MUTATED EAF2 WILD-TYPE 
             7            282 
[1] "PHF20 MUTATION ANALYSIS"
[1] 3
  PHF20 MUTATED PHF20 WILD-TYPE 
             11             278 
  PHF20 MUTATED PHF20 WILD-TYPE 
             11             278 
[1] "UBXN6 MUTATION ANALYSIS"
[1] 3
  UBXN6 MUTATED UBXN6 WILD-TYPE 
             12             277 
  UBXN6 MUTATED UBXN6 WILD-TYPE 
             12             277 
[1] "ZNF367 MUTATION ANALYSIS"
[1] 3
  ZNF367 MUTATED ZNF367 WILD-TYPE 
               4              285 
  ZNF367 MUTATED ZNF367 WILD-TYPE 
               4              285 
[1] "NEK8 MUTATION ANALYSIS"
[1] 3
  NEK8 MUTATED NEK8 WILD-TYPE 
            11            278 
  NEK8 MUTATED NEK8 WILD-TYPE 
            11            278 
[1] "ZNF292 MUTATION ANALYSIS"
[1] 3
  ZNF292 MUTATED ZNF292 WILD-TYPE 
              21              268 
  ZNF292 MUTATED ZNF292 WILD-TYPE 
              21              268 
[1] "NT5DC1 MUTATION ANALYSIS"
[1] 3
  NT5DC1 MUTATED NT5DC1 WILD-TYPE 
               6              283 
  NT5DC1 MUTATED NT5DC1 WILD-TYPE 
               6              283 
[1] "DUSP9 MUTATION ANALYSIS"
[1] 3
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              5             284 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              5             284 
[1] "ABCA5 MUTATION ANALYSIS"
[1] 3
  ABCA5 MUTATED ABCA5 WILD-TYPE 
             20             269 
  ABCA5 MUTATED ABCA5 WILD-TYPE 
             20             269 
[1] "GFOD1 MUTATION ANALYSIS"
[1] 3
  GFOD1 MUTATED GFOD1 WILD-TYPE 
             13             276 
  GFOD1 MUTATED GFOD1 WILD-TYPE 
             13             276 
[1] "ZNF334 MUTATION ANALYSIS"
[1] 3
  ZNF334 MUTATED ZNF334 WILD-TYPE 
              12              277 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
              12              277 
[1] "MUT MUTATION ANALYSIS"
[1] 3
  MUT MUTATED MUT WILD-TYPE 
            6           283 
  MUT MUTATED MUT WILD-TYPE 
            6           283 
[1] "MGST2 MUTATION ANALYSIS"
[1] 3
  MGST2 MUTATED MGST2 WILD-TYPE 
              3             286 
  MGST2 MUTATED MGST2 WILD-TYPE 
              3             286 
[1] "GPATCH4 MUTATION ANALYSIS"
[1] 3
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
                8               281 
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
                8               281 
[1] "MAP2K1 MUTATION ANALYSIS"
[1] 3
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
               5              284 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
               5              284 
[1] "TCEAL5 MUTATION ANALYSIS"
[1] 3
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
               6              283 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
               6              283 
[1] "GANAB MUTATION ANALYSIS"
[1] 3
  GANAB MUTATED GANAB WILD-TYPE 
             10             279 
  GANAB MUTATED GANAB WILD-TYPE 
             10             279 
[1] "PIAS1 MUTATION ANALYSIS"
[1] 3
  PIAS1 MUTATED PIAS1 WILD-TYPE 
             10             279 
  PIAS1 MUTATED PIAS1 WILD-TYPE 
             10             279 
[1] "YLPM1 MUTATION ANALYSIS"
[1] 3
  YLPM1 MUTATED YLPM1 WILD-TYPE 
             18             271 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
             18             271 
[1] "SMAD7 MUTATION ANALYSIS"
[1] 3
  SMAD7 MUTATED SMAD7 WILD-TYPE 
              5             284 
  SMAD7 MUTATED SMAD7 WILD-TYPE 
              5             284 
[1] "PPARGC1B MUTATION ANALYSIS"
[1] 3
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 7                282 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 7                282 
[1] "TSPYL5 MUTATION ANALYSIS"
[1] 3
  TSPYL5 MUTATED TSPYL5 WILD-TYPE 
               9              280 
  TSPYL5 MUTATED TSPYL5 WILD-TYPE 
               9              280 
[1] "UPK2 MUTATION ANALYSIS"
[1] 3
  UPK2 MUTATED UPK2 WILD-TYPE 
             3            286 
  UPK2 MUTATED UPK2 WILD-TYPE 
             3            286 
[1] "BCKDHA MUTATION ANALYSIS"
[1] 3
  BCKDHA MUTATED BCKDHA WILD-TYPE 
              12              277 
  BCKDHA MUTATED BCKDHA WILD-TYPE 
              12              277 
[1] "BRD3 MUTATION ANALYSIS"
[1] 3
  BRD3 MUTATED BRD3 WILD-TYPE 
            16            273 
  BRD3 MUTATED BRD3 WILD-TYPE 
            16            273 
[1] "PNMT MUTATION ANALYSIS"
[1] 3
  PNMT MUTATED PNMT WILD-TYPE 
             8            281 
  PNMT MUTATED PNMT WILD-TYPE 
             8            281 
[1] "IGSF21 MUTATION ANALYSIS"
[1] 3
  IGSF21 MUTATED IGSF21 WILD-TYPE 
               3              286 
  IGSF21 MUTATED IGSF21 WILD-TYPE 
               3              286 
[1] "TAS2R10 MUTATION ANALYSIS"
[1] 3
  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
                3               286 
  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
                3               286 
[1] "TNKS1BP1 MUTATION ANALYSIS"
[1] 3
  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
                19                270 
  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
                19                270 
[1] "KIRREL2 MUTATION ANALYSIS"
[1] 3
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
               12               277 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
               12               277 
[1] "NID2 MUTATION ANALYSIS"
[1] 3
  NID2 MUTATED NID2 WILD-TYPE 
            17            272 
  NID2 MUTATED NID2 WILD-TYPE 
            17            272 
[1] "FOXQ1 MUTATION ANALYSIS"
[1] 3
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              3             286 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              3             286 
[1] "SMAD2 MUTATION ANALYSIS"
[1] 3
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              9             280 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              9             280 
[1] "LARP1 MUTATION ANALYSIS"
[1] 3
  LARP1 MUTATED LARP1 WILD-TYPE 
             10             279 
  LARP1 MUTATED LARP1 WILD-TYPE 
             10             279 
[1] "FAM186B MUTATION ANALYSIS"
[1] 3
  FAM186B MUTATED FAM186B WILD-TYPE 
               10               279 
  FAM186B MUTATED FAM186B WILD-TYPE 
               10               279 
[1] "TBC1D23 MUTATION ANALYSIS"
[1] 3
  TBC1D23 MUTATED TBC1D23 WILD-TYPE 
                4               285 
  TBC1D23 MUTATED TBC1D23 WILD-TYPE 
                4               285 
[1] "UGP2 MUTATION ANALYSIS"
[1] 3
  UGP2 MUTATED UGP2 WILD-TYPE 
             7            282 
  UGP2 MUTATED UGP2 WILD-TYPE 
             7            282 
[1] "FBN3 MUTATION ANALYSIS"
[1] 3
  FBN3 MUTATED FBN3 WILD-TYPE 
            28            261 
  FBN3 MUTATED FBN3 WILD-TYPE 
            28            261 
[1] "IK MUTATION ANALYSIS"
[1] 3
  IK MUTATED IK WILD-TYPE 
           6          283 
  IK MUTATED IK WILD-TYPE 
           6          283 
[1] "FAHD2B MUTATION ANALYSIS"
[1] 3
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               5              284 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               5              284 
[1] "GPC4 MUTATION ANALYSIS"
[1] 3
  GPC4 MUTATED GPC4 WILD-TYPE 
             9            280 
  GPC4 MUTATED GPC4 WILD-TYPE 
             9            280 
[1] "CLGN MUTATION ANALYSIS"
[1] 3
  CLGN MUTATED CLGN WILD-TYPE 
             8            281 
  CLGN MUTATED CLGN WILD-TYPE 
             8            281 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           25           264 
  NF1 MUTATED NF1 WILD-TYPE 
           25           264 
[1] "LCE1A MUTATION ANALYSIS"
[1] 3
  LCE1A MUTATED LCE1A WILD-TYPE 
              3             286 
  LCE1A MUTATED LCE1A WILD-TYPE 
              3             286 
[1] "NBN MUTATION ANALYSIS"
[1] 3
  NBN MUTATED NBN WILD-TYPE 
           13           276 
  NBN MUTATED NBN WILD-TYPE 
           13           276 
[1] "PRKAR1B MUTATION ANALYSIS"
[1] 3
  PRKAR1B MUTATED PRKAR1B WILD-TYPE 
                5               284 
  PRKAR1B MUTATED PRKAR1B WILD-TYPE 
                5               284 
[1] "PPP1R13B MUTATION ANALYSIS"
[1] 3
  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
                10                279 
  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
                10                279 
[1] "PHACTR1 MUTATION ANALYSIS"
[1] 3
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
                9               280 
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
                9               280 
[1] "DHRS9 MUTATION ANALYSIS"
[1] 3
  DHRS9 MUTATED DHRS9 WILD-TYPE 
              9             280 
  DHRS9 MUTATED DHRS9 WILD-TYPE 
              9             280 
[1] "PRICKLE4 MUTATION ANALYSIS"
[1] 3
  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
                 6                283 
  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
                 6                283 
[1] "TRIM46 MUTATION ANALYSIS"
[1] 3
  TRIM46 MUTATED TRIM46 WILD-TYPE 
              12              277 
  TRIM46 MUTATED TRIM46 WILD-TYPE 
              12              277 
[1] "FOXJ1 MUTATION ANALYSIS"
[1] 3
  FOXJ1 MUTATED FOXJ1 WILD-TYPE 
              5             284 
  FOXJ1 MUTATED FOXJ1 WILD-TYPE 
              5             284 
[1] "DCHS1 MUTATION ANALYSIS"
[1] 3
  DCHS1 MUTATED DCHS1 WILD-TYPE 
             29             260 
  DCHS1 MUTATED DCHS1 WILD-TYPE 
             29             260 
[1] "HLA-F MUTATION ANALYSIS"
[1] 3
  HLA-F MUTATED HLA-F WILD-TYPE 
             11             278 
  HLA-F MUTATED HLA-F WILD-TYPE 
             11             278 
[1] "WNT9A MUTATION ANALYSIS"
[1] 3
  WNT9A MUTATED WNT9A WILD-TYPE 
              8             281 
  WNT9A MUTATED WNT9A WILD-TYPE 
              8             281 
[1] "PPL MUTATION ANALYSIS"
[1] 3
  PPL MUTATED PPL WILD-TYPE 
           16           273 
  PPL MUTATED PPL WILD-TYPE 
           16           273 
[1] "PTOV1 MUTATION ANALYSIS"
[1] 3
  PTOV1 MUTATED PTOV1 WILD-TYPE 
              9             280 
  PTOV1 MUTATED PTOV1 WILD-TYPE 
              9             280 
[1] "PCCA MUTATION ANALYSIS"
[1] 3
  PCCA MUTATED PCCA WILD-TYPE 
             8            281 
  PCCA MUTATED PCCA WILD-TYPE 
             8            281 
[1] "TAF6 MUTATION ANALYSIS"
[1] 3
  TAF6 MUTATED TAF6 WILD-TYPE 
            12            277 
  TAF6 MUTATED TAF6 WILD-TYPE 
            12            277 
[1] "ITGA7 MUTATION ANALYSIS"
[1] 3
  ITGA7 MUTATED ITGA7 WILD-TYPE 
             14             275 
  ITGA7 MUTATED ITGA7 WILD-TYPE 
             14             275 
[1] "C11ORF63 MUTATION ANALYSIS"
[1] 3
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
                15                274 
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
                15                274 
[1] "ENOSF1 MUTATION ANALYSIS"
[1] 3
  ENOSF1 MUTATED ENOSF1 WILD-TYPE 
               7              282 
  ENOSF1 MUTATED ENOSF1 WILD-TYPE 
               7              282 
[1] "SLC38A6 MUTATION ANALYSIS"
[1] 3
  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
                8               281 
  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
                8               281 
[1] "KCNC1 MUTATION ANALYSIS"
[1] 3
  KCNC1 MUTATED KCNC1 WILD-TYPE 
              7             282 
  KCNC1 MUTATED KCNC1 WILD-TYPE 
              7             282 
[1] "AMPD3 MUTATION ANALYSIS"
[1] 3
  AMPD3 MUTATED AMPD3 WILD-TYPE 
             19             270 
  AMPD3 MUTATED AMPD3 WILD-TYPE 
             19             270 
[1] "PPARG MUTATION ANALYSIS"
[1] 3
  PPARG MUTATED PPARG WILD-TYPE 
              4             285 
  PPARG MUTATED PPARG WILD-TYPE 
              4             285 
[1] "TRIM27 MUTATION ANALYSIS"
[1] 3
  TRIM27 MUTATED TRIM27 WILD-TYPE 
               5              284 
  TRIM27 MUTATED TRIM27 WILD-TYPE 
               5              284 
[1] "MMP3 MUTATION ANALYSIS"
[1] 3
  MMP3 MUTATED MMP3 WILD-TYPE 
             8            281 
  MMP3 MUTATED MMP3 WILD-TYPE 
             8            281 
[1] "IDE MUTATION ANALYSIS"
[1] 3
  IDE MUTATED IDE WILD-TYPE 
            9           280 
  IDE MUTATED IDE WILD-TYPE 
            9           280 
[1] "LARP7 MUTATION ANALYSIS"
[1] 3
  LARP7 MUTATED LARP7 WILD-TYPE 
              3             286 
  LARP7 MUTATED LARP7 WILD-TYPE 
              3             286 
[1] "KIF6 MUTATION ANALYSIS"
[1] 3
  KIF6 MUTATED KIF6 WILD-TYPE 
             7            282 
  KIF6 MUTATED KIF6 WILD-TYPE 
             7            282 
[1] "PLEKHH3 MUTATION ANALYSIS"
[1] 3
  PLEKHH3 MUTATED PLEKHH3 WILD-TYPE 
                9               280 
  PLEKHH3 MUTATED PLEKHH3 WILD-TYPE 
                9               280 
[1] "WSB2 MUTATION ANALYSIS"
[1] 3
  WSB2 MUTATED WSB2 WILD-TYPE 
             9            280 
  WSB2 MUTATED WSB2 WILD-TYPE 
             9            280 
[1] "KIAA1609 MUTATION ANALYSIS"
[1] 3
  KIAA1609 MUTATED KIAA1609 WILD-TYPE 
                 7                282 
  KIAA1609 MUTATED KIAA1609 WILD-TYPE 
                 7                282 
[1] "AKAP11 MUTATION ANALYSIS"
[1] 3
  AKAP11 MUTATED AKAP11 WILD-TYPE 
              14              275 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
              14              275 
[1] "VASH1 MUTATION ANALYSIS"
[1] 3
  VASH1 MUTATED VASH1 WILD-TYPE 
              7             282 
  VASH1 MUTATED VASH1 WILD-TYPE 
              7             282 
[1] "IFNA17 MUTATION ANALYSIS"
[1] 3
  IFNA17 MUTATED IFNA17 WILD-TYPE 
               4              285 
  IFNA17 MUTATED IFNA17 WILD-TYPE 
               4              285 
[1] "SBF1 MUTATION ANALYSIS"
[1] 3
  SBF1 MUTATED SBF1 WILD-TYPE 
            27            262 
  SBF1 MUTATED SBF1 WILD-TYPE 
            27            262 
[1] "SCN9A MUTATION ANALYSIS"
[1] 3
  SCN9A MUTATED SCN9A WILD-TYPE 
             28             261 
  SCN9A MUTATED SCN9A WILD-TYPE 
             28             261 
[1] "KIAA0586 MUTATION ANALYSIS"
[1] 3
  KIAA0586 MUTATED KIAA0586 WILD-TYPE 
                10                279 
  KIAA0586 MUTATED KIAA0586 WILD-TYPE 
                10                279 
[1] "MACF1 MUTATION ANALYSIS"
[1] 3
  MACF1 MUTATED MACF1 WILD-TYPE 
             45             244 
  MACF1 MUTATED MACF1 WILD-TYPE 
             45             244 
[1] "DYRK1A MUTATION ANALYSIS"
[1] 3
  DYRK1A MUTATED DYRK1A WILD-TYPE 
               9              280 
  DYRK1A MUTATED DYRK1A WILD-TYPE 
               9              280 
[1] "GALK1 MUTATION ANALYSIS"
[1] 3
  GALK1 MUTATED GALK1 WILD-TYPE 
              4             285 
  GALK1 MUTATED GALK1 WILD-TYPE 
              4             285 
[1] "DENND1C MUTATION ANALYSIS"
[1] 3
  DENND1C MUTATED DENND1C WILD-TYPE 
                7               282 
  DENND1C MUTATED DENND1C WILD-TYPE 
                7               282 
[1] "CNKSR1 MUTATION ANALYSIS"
[1] 3
  CNKSR1 MUTATED CNKSR1 WILD-TYPE 
               7              282 
  CNKSR1 MUTATED CNKSR1 WILD-TYPE 
               7              282 
[1] "MYCT1 MUTATION ANALYSIS"
[1] 3
  MYCT1 MUTATED MYCT1 WILD-TYPE 
              6             283 
  MYCT1 MUTATED MYCT1 WILD-TYPE 
              6             283 
[1] "ATRIP MUTATION ANALYSIS"
[1] 3
  ATRIP MUTATED ATRIP WILD-TYPE 
              5             284 
  ATRIP MUTATED ATRIP WILD-TYPE 
              5             284 
[1] "TIMP3 MUTATION ANALYSIS"
[1] 3
  TIMP3 MUTATED TIMP3 WILD-TYPE 
              6             283 
  TIMP3 MUTATED TIMP3 WILD-TYPE 
              6             283 
[1] "ELK3 MUTATION ANALYSIS"
[1] 3
  ELK3 MUTATED ELK3 WILD-TYPE 
             6            283 
  ELK3 MUTATED ELK3 WILD-TYPE 
             6            283 
[1] "CD3EAP MUTATION ANALYSIS"
[1] 3
  CD3EAP MUTATED CD3EAP WILD-TYPE 
               7              282 
  CD3EAP MUTATED CD3EAP WILD-TYPE 
               7              282 
[1] "MAPK15 MUTATION ANALYSIS"
[1] 3
  MAPK15 MUTATED MAPK15 WILD-TYPE 
               7              282 
  MAPK15 MUTATED MAPK15 WILD-TYPE 
               7              282 
[1] "PARP15 MUTATION ANALYSIS"
[1] 3
  PARP15 MUTATED PARP15 WILD-TYPE 
               4              285 
  PARP15 MUTATED PARP15 WILD-TYPE 
               4              285 
[1] "TM6SF1 MUTATION ANALYSIS"
[1] 3
  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
               6              283 
  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
               6              283 
[1] "DDX50 MUTATION ANALYSIS"
[1] 3
  DDX50 MUTATED DDX50 WILD-TYPE 
             11             278 
  DDX50 MUTATED DDX50 WILD-TYPE 
             11             278 
[1] "CCDC27 MUTATION ANALYSIS"
[1] 3
  CCDC27 MUTATED CCDC27 WILD-TYPE 
               6              283 
  CCDC27 MUTATED CCDC27 WILD-TYPE 
               6              283 
[1] "EPHB6 MUTATION ANALYSIS"
[1] 3
  EPHB6 MUTATED EPHB6 WILD-TYPE 
             11             278 
  EPHB6 MUTATED EPHB6 WILD-TYPE 
             11             278 
[1] "TRIP11 MUTATION ANALYSIS"
[1] 3
  TRIP11 MUTATED TRIP11 WILD-TYPE 
              13              276 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
              13              276 
[1] "ITGAV MUTATION ANALYSIS"
[1] 3
  ITGAV MUTATED ITGAV WILD-TYPE 
             13             276 
  ITGAV MUTATED ITGAV WILD-TYPE 
             13             276 
[1] "BCL2L14 MUTATION ANALYSIS"
[1] 3
  BCL2L14 MUTATED BCL2L14 WILD-TYPE 
                3               286 
  BCL2L14 MUTATED BCL2L14 WILD-TYPE 
                3               286 
[1] "CDX2 MUTATION ANALYSIS"
[1] 3
  CDX2 MUTATED CDX2 WILD-TYPE 
             3            286 
  CDX2 MUTATED CDX2 WILD-TYPE 
             3            286 
[1] "SLC7A10 MUTATION ANALYSIS"
[1] 3
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                5               284 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                5               284 
[1] "RGS2 MUTATION ANALYSIS"
[1] 3
  RGS2 MUTATED RGS2 WILD-TYPE 
             3            286 
  RGS2 MUTATED RGS2 WILD-TYPE 
             3            286 
[1] "SAMD9L MUTATION ANALYSIS"
[1] 3
  SAMD9L MUTATED SAMD9L WILD-TYPE 
              18              271 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
              18              271 
[1] "DUSP11 MUTATION ANALYSIS"
[1] 3
  DUSP11 MUTATED DUSP11 WILD-TYPE 
               4              285 
  DUSP11 MUTATED DUSP11 WILD-TYPE 
               4              285 
[1] "MRPL2 MUTATION ANALYSIS"
[1] 3
  MRPL2 MUTATED MRPL2 WILD-TYPE 
              6             283 
  MRPL2 MUTATED MRPL2 WILD-TYPE 
              6             283 
[1] "SLC4A3 MUTATION ANALYSIS"
[1] 3
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
              15              274 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
              15              274 
[1] "ZDHHC5 MUTATION ANALYSIS"
[1] 3
  ZDHHC5 MUTATED ZDHHC5 WILD-TYPE 
              10              279 
  ZDHHC5 MUTATED ZDHHC5 WILD-TYPE 
              10              279 
[1] "GCDH MUTATION ANALYSIS"
[1] 3
  GCDH MUTATED GCDH WILD-TYPE 
             8            281 
  GCDH MUTATED GCDH WILD-TYPE 
             8            281 
[1] "BTNL8 MUTATION ANALYSIS"
[1] 3
  BTNL8 MUTATED BTNL8 WILD-TYPE 
              6             283 
  BTNL8 MUTATED BTNL8 WILD-TYPE 
              6             283 
[1] "RASA2 MUTATION ANALYSIS"
[1] 3
  RASA2 MUTATED RASA2 WILD-TYPE 
              8             281 
  RASA2 MUTATED RASA2 WILD-TYPE 
              8             281 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              10              279 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              10              279 
[1] "CDC5L MUTATION ANALYSIS"
[1] 3
  CDC5L MUTATED CDC5L WILD-TYPE 
             15             274 
  CDC5L MUTATED CDC5L WILD-TYPE 
             15             274 
[1] "COL20A1 MUTATION ANALYSIS"
[1] 3
  COL20A1 MUTATED COL20A1 WILD-TYPE 
               18               271 
  COL20A1 MUTATED COL20A1 WILD-TYPE 
               18               271 
[1] "AP3M2 MUTATION ANALYSIS"
[1] 3
  AP3M2 MUTATED AP3M2 WILD-TYPE 
             10             279 
  AP3M2 MUTATED AP3M2 WILD-TYPE 
             10             279 
[1] "NAA16 MUTATION ANALYSIS"
[1] 3
  NAA16 MUTATED NAA16 WILD-TYPE 
              8             281 
  NAA16 MUTATED NAA16 WILD-TYPE 
              8             281 
[1] "NPR3 MUTATION ANALYSIS"
[1] 3
  NPR3 MUTATED NPR3 WILD-TYPE 
            11            278 
  NPR3 MUTATED NPR3 WILD-TYPE 
            11            278 
[1] "COX8C MUTATION ANALYSIS"
[1] 3
  COX8C MUTATED COX8C WILD-TYPE 
              4             285 
  COX8C MUTATED COX8C WILD-TYPE 
              4             285 
[1] "KLHDC8B MUTATION ANALYSIS"
[1] 3
  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
                8               281 
  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
                8               281 
[1] "ZBTB40 MUTATION ANALYSIS"
[1] 3
  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
              10              279 
  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
              10              279 
[1] "FOLH1 MUTATION ANALYSIS"
[1] 3
  FOLH1 MUTATED FOLH1 WILD-TYPE 
             11             278 
  FOLH1 MUTATED FOLH1 WILD-TYPE 
             11             278 
[1] "TXLNG MUTATION ANALYSIS"
[1] 3
  TXLNG MUTATED TXLNG WILD-TYPE 
              7             282 
  TXLNG MUTATED TXLNG WILD-TYPE 
              7             282 
[1] "SFTPC MUTATION ANALYSIS"
[1] 3
  SFTPC MUTATED SFTPC WILD-TYPE 
              3             286 
  SFTPC MUTATED SFTPC WILD-TYPE 
              3             286 
[1] "P2RX1 MUTATION ANALYSIS"
[1] 3
  P2RX1 MUTATED P2RX1 WILD-TYPE 
              3             286 
  P2RX1 MUTATED P2RX1 WILD-TYPE 
              3             286 
[1] "CORIN MUTATION ANALYSIS"
[1] 3
  CORIN MUTATED CORIN WILD-TYPE 
             10             279 
  CORIN MUTATED CORIN WILD-TYPE 
             10             279 
[1] "ACSS2 MUTATION ANALYSIS"
[1] 3
  ACSS2 MUTATED ACSS2 WILD-TYPE 
              9             280 
  ACSS2 MUTATED ACSS2 WILD-TYPE 
              9             280 
[1] "CD1E MUTATION ANALYSIS"
[1] 3
  CD1E MUTATED CD1E WILD-TYPE 
             7            282 
  CD1E MUTATED CD1E WILD-TYPE 
             7            282 
[1] "SCN10A MUTATION ANALYSIS"
[1] 3
  SCN10A MUTATED SCN10A WILD-TYPE 
              28              261 
  SCN10A MUTATED SCN10A WILD-TYPE 
              28              261 
[1] "CBLN3 MUTATION ANALYSIS"
[1] 3
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              5             284 
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              5             284 
[1] "DGKD MUTATION ANALYSIS"
[1] 3
  DGKD MUTATED DGKD WILD-TYPE 
             6            283 
  DGKD MUTATED DGKD WILD-TYPE 
             6            283 
[1] "MAGI2 MUTATION ANALYSIS"
[1] 3
  MAGI2 MUTATED MAGI2 WILD-TYPE 
             28             261 
  MAGI2 MUTATED MAGI2 WILD-TYPE 
             28             261 
[1] "FIGNL1 MUTATION ANALYSIS"
[1] 3
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
               9              280 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
               9              280 
[1] "STK36 MUTATION ANALYSIS"
[1] 3
  STK36 MUTATED STK36 WILD-TYPE 
             10             279 
  STK36 MUTATED STK36 WILD-TYPE 
             10             279 
[1] "USP13 MUTATION ANALYSIS"
[1] 3
  USP13 MUTATED USP13 WILD-TYPE 
             11             278 
  USP13 MUTATED USP13 WILD-TYPE 
             11             278 
[1] "CALCRL MUTATION ANALYSIS"
[1] 3
  CALCRL MUTATED CALCRL WILD-TYPE 
               8              281 
  CALCRL MUTATED CALCRL WILD-TYPE 
               8              281 
[1] "AFP MUTATION ANALYSIS"
[1] 3
  AFP MUTATED AFP WILD-TYPE 
            3           286 
  AFP MUTATED AFP WILD-TYPE 
            3           286 
[1] "DISP2 MUTATION ANALYSIS"
[1] 3
  DISP2 MUTATED DISP2 WILD-TYPE 
             15             274 
  DISP2 MUTATED DISP2 WILD-TYPE 
             15             274 
[1] "MGA MUTATION ANALYSIS"
[1] 3
  MGA MUTATED MGA WILD-TYPE 
           25           264 
  MGA MUTATED MGA WILD-TYPE 
           25           264 
[1] "PPP1R12C MUTATION ANALYSIS"
[1] 3
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
                 5                284 
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
                 5                284 
[1] "UNC50 MUTATION ANALYSIS"
[1] 3
  UNC50 MUTATED UNC50 WILD-TYPE 
              3             286 
  UNC50 MUTATED UNC50 WILD-TYPE 
              3             286 
[1] "CNGA4 MUTATION ANALYSIS"
[1] 3
  CNGA4 MUTATED CNGA4 WILD-TYPE 
             18             271 
  CNGA4 MUTATED CNGA4 WILD-TYPE 
             18             271 
[1] "C3 MUTATION ANALYSIS"
[1] 3
  C3 MUTATED C3 WILD-TYPE 
          25          264 
  C3 MUTATED C3 WILD-TYPE 
          25          264 
[1] "GPX6 MUTATION ANALYSIS"
[1] 3
  GPX6 MUTATED GPX6 WILD-TYPE 
             4            285 
  GPX6 MUTATED GPX6 WILD-TYPE 
             4            285 
[1] "KANK4 MUTATION ANALYSIS"
[1] 3
  KANK4 MUTATED KANK4 WILD-TYPE 
             10             279 
  KANK4 MUTATED KANK4 WILD-TYPE 
             10             279 
[1] "CASP1 MUTATION ANALYSIS"
[1] 3
  CASP1 MUTATED CASP1 WILD-TYPE 
              4             285 
  CASP1 MUTATED CASP1 WILD-TYPE 
              4             285 
[1] "ELL2 MUTATION ANALYSIS"
[1] 3
  ELL2 MUTATED ELL2 WILD-TYPE 
            12            277 
  ELL2 MUTATED ELL2 WILD-TYPE 
            12            277 
[1] "PIK3C2G MUTATION ANALYSIS"
[1] 3
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
               10               279 
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
               10               279 
[1] "KIAA0664 MUTATION ANALYSIS"
[1] 3
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
                13                276 
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
                13                276 
[1] "SOS2 MUTATION ANALYSIS"
[1] 3
  SOS2 MUTATED SOS2 WILD-TYPE 
            19            270 
  SOS2 MUTATED SOS2 WILD-TYPE 
            19            270 
[1] "ATL3 MUTATION ANALYSIS"
[1] 3
  ATL3 MUTATED ATL3 WILD-TYPE 
            12            277 
  ATL3 MUTATED ATL3 WILD-TYPE 
            12            277 
[1] "PEG3 MUTATION ANALYSIS"
[1] 3
  PEG3 MUTATED PEG3 WILD-TYPE 
            31            258 
  PEG3 MUTATED PEG3 WILD-TYPE 
            31            258 
[1] "SMARCAL1 MUTATION ANALYSIS"
[1] 3
  SMARCAL1 MUTATED SMARCAL1 WILD-TYPE 
                13                276 
  SMARCAL1 MUTATED SMARCAL1 WILD-TYPE 
                13                276 
[1] "THBS1 MUTATION ANALYSIS"
[1] 3
  THBS1 MUTATED THBS1 WILD-TYPE 
             15             274 
  THBS1 MUTATED THBS1 WILD-TYPE 
             15             274 
[1] "PUS7 MUTATION ANALYSIS"
[1] 3
  PUS7 MUTATED PUS7 WILD-TYPE 
            10            279 
  PUS7 MUTATED PUS7 WILD-TYPE 
            10            279 
[1] "RALGDS MUTATION ANALYSIS"
[1] 3
  RALGDS MUTATED RALGDS WILD-TYPE 
              13              276 
  RALGDS MUTATED RALGDS WILD-TYPE 
              13              276 
[1] "CNTROB MUTATION ANALYSIS"
[1] 3
  CNTROB MUTATED CNTROB WILD-TYPE 
               6              283 
  CNTROB MUTATED CNTROB WILD-TYPE 
               6              283 
[1] "PFAS MUTATION ANALYSIS"
[1] 3
  PFAS MUTATED PFAS WILD-TYPE 
             9            280 
  PFAS MUTATED PFAS WILD-TYPE 
             9            280 
[1] "TCF7 MUTATION ANALYSIS"
[1] 3
  TCF7 MUTATED TCF7 WILD-TYPE 
             9            280 
  TCF7 MUTATED TCF7 WILD-TYPE 
             9            280 
[1] "GPATCH8 MUTATION ANALYSIS"
[1] 3
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
               23               266 
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
               23               266 
[1] "PSD MUTATION ANALYSIS"
[1] 3
  PSD MUTATED PSD WILD-TYPE 
           16           273 
  PSD MUTATED PSD WILD-TYPE 
           16           273 
[1] "MMEL1 MUTATION ANALYSIS"
[1] 3
  MMEL1 MUTATED MMEL1 WILD-TYPE 
              6             283 
  MMEL1 MUTATED MMEL1 WILD-TYPE 
              6             283 
[1] "OSBPL2 MUTATION ANALYSIS"
[1] 3
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
               7              282 
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
               7              282 
[1] "TOX MUTATION ANALYSIS"
[1] 3
  TOX MUTATED TOX WILD-TYPE 
            9           280 
  TOX MUTATED TOX WILD-TYPE 
            9           280 
[1] "ROCK1 MUTATION ANALYSIS"
[1] 3
  ROCK1 MUTATED ROCK1 WILD-TYPE 
             16             273 
  ROCK1 MUTATED ROCK1 WILD-TYPE 
             16             273 
[1] "LRP12 MUTATION ANALYSIS"
[1] 3
  LRP12 MUTATED LRP12 WILD-TYPE 
             23             266 
  LRP12 MUTATED LRP12 WILD-TYPE 
             23             266 
[1] "C19ORF70 MUTATION ANALYSIS"
[1] 3
  C19ORF70 MUTATED C19ORF70 WILD-TYPE 
                 6                283 
  C19ORF70 MUTATED C19ORF70 WILD-TYPE 
                 6                283 
[1] "KIAA1217 MUTATION ANALYSIS"
[1] 3
  KIAA1217 MUTATED KIAA1217 WILD-TYPE 
                19                270 
  KIAA1217 MUTATED KIAA1217 WILD-TYPE 
                19                270 
[1] "CENPN MUTATION ANALYSIS"
[1] 3
  CENPN MUTATED CENPN WILD-TYPE 
              4             285 
  CENPN MUTATED CENPN WILD-TYPE 
              4             285 
[1] "MAN2B1 MUTATION ANALYSIS"
[1] 3
  MAN2B1 MUTATED MAN2B1 WILD-TYPE 
              16              273 
  MAN2B1 MUTATED MAN2B1 WILD-TYPE 
              16              273 
[1] "KIAA0226 MUTATION ANALYSIS"
[1] 3
  KIAA0226 MUTATED KIAA0226 WILD-TYPE 
                12                277 
  KIAA0226 MUTATED KIAA0226 WILD-TYPE 
                12                277 
[1] "SP6 MUTATION ANALYSIS"
[1] 3
  SP6 MUTATED SP6 WILD-TYPE 
            3           286 
  SP6 MUTATED SP6 WILD-TYPE 
            3           286 
[1] "CHST9 MUTATION ANALYSIS"
[1] 3
  CHST9 MUTATED CHST9 WILD-TYPE 
              6             283 
  CHST9 MUTATED CHST9 WILD-TYPE 
              6             283 
[1] "ETV1 MUTATION ANALYSIS"
[1] 3
  ETV1 MUTATED ETV1 WILD-TYPE 
            10            279 
  ETV1 MUTATED ETV1 WILD-TYPE 
            10            279 
[1] "NOL6 MUTATION ANALYSIS"
[1] 3
  NOL6 MUTATED NOL6 WILD-TYPE 
            17            272 
  NOL6 MUTATED NOL6 WILD-TYPE 
            17            272 
[1] "TAC4 MUTATION ANALYSIS"
[1] 3
  TAC4 MUTATED TAC4 WILD-TYPE 
             3            286 
  TAC4 MUTATED TAC4 WILD-TYPE 
             3            286 
[1] "RNMT MUTATION ANALYSIS"
[1] 3
  RNMT MUTATED RNMT WILD-TYPE 
             8            281 
  RNMT MUTATED RNMT WILD-TYPE 
             8            281 
[1] "HOOK1 MUTATION ANALYSIS"
[1] 3
  HOOK1 MUTATED HOOK1 WILD-TYPE 
              6             283 
  HOOK1 MUTATED HOOK1 WILD-TYPE 
              6             283 
[1] "CCDC25 MUTATION ANALYSIS"
[1] 3
  CCDC25 MUTATED CCDC25 WILD-TYPE 
               3              286 
  CCDC25 MUTATED CCDC25 WILD-TYPE 
               3              286 
[1] "IQSEC2 MUTATION ANALYSIS"
[1] 3
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
              12              277 
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
              12              277 
[1] "IBTK MUTATION ANALYSIS"
[1] 3
  IBTK MUTATED IBTK WILD-TYPE 
            18            271 
  IBTK MUTATED IBTK WILD-TYPE 
            18            271 
[1] "TDRD3 MUTATION ANALYSIS"
[1] 3
  TDRD3 MUTATED TDRD3 WILD-TYPE 
             11             278 
  TDRD3 MUTATED TDRD3 WILD-TYPE 
             11             278 
[1] "HS6ST2 MUTATION ANALYSIS"
[1] 3
  HS6ST2 MUTATED HS6ST2 WILD-TYPE 
               7              282 
  HS6ST2 MUTATED HS6ST2 WILD-TYPE 
               7              282 
[1] "EPB41L5 MUTATION ANALYSIS"
[1] 3
  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
                8               281 
  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
                8               281 
[1] "ARID5B MUTATION ANALYSIS"
[1] 3
  ARID5B MUTATED ARID5B WILD-TYPE 
              11              278 
  ARID5B MUTATED ARID5B WILD-TYPE 
              11              278 
[1] "HECA MUTATION ANALYSIS"
[1] 3
  HECA MUTATED HECA WILD-TYPE 
            12            277 
  HECA MUTATED HECA WILD-TYPE 
            12            277 
[1] "RHOBTB2 MUTATION ANALYSIS"
[1] 3
  RHOBTB2 MUTATED RHOBTB2 WILD-TYPE 
               16               273 
  RHOBTB2 MUTATED RHOBTB2 WILD-TYPE 
               16               273 
[1] "EML3 MUTATION ANALYSIS"
[1] 3
  EML3 MUTATED EML3 WILD-TYPE 
            10            279 
  EML3 MUTATED EML3 WILD-TYPE 
            10            279 
[1] "EIF2C4 MUTATION ANALYSIS"
[1] 3
  EIF2C4 MUTATED EIF2C4 WILD-TYPE 
              10              279 
  EIF2C4 MUTATED EIF2C4 WILD-TYPE 
              10              279 
[1] "LSS MUTATION ANALYSIS"
[1] 3
  LSS MUTATED LSS WILD-TYPE 
            9           280 
  LSS MUTATED LSS WILD-TYPE 
            9           280 
[1] "MMP10 MUTATION ANALYSIS"
[1] 3
  MMP10 MUTATED MMP10 WILD-TYPE 
              8             281 
  MMP10 MUTATED MMP10 WILD-TYPE 
              8             281 
[1] "SLC7A13 MUTATION ANALYSIS"
[1] 3
  SLC7A13 MUTATED SLC7A13 WILD-TYPE 
                9               280 
  SLC7A13 MUTATED SLC7A13 WILD-TYPE 
                9               280 
[1] "FANCA MUTATION ANALYSIS"
[1] 3
  FANCA MUTATED FANCA WILD-TYPE 
              7             282 
  FANCA MUTATED FANCA WILD-TYPE 
              7             282 
[1] "CLIP1 MUTATION ANALYSIS"
[1] 3
  CLIP1 MUTATED CLIP1 WILD-TYPE 
             15             274 
  CLIP1 MUTATED CLIP1 WILD-TYPE 
             15             274 
[1] "ZNF217 MUTATION ANALYSIS"
[1] 3
  ZNF217 MUTATED ZNF217 WILD-TYPE 
              14              275 
  ZNF217 MUTATED ZNF217 WILD-TYPE 
              14              275 
[1] "SLA MUTATION ANALYSIS"
[1] 3
  SLA MUTATED SLA WILD-TYPE 
            4           285 
  SLA MUTATED SLA WILD-TYPE 
            4           285 
[1] "HDAC4 MUTATION ANALYSIS"
[1] 3
  HDAC4 MUTATED HDAC4 WILD-TYPE 
             22             267 
  HDAC4 MUTATED HDAC4 WILD-TYPE 
             22             267 
[1] "AHI1 MUTATION ANALYSIS"
[1] 3
  AHI1 MUTATED AHI1 WILD-TYPE 
             9            280 
  AHI1 MUTATED AHI1 WILD-TYPE 
             9            280 
[1] "CLSTN1 MUTATION ANALYSIS"
[1] 3
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
              11              278 
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
              11              278 
[1] "PPM1H MUTATION ANALYSIS"
[1] 3
  PPM1H MUTATED PPM1H WILD-TYPE 
              8             281 
  PPM1H MUTATED PPM1H WILD-TYPE 
              8             281 
[1] "KYNU MUTATION ANALYSIS"
[1] 3
  KYNU MUTATED KYNU WILD-TYPE 
            10            279 
  KYNU MUTATED KYNU WILD-TYPE 
            10            279 
[1] "MLL4 MUTATION ANALYSIS"
[1] 3
  MLL4 MUTATED MLL4 WILD-TYPE 
            23            266 
  MLL4 MUTATED MLL4 WILD-TYPE 
            23            266 
[1] "PHKG2 MUTATION ANALYSIS"
[1] 3
  PHKG2 MUTATED PHKG2 WILD-TYPE 
             12             277 
  PHKG2 MUTATED PHKG2 WILD-TYPE 
             12             277 
[1] "OR4C16 MUTATION ANALYSIS"
[1] 3
  OR4C16 MUTATED OR4C16 WILD-TYPE 
              13              276 
  OR4C16 MUTATED OR4C16 WILD-TYPE 
              13              276 
[1] "NUAK1 MUTATION ANALYSIS"
[1] 3
  NUAK1 MUTATED NUAK1 WILD-TYPE 
             16             273 
  NUAK1 MUTATED NUAK1 WILD-TYPE 
             16             273 
[1] "FAM82A1 MUTATION ANALYSIS"
[1] 3
  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
                4               285 
  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
                4               285 
[1] "RASSF5 MUTATION ANALYSIS"
[1] 3
  RASSF5 MUTATED RASSF5 WILD-TYPE 
               4              285 
  RASSF5 MUTATED RASSF5 WILD-TYPE 
               4              285 
[1] "MTMR11 MUTATION ANALYSIS"
[1] 3
  MTMR11 MUTATED MTMR11 WILD-TYPE 
               8              281 
  MTMR11 MUTATED MTMR11 WILD-TYPE 
               8              281 
[1] "KRT222 MUTATION ANALYSIS"
[1] 3
  KRT222 MUTATED KRT222 WILD-TYPE 
               5              284 
  KRT222 MUTATED KRT222 WILD-TYPE 
               5              284 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "RADIATION_THERAPY"                     
[14] "HISTOLOGICAL_TYPE"                     
[15] "RADIATIONS_RADIATION_REGIMENINDICATION"
[16] "COMPLETENESS_OF_RESECTION"             
[17] "NUMBER_OF_LYMPH_NODES"                 
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCH_NUMBER"                          

Input Data has 20 rows and 289 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=74,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=183,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "2"                "246"                 
freq.contrast "246"              "2"                   
both >= 3     "FALSE"            "FALSE"               
Variable 20:'BATCH_NUMBER':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 289 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "PATHOLOGY_M_STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL_TYPE"                     
 [8] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [9] "COMPLETENESS_OF_RESECTION"             
[10] "NUMBER_OF_LYMPH_NODES"                 
[11] "RACE"                                  
YEARS_TO_BIRTH, nv=52, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=11, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 11  72 122  75 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 11  72 122  75 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 11  72 122  75 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 11  72 122  75 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
93 81 50 53 
[1] "table(vv)"
vv
N0 N1 N2 N3 
93 81 50 53 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 N3 
93 81 50 53 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


N0 N1 N2 N3 
93 81 50 53 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=7, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=27, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   89 37
  TP53 WILD-TYPE 92 43
  TP53 MUTATED TP53 WILD-TYPE 
           126            135 
  TP53 MUTATED TP53 WILD-TYPE 
            37             43 
$`TP53 MUTATED`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       11.70         6.61         6.97        17.29        13.68        19.33 
TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
        9.17        31.20        32.94         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8077 TCGA-BR-8080 
       15.42        28.01        28.73         3.45         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       20.55        12.95         2.66         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 
        6.18        19.50        14.04         5.39        25.18        20.22 
TCGA-BR-8487 TCGA-BR-8590 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 
        1.12         9.34        11.54        16.44         9.86        10.68 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IY 
       13.87         7.53        22.26         1.48        13.41        12.89 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 
       13.51        20.65        20.42         1.15        13.64         3.25 
TCGA-CD-5800 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 
       13.15         0.39         0.07         0.07         0.07         0.10 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.16         0.10         0.13         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4438 
       12.43        11.61        12.20        20.02         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
        4.01        47.05        19.07        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 
        6.97        36.00         6.02       105.07        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
        4.01        69.04        12.66        19.13        18.84        18.54 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU 
       10.55        11.31        12.33        14.66        21.14        16.44 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 
        7.99        14.47        72.23         3.48        19.53        17.06 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8604 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       12.10         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H3 
        8.98         0.10         6.25        10.19        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IP-7968 
       23.84        27.42        21.21         3.45        18.81         2.53 

$`TP53 WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
       26.70         4.64         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6563 
        9.57         6.61        34.68        15.95        13.87        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-7196 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 
       21.11        30.90        12.82        18.15        15.32        12.43 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 
        9.07        12.76        18.71        17.49        14.43        12.26 
TCGA-BR-8284 TCGA-BR-8291 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        8.05        16.31         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8589 
        0.26        15.85         3.72         9.21        12.79        15.81 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8686 
       13.45         6.28         7.53         0.49        15.81        15.68 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 
        8.22        12.56         6.08        13.51         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QL TCGA-BR-A4QM 
       14.17         0.53         0.66        19.36        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8527 TCGA-CD-8529 
        2.83        13.18         0.30         0.07         0.07         0.13 
TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
        0.10         0.10         6.58         0.10        12.62         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 
       27.02        15.95         1.02         8.05        14.01        29.98 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4475 TCGA-CG-5719 TCGA-CG-5720 
       12.03         0.00         9.01        22.98         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
        0.99        12.03        65.10        21.07         7.99        12.36 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-8570 TCGA-D7-8572 
       11.93        20.55        18.61        17.85        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       19.50        17.19        18.21        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-A448 
       15.16        13.78        14.76         0.62        16.24        21.27 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HU-8249 
       14.07        22.29        59.54         5.03        13.58        14.17 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       11.41        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H5 
       11.84        24.20         6.51         0.26         2.10        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-IN-8663 
        9.67         8.88         3.39 

  TP53 MUTATED TP53 WILD-TYPE 
          0.07           0.00 
  TP53 MUTATED TP53 WILD-TYPE 
        105.07          65.10 
  TP53 MUTATED TP53 WILD-TYPE 
        12.725         12.560 
[1] "0.1 - 105.1 (12.7)" "0.0 - 65.1 (12.6)" 
[1] "hr=" "1.3"
D1V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TP53 MUTATED         0        5       14       14        18        21
  TP53 WILD-TYPE       1        4       13       12        13        23
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TP53 MUTATED           1         27         14         11        7
  TP53 WILD-TYPE         2         22         22         13       17
D1V3, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  STAGE I               0              1
  STAGE IA              5              4
  STAGE IB             14             13
  STAGE II             14             12
  STAGE IIA            18             13
  STAGE IIB            21             23
  STAGE III             1              2
  STAGE IIIA           27             22
  STAGE IIIB           14             22
  STAGE IIIC           11             13
  STAGE IV              7             17
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  TP53 MUTATED    5 37 63 30
  TP53 WILD-TYPE  6 35 59 45
D1V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1            5              6
  T2           37             35
  T3           63             59
  T4           30             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  TP53 MUTATED   50 38 23 22
  TP53 WILD-TYPE 43 43 27 31
D1V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           50             43
  N1           38             43
  N2           23             27
  N3           22             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                cls
clus               0   1
  TP53 MUTATED   124   4
  TP53 WILD-TYPE 133  14
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    124    4
  TP53 WILD-TYPE  133   14
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0          124            133
  1            4             14
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus              0  1
  TP53 MUTATED   53 84
  TP53 WILD-TYPE 57 95
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     53   84
  TP53 WILD-TYPE   57   95
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           53             57
  MALE             84             95
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TP53 MUTATED                                      20
  TP53 WILD-TYPE                                    30
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TP53 MUTATED                                                       59
  TP53 WILD-TYPE                                                     76
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TP53 MUTATED                                                                  23
  TP53 WILD-TYPE                                                                17
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TP53 MUTATED                                                 22
  TP53 WILD-TYPE                                               16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TP53 MUTATED                                                          7
  TP53 WILD-TYPE                                                        9
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TP53 MUTATED                                                           4
  TP53 WILD-TYPE                                                         2
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TP53 MUTATED                                          2
  TP53 WILD-TYPE                                        1
D1V8, multiclass
                                                                   clus
vv                                                                  TP53 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       20
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      59
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           23
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            22
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     2
                                                                   clus
vv                                                                  TP53 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         30
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        76
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       1
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
                cls
clus               0   1
  TP53 MUTATED     3 134
  TP53 WILD-TYPE   2 150
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      3  134
  TP53 WILD-TYPE    2  150
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO             3              2
  YES          134            150
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TP53 MUTATED   114   3   2   9
  TP53 WILD-TYPE 113   7   8  15
D1V10, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0          114            113
  R1            3              7
  R2            2              8
  RX            9             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED      38                         3    78
  TP53 WILD-TYPE    38                         1    90
D1V12, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                               38             38
  BLACK OR AFRICAN AMERICAN            3              1
  WHITE                               78             90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = ARID1A MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED    55  24
  ARID1A WILD-TYPE 126  56
  ARID1A MUTATED ARID1A WILD-TYPE 
              79              182 
  ARID1A MUTATED ARID1A WILD-TYPE 
              24               56 
$`ARID1A MUTATED`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-6452 
       26.70        11.70         6.97         7.43        30.90        34.68 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6707 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 
       13.87        17.29        19.89        30.90        32.94        12.82 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       15.32        12.43        14.43        12.26        20.55         8.05 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8368 TCGA-BR-8372 
        6.18        19.50         0.26        17.52         4.31        19.17 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8677 
        0.26        15.85         1.12        15.81        13.45         0.49 
TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A453 TCGA-BR-A4J1 TCGA-BR-A4J8 
       15.81        15.68         8.22         6.08         0.72        13.51 
TCGA-BR-A4PE TCGA-BR-A4QL TCGA-CD-5803 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MJ 
       20.42        11.57         0.07         0.10         6.58        12.62 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-5721 
       15.95         1.02         8.05         9.01         7.07         6.02 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-6521 
      105.07        28.96        65.10        21.07        12.36        18.54 
TCGA-D7-6524 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-F1-6874 
       17.85        20.91        16.44         5.92        15.16        14.47 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BE TCGA-HJ-7597 
       14.07        22.29        17.06         0.56        11.08        26.47 
TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GH 
       10.62         5.59        12.30        11.84        24.20        11.77 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H4 
       29.98         0.10         6.25        10.19        19.36        23.84 
TCGA-HU-A4H8 
        8.88 

$`ARID1A WILD-TYPE`
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        6.61         4.64        18.35         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       15.95        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       32.78        25.61        18.05         8.98        21.11        31.20 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        0.69         9.60        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
       15.58         7.40        22.19         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
        3.32        11.80        14.79         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        9.21        20.22        12.79         9.34         6.28         7.53 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       11.54        16.44         9.86        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4PD 
        8.98        14.17         0.53         0.66        19.36        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.18         0.30         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 
       12.20         0.10        20.02         3.02        27.02         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00        18.97        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 
       36.00         1.02         0.99         0.99        12.03        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
        4.01        69.04         7.99        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       20.55        18.84        18.61        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       21.14        14.27        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8209 
       16.24        72.23        21.27         3.48        19.53        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        5.03        13.58         5.52         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD 
       11.41        12.10         0.76        24.30         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
       25.81         8.98         6.51         0.26         2.10        12.95 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       12.30         9.67        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.07             0.00 
  ARID1A MUTATED ARID1A WILD-TYPE 
          105.07            79.07 
  ARID1A MUTATED ARID1A WILD-TYPE 
          13.450           12.495 
[1] "0.1 - 105.1 (13.4)" "0.0 - 79.1 (12.5)" 
[1] "hr=" "1.1"
D2V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARID1A MUTATED         1        4       10        7        10        15
  ARID1A WILD-TYPE       0        5       17       19        21        29
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID1A MUTATED           1          9          7         11        8
  ARID1A WILD-TYPE         2         40         29         13       16
D2V3, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                 1                0
  STAGE IA                4                5
  STAGE IB               10               17
  STAGE II                7               19
  STAGE IIA              10               21
  STAGE IIB              15               29
  STAGE III               1                2
  STAGE IIIA              9               40
  STAGE IIIB              7               29
  STAGE IIIC             11               13
  STAGE IV                8               16
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  ARID1A MUTATED    7 22 31 26
  ARID1A WILD-TYPE  4 50 91 49
D2V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1              7                4
  T2             22               50
  T3             31               91
  T4             26               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ARID1A MUTATED   29 26 15 16
  ARID1A WILD-TYPE 64 55 35 37
D2V5, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  N0             29               64
  N1             26               55
  N2             15               35
  N3             16               37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                  cls
clus                 0   1
  ARID1A MUTATED    77   5
  ARID1A WILD-TYPE 180  13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     77    5
  ARID1A WILD-TYPE  180   13
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0             77              180
  1              5               13
[1] 2 2
[1] FALSE
D2V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED    40  50
  ARID1A WILD-TYPE  70 129
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     40   50
  ARID1A WILD-TYPE   70  129
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE             40               70
  MALE               50              129
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ARID1A MUTATED                                      13
  ARID1A WILD-TYPE                                    37
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ARID1A MUTATED                                                       47
  ARID1A WILD-TYPE                                                     88
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ARID1A MUTATED                                                                  14
  ARID1A WILD-TYPE                                                                26
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ARID1A MUTATED                                                 12
  ARID1A WILD-TYPE                                               26
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ARID1A MUTATED                                                          1
  ARID1A WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ARID1A MUTATED                                                           1
  ARID1A WILD-TYPE                                                         5
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ARID1A MUTATED                                          2
  ARID1A WILD-TYPE                                        1
D2V8, multiclass
                                                                   clus
vv                                                                  ARID1A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        47
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
                                                                   clus
vv                                                                  ARID1A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           37
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          88
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               26
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                26
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
                  cls
clus                 0   1
  ARID1A MUTATED     1  89
  ARID1A WILD-TYPE   4 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      1   89
  ARID1A WILD-TYPE    4  195
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO               1                4
  YES             89              195
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ARID1A MUTATED    69   3   2  11
  ARID1A WILD-TYPE 158   7   8  13
D2V10, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0             69              158
  R1              3                7
  R2              2                8
  RX             11               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED      22                         2    54
  ARID1A WILD-TYPE    54                         2   114
D2V12, multiclass
                           clus
vv                          ARID1A MUTATED ARID1A WILD-TYPE
  ASIAN                                 22               54
  BLACK OR AFRICAN AMERICAN              2                2
  WHITE                                 54              114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RNF43 MUTATION ANALYSIS
D3V1, survival
                 sevent
clus2               0   1
  RNF43 MUTATED    28  13
  RNF43 WILD-TYPE 153  67
  RNF43 MUTATED RNF43 WILD-TYPE 
             41             220 
  RNF43 MUTATED RNF43 WILD-TYPE 
             13              67 
$`RNF43 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7707 
        6.97        30.90        34.68        32.94        24.76        23.93 
TCGA-BR-7851 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       12.43        12.26        20.55         6.18        19.50         0.26 
TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8591 
        4.31        19.17        15.85         1.12        12.79        13.45 
TCGA-BR-A44U TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4306 
       13.87        11.57         5.13         0.10         6.58         1.02 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5728 
        9.01         7.07         0.99         6.02        28.96        65.10 
TCGA-CG-5733 TCGA-D7-A4YT TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-A4G9 TCGA-HU-A4GN 
       21.07        14.27        11.08        26.47        24.20        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 
        0.10         6.51        19.36        23.84         8.88 

$`RNF43 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       31.20        12.82         9.21        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 
       17.49        14.43         0.69         9.60         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8364 
        2.66        16.31         2.20        15.58         7.40        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       20.22        15.81         9.34         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       10.68        12.56         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        1.15        13.64         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
       29.98        47.05        19.07        12.03         0.00        18.97 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5722 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
      105.07        12.03        79.07         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8243 
       59.54         5.03        13.58         0.56         5.52         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        11.84         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       25.81        11.77         8.98         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
        2.10        12.95        12.30         9.67        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  RNF43 MUTATED RNF43 WILD-TYPE 
            0.1             0.0 
  RNF43 MUTATED RNF43 WILD-TYPE 
          65.10          105.07 
  RNF43 MUTATED RNF43 WILD-TYPE 
         12.790          12.605 
[1] "0.1 - 65.1 (12.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D3V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RNF43 MUTATED         1        3        8        1         8         5
  RNF43 WILD-TYPE       0        6       19       25        23        39
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF43 MUTATED           0          5          2          6        6
  RNF43 WILD-TYPE         3         44         34         18       18
D3V3, multiclass
            clus
vv           RNF43 MUTATED RNF43 WILD-TYPE
  STAGE I                1               0
  STAGE IA               3               6
  STAGE IB               8              19
  STAGE II               1              25
  STAGE IIA              8              23
  STAGE IIB              5              39
  STAGE III              0               3
  STAGE IIIA             5              44
  STAGE IIIB             2              34
  STAGE IIIC             6              18
  STAGE IV               6              18
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RNF43 MUTATED     6  12  14  15
  RNF43 WILD-TYPE   5  60 108  60
D3V4, multiclass
    clus
vv   RNF43 MUTATED RNF43 WILD-TYPE
  T1             6               5
  T2            12              60
  T3            14             108
  T4            15              60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  RNF43 MUTATED   23  7  8  9
  RNF43 WILD-TYPE 70 74 42 44
D3V5, multiclass
    clus
vv   RNF43 MUTATED RNF43 WILD-TYPE
  N0            23              70
  N1             7              74
  N2             8              42
  N3             9              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                 cls
clus                0   1
  RNF43 MUTATED    43   3
  RNF43 WILD-TYPE 214  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED     43    3
  RNF43 WILD-TYPE  214   15
   clus
vv  RNF43 MUTATED RNF43 WILD-TYPE
  0            43             214
  1             3              15
[1] 2 2
[1] FALSE
D3V7, binary
                 cls
clus                0   1
  RNF43 MUTATED    26  23
  RNF43 WILD-TYPE  84 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED     26   23
  RNF43 WILD-TYPE   84  156
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  FEMALE            26              84
  MALE              23             156
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RNF43 MUTATED                                       4
  RNF43 WILD-TYPE                                    46
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RNF43 MUTATED                                                       28
  RNF43 WILD-TYPE                                                    107
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RNF43 MUTATED                                                                   8
  RNF43 WILD-TYPE                                                                32
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RNF43 MUTATED                                                  7
  RNF43 WILD-TYPE                                               31
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RNF43 MUTATED                                                          0
  RNF43 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RNF43 MUTATED                                                           1
  RNF43 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RNF43 MUTATED                                          1
  RNF43 WILD-TYPE                                        2
D3V8, multiclass
                                                                   clus
vv                                                                  RNF43 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       28
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  RNF43 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        107
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               31
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, binary
                 cls
clus                0   1
  RNF43 MUTATED     0  49
  RNF43 WILD-TYPE   5 235
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED      0   49
  RNF43 WILD-TYPE    5  235
     clus
vv    RNF43 MUTATED RNF43 WILD-TYPE
  NO              0               5
  YES            49             235
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RNF43 MUTATED    37   1   3   7
  RNF43 WILD-TYPE 190   9   7  17
D3V10, multiclass
    clus
vv   RNF43 MUTATED RNF43 WILD-TYPE
  R0            37             190
  R1             1               9
  R2             3               7
  RX             7              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RNF43 MUTATED       9                         2    28
  RNF43 WILD-TYPE    67                         2   140
D3V12, multiclass
                           clus
vv                          RNF43 MUTATED RNF43 WILD-TYPE
  ASIAN                                 9              67
  BLACK OR AFRICAN AMERICAN             2               2
  WHITE                                28             140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = LARP4B MUTATION ANALYSIS
D4V1, survival
                  sevent
clus2                0   1
  LARP4B MUTATED    17   4
  LARP4B WILD-TYPE 164  76
  LARP4B MUTATED LARP4B WILD-TYPE 
              21              240 
  LARP4B MUTATED LARP4B WILD-TYPE 
               4               76 
$`LARP4B MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8368 TCGA-BR-8372 
        6.97        30.90        32.78        23.93         4.31        19.17 
TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8535 TCGA-CD-A4MG TCGA-CD-A4MI 
       13.45        15.81        11.57         0.13         6.58         0.10 
TCGA-CG-5721 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5578 TCGA-F1-6874 TCGA-HU-8602 
        6.02        65.10        21.07        12.66        14.47        11.41 
TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GT 
       11.84        29.98         6.51 

$`LARP4B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 
       31.20        32.94        12.82         9.21        24.76        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       15.81         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 
       79.07         4.01        69.04         7.99        12.36        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.99        16.24        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  LARP4B MUTATED LARP4B WILD-TYPE 
             0.1              0.0 
  LARP4B MUTATED LARP4B WILD-TYPE 
           65.10           105.07 
  LARP4B MUTATED LARP4B WILD-TYPE 
          12.660           12.605 
[1] "0.1 - 65.1 (12.7)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.9"
D4V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LARP4B MUTATED         0        0        4        0         4         2
  LARP4B WILD-TYPE       1        9       23       26        27        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LARP4B MUTATED           0          5          2          2        3
  LARP4B WILD-TYPE         3         44         34         22       21
D4V3, multiclass
            clus
vv           LARP4B MUTATED LARP4B WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                4               23
  STAGE II                0               26
  STAGE IIA               4               27
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              5               44
  STAGE IIIB              2               34
  STAGE IIIC              2               22
  STAGE IV                3               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LARP4B MUTATED     1   7  10   7
  LARP4B WILD-TYPE  10  65 112  68
D4V4, multiclass
    clus
vv   LARP4B MUTATED LARP4B WILD-TYPE
  T1              1               10
  T2              7               65
  T3             10              112
  T4              7               68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  LARP4B MUTATED    9  6  4  3
  LARP4B WILD-TYPE 84 75 46 50
D4V5, multiclass
    clus
vv   LARP4B MUTATED LARP4B WILD-TYPE
  N0              9               84
  N1              6               75
  N2              4               46
  N3              3               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                  cls
clus                 0   1
  LARP4B MUTATED    24   1
  LARP4B WILD-TYPE 233  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED     24    1
  LARP4B WILD-TYPE  233   17
   clus
vv  LARP4B MUTATED LARP4B WILD-TYPE
  0             24              233
  1              1               17
[1] 2 2
[1] FALSE
D4V7, binary
                  cls
clus                 0   1
  LARP4B MUTATED    16  11
  LARP4B WILD-TYPE  94 168
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED     16   11
  LARP4B WILD-TYPE   94  168
        clus
vv       LARP4B MUTATED LARP4B WILD-TYPE
  FEMALE             16               94
  MALE               11              168
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  LARP4B MUTATED                                       3
  LARP4B WILD-TYPE                                    47
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LARP4B MUTATED                                                       16
  LARP4B WILD-TYPE                                                    119
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LARP4B MUTATED                                                                   4
  LARP4B WILD-TYPE                                                                36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  LARP4B MUTATED                                                  4
  LARP4B WILD-TYPE                                               34
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  LARP4B MUTATED                                                          0
  LARP4B WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  LARP4B MUTATED                                                           0
  LARP4B WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  LARP4B MUTATED                                          0
  LARP4B WILD-TYPE                                        3
D4V8, multiclass
                                                                   clus
vv                                                                  LARP4B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  LARP4B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         119
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
                  cls
clus                 0   1
  LARP4B MUTATED     0  27
  LARP4B WILD-TYPE   5 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED      0   27
  LARP4B WILD-TYPE    5  257
     clus
vv    LARP4B MUTATED LARP4B WILD-TYPE
  NO               0                5
  YES             27              257
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  LARP4B MUTATED    16   0   0   8
  LARP4B WILD-TYPE 211  10  10  16
D4V10, multiclass
    clus
vv   LARP4B MUTATED LARP4B WILD-TYPE
  R0             16              211
  R1              0               10
  R2              0               10
  RX              8               16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LARP4B MUTATED       8                         0    16
  LARP4B WILD-TYPE    68                         4   152
D4V12, multiclass
                           clus
vv                          LARP4B MUTATED LARP4B WILD-TYPE
  ASIAN                                  8               68
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                 16              152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = XYLT2 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  XYLT2 MUTATED    23   5
  XYLT2 WILD-TYPE 158  75
  XYLT2 MUTATED XYLT2 WILD-TYPE 
             28             233 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
              5              75 
$`XYLT2 MUTATED`
TCGA-B7-5816 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-8078 
       26.70        32.78        23.93        28.73        12.43        12.26 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8368 
       20.55         8.05         6.18        19.50         0.26         4.31 
TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI 
       15.85         1.12        13.45         0.10         6.58         0.10 
TCGA-CD-A4MJ TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 TCGA-FP-A4BE TCGA-HU-8602 
       12.62       105.07        65.10        21.07        11.08        11.41 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H8 
        6.25        10.19        19.36         8.88 

$`XYLT2 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 
       15.42        28.01        18.15        15.32         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 
       12.76        18.71        17.49        14.43         0.69         9.60 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        19.17        14.79         0.26         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.20        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         6.02         0.99        12.03        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GY 
       11.77        29.98         8.98         0.10         6.51         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
        2.10        12.95        23.84        12.30         9.67        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  XYLT2 MUTATED XYLT2 WILD-TYPE 
            0.1             0.0 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
         105.07           79.07 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
         12.345          12.760 
[1] "0.1 - 105.1 (12.3)" "0.0 - 79.1 (12.8)" 
[1] "hr=" "2.2"
D5V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XYLT2 MUTATED         1        0        6        3         5         6
  XYLT2 WILD-TYPE       0        9       21       23        26        38
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XYLT2 MUTATED           0          2          2          6        1
  XYLT2 WILD-TYPE         3         47         34         18       23
D5V3, multiclass
            clus
vv           XYLT2 MUTATED XYLT2 WILD-TYPE
  STAGE I                1               0
  STAGE IA               0               9
  STAGE IB               6              21
  STAGE II               3              23
  STAGE IIA              5              26
  STAGE IIB              6              38
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             2              34
  STAGE IIIC             6              18
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  XYLT2 MUTATED     2   8   9  13
  XYLT2 WILD-TYPE   9  64 113  62
D5V4, multiclass
    clus
vv   XYLT2 MUTATED XYLT2 WILD-TYPE
  T1             2               9
  T2             8              64
  T3             9             113
  T4            13              62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  XYLT2 MUTATED   17  6  4  5
  XYLT2 WILD-TYPE 76 75 46 48
D5V5, multiclass
    clus
vv   XYLT2 MUTATED XYLT2 WILD-TYPE
  N0            17              76
  N1             6              75
  N2             4              46
  N3             5              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                 cls
clus                0   1
  XYLT2 MUTATED    31   0
  XYLT2 WILD-TYPE 226  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XYLT2 MUTATED     31    0
  XYLT2 WILD-TYPE  226   18
   clus
vv  XYLT2 MUTATED XYLT2 WILD-TYPE
  0            31             226
  1             0              18
[1] 2 2
[1] FALSE
D5V7, binary
                 cls
clus                0   1
  XYLT2 MUTATED    18  14
  XYLT2 WILD-TYPE  92 165
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XYLT2 MUTATED     18   14
  XYLT2 WILD-TYPE   92  165
        clus
vv       XYLT2 MUTATED XYLT2 WILD-TYPE
  FEMALE            18              92
  MALE              14             165
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  XYLT2 MUTATED                                       6
  XYLT2 WILD-TYPE                                    44
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XYLT2 MUTATED                                                       19
  XYLT2 WILD-TYPE                                                    116
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XYLT2 MUTATED                                                                   5
  XYLT2 WILD-TYPE                                                                35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  XYLT2 MUTATED                                                  1
  XYLT2 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  XYLT2 MUTATED                                                          1
  XYLT2 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  XYLT2 MUTATED                                                           0
  XYLT2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  XYLT2 MUTATED                                          0
  XYLT2 WILD-TYPE                                        3
D5V8, multiclass
                                                                   clus
vv                                                                  XYLT2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       19
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  XYLT2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          44
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        116
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
                 cls
clus                0   1
  XYLT2 MUTATED     1  31
  XYLT2 WILD-TYPE   4 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XYLT2 MUTATED      1   31
  XYLT2 WILD-TYPE    4  253
     clus
vv    XYLT2 MUTATED XYLT2 WILD-TYPE
  NO              1               4
  YES            31             253
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  XYLT2 MUTATED    27   0   0   2
  XYLT2 WILD-TYPE 200  10  10  22
D5V10, multiclass
    clus
vv   XYLT2 MUTATED XYLT2 WILD-TYPE
  R0            27             200
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XYLT2 MUTATED       9                         2    17
  XYLT2 WILD-TYPE    67                         2   151
D5V12, multiclass
                           clus
vv                          XYLT2 MUTATED XYLT2 WILD-TYPE
  ASIAN                                 9              67
  BLACK OR AFRICAN AMERICAN             2               2
  WHITE                                17             151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = B2M MUTATION ANALYSIS
D6V1, survival
               sevent
clus2             0   1
  B2M MUTATED    15   0
  B2M WILD-TYPE 166  80
  B2M MUTATED B2M WILD-TYPE 
           15           246 
  B2M MUTATED B2M WILD-TYPE 
            0            80 
$`B2M MUTATED`
TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 
       32.78        32.94        23.93        15.85         1.12        13.45 
TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-8570 
       11.57         0.10         0.10         6.02        65.10        24.72 
TCGA-FP-A4BE TCGA-HU-A4GX TCGA-HU-A4H8 
       11.08        10.19         8.88 

$`B2M WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        0.26         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        15.81         9.34         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.13         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        28.96        79.07         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51         6.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  B2M MUTATED B2M WILD-TYPE 
          0.1           0.0 
  B2M MUTATED B2M WILD-TYPE 
        65.10        105.07 
  B2M MUTATED B2M WILD-TYPE 
        11.57         12.64 
[1] "0.1 - 65.1 (11.6)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "2.8e+07"
D6V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  B2M MUTATED         1        0        3        1         4         0
  B2M WILD-TYPE       0        9       24       25        27        44
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  B2M MUTATED           0          0          3          3        1
  B2M WILD-TYPE         3         49         33         21       23
D6V3, multiclass
            clus
vv           B2M MUTATED B2M WILD-TYPE
  STAGE I              1             0
  STAGE IA             0             9
  STAGE IB             3            24
  STAGE II             1            25
  STAGE IIA            4            27
  STAGE IIB            0            44
  STAGE III            0             3
  STAGE IIIA           0            49
  STAGE IIIB           3            33
  STAGE IIIC           3            21
  STAGE IV             1            23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  B2M MUTATED     2   2   8   4
  B2M WILD-TYPE   9  70 114  71
D6V4, multiclass
    clus
vv   B2M MUTATED B2M WILD-TYPE
  T1           2             9
  T2           2            70
  T3           8           114
  T4           4            71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  B2M MUTATED    7  5  1  4
  B2M WILD-TYPE 86 76 49 49
D6V5, multiclass
    clus
vv   B2M MUTATED B2M WILD-TYPE
  N0           7            86
  N1           5            76
  N2           1            49
  N3           4            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
               cls
clus              0   1
  B2M MUTATED    16   0
  B2M WILD-TYPE 241  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED     16    0
  B2M WILD-TYPE  241   18
   clus
vv  B2M MUTATED B2M WILD-TYPE
  0          16           241
  1           0            18
[1] 2 2
[1] FALSE
D6V7, binary
               cls
clus              0   1
  B2M MUTATED     9   8
  B2M WILD-TYPE 101 171
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED      9    8
  B2M WILD-TYPE  101  171
        clus
vv       B2M MUTATED B2M WILD-TYPE
  FEMALE           9           101
  MALE             8           171
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  B2M MUTATED                                       1
  B2M WILD-TYPE                                    49
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  B2M MUTATED                                                       12
  B2M WILD-TYPE                                                    123
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  B2M MUTATED                                                                   2
  B2M WILD-TYPE                                                                38
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  B2M MUTATED                                                  2
  B2M WILD-TYPE                                               36
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  B2M MUTATED                                                          0
  B2M WILD-TYPE                                                       16
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  B2M MUTATED                                                           0
  B2M WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  B2M MUTATED                                          0
  B2M WILD-TYPE                                        3
D6V8, multiclass
                                                                   clus
vv                                                                  B2M MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                     12
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  B2M WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      123
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
               cls
clus              0   1
  B2M MUTATED     0  17
  B2M WILD-TYPE   5 267
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED      0   17
  B2M WILD-TYPE    5  267
     clus
vv    B2M MUTATED B2M WILD-TYPE
  NO            0             5
  YES          17           267
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  B2M MUTATED    15   0   0   1
  B2M WILD-TYPE 212  10  10  23
D6V10, multiclass
    clus
vv   B2M MUTATED B2M WILD-TYPE
  R0          15           212
  R1           0            10
  R2           0            10
  RX           1            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  B2M MUTATED       4                         2     9
  B2M WILD-TYPE    72                         2   159
D6V12, multiclass
                           clus
vv                          B2M MUTATED B2M WILD-TYPE
  ASIAN                               4            72
  BLACK OR AFRICAN AMERICAN           2             2
  WHITE                               9           159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = BZRAP1 MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2                0   1
  BZRAP1 MUTATED    31  10
  BZRAP1 WILD-TYPE 150  70
  BZRAP1 MUTATED BZRAP1 WILD-TYPE 
              41              220 
  BZRAP1 MUTATED BZRAP1 WILD-TYPE 
              10               70 
$`BZRAP1 MUTATED`
TCGA-B7-5816 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-8059 TCGA-BR-8078 
       26.70        32.78        23.93        12.43        14.43        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8363 TCGA-BR-8365 
        9.60        20.55         8.05         2.20         0.26        17.52 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8483 TCGA-BR-A4CQ TCGA-BR-A4J2 
       26.33         4.31        19.17         5.39        22.26        14.17 
TCGA-BR-A4J4 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.53         0.07         0.07         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A48A TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-8570 
        0.10         0.13        12.43         6.02       105.07        24.72 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8211 
       19.50        17.19        14.66        17.06        59.54        13.58 
TCGA-HU-8243 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GH 
        5.92         0.76        24.30        12.30        11.77 

$`BZRAP1 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       15.42        28.01        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8286 
        9.07        12.76        18.71        17.49         0.69        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        16.31        15.58         7.40         6.18        19.50 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       22.19         0.95        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        0.26        15.85         3.72        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.72         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8526 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.07         0.10         0.10         3.42         9.34        11.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       11.31        12.33        16.80        18.21        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8210 TCGA-FP-8631 
        3.48        19.53        14.07        22.29         5.03         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       11.08         5.52        26.47        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       12.10        10.62         5.59        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       22.75        25.81        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  BZRAP1 MUTATED BZRAP1 WILD-TYPE 
            0.07             0.00 
  BZRAP1 MUTATED BZRAP1 WILD-TYPE 
          105.07            79.07 
  BZRAP1 MUTATED BZRAP1 WILD-TYPE 
           12.43            12.71 
[1] "0.1 - 105.1 (12.4)" "0.0 - 79.1 (12.7)" 
[1] "hr=" "1.3"
D7V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BZRAP1 MUTATED         1        3        5        5         5         8
  BZRAP1 WILD-TYPE       0        6       22       21        26        36
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BZRAP1 MUTATED           1          6          4          4        2
  BZRAP1 WILD-TYPE         2         43         32         20       22
D7V3, multiclass
            clus
vv           BZRAP1 MUTATED BZRAP1 WILD-TYPE
  STAGE I                 1                0
  STAGE IA                3                6
  STAGE IB                5               22
  STAGE II                5               21
  STAGE IIA               5               26
  STAGE IIB               8               36
  STAGE III               1                2
  STAGE IIIA              6               43
  STAGE IIIB              4               32
  STAGE IIIC              4               20
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BZRAP1 MUTATED     4   7  19  15
  BZRAP1 WILD-TYPE   7  65 103  60
D7V4, multiclass
    clus
vv   BZRAP1 MUTATED BZRAP1 WILD-TYPE
  T1              4                7
  T2              7               65
  T3             19              103
  T4             15               60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  BZRAP1 MUTATED   24 10  2  8
  BZRAP1 WILD-TYPE 69 71 48 45
D7V5, multiclass
    clus
vv   BZRAP1 MUTATED BZRAP1 WILD-TYPE
  N0             24               69
  N1             10               71
  N2              2               48
  N3              8               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                  cls
clus                 0   1
  BZRAP1 MUTATED    41   1
  BZRAP1 WILD-TYPE 216  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BZRAP1 MUTATED     41    1
  BZRAP1 WILD-TYPE  216   17
   clus
vv  BZRAP1 MUTATED BZRAP1 WILD-TYPE
  0             41              216
  1              1               17
[1] 2 2
[1] FALSE
D7V7, binary
                  cls
clus                 0   1
  BZRAP1 MUTATED    17  29
  BZRAP1 WILD-TYPE  93 150
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BZRAP1 MUTATED     17   29
  BZRAP1 WILD-TYPE   93  150
        clus
vv       BZRAP1 MUTATED BZRAP1 WILD-TYPE
  FEMALE             17               93
  MALE               29              150
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  BZRAP1 MUTATED                                       7
  BZRAP1 WILD-TYPE                                    43
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BZRAP1 MUTATED                                                       22
  BZRAP1 WILD-TYPE                                                    113
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BZRAP1 MUTATED                                                                   7
  BZRAP1 WILD-TYPE                                                                33
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  BZRAP1 MUTATED                                                  6
  BZRAP1 WILD-TYPE                                               32
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  BZRAP1 MUTATED                                                          3
  BZRAP1 WILD-TYPE                                                       13
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  BZRAP1 MUTATED                                                           1
  BZRAP1 WILD-TYPE                                                         5
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  BZRAP1 MUTATED                                          0
  BZRAP1 WILD-TYPE                                        3
D7V8, multiclass
                                                                   clus
vv                                                                  BZRAP1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  BZRAP1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           43
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         113
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
                  cls
clus                 0   1
  BZRAP1 MUTATED     0  46
  BZRAP1 WILD-TYPE   5 238
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BZRAP1 MUTATED      0   46
  BZRAP1 WILD-TYPE    5  238
     clus
vv    BZRAP1 MUTATED BZRAP1 WILD-TYPE
  NO               0                5
  YES             46              238
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  BZRAP1 MUTATED    42   1   0   2
  BZRAP1 WILD-TYPE 185   9  10  22
D7V10, multiclass
    clus
vv   BZRAP1 MUTATED BZRAP1 WILD-TYPE
  R0             42              185
  R1              1                9
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BZRAP1 MUTATED      16                         1    26
  BZRAP1 WILD-TYPE    60                         3   142
D7V12, multiclass
                           clus
vv                          BZRAP1 MUTATED BZRAP1 WILD-TYPE
  ASIAN                                 16               60
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                 26              142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = KRAS MUTATION ANALYSIS
D8V1, survival
                sevent
clus2              0   1
  KRAS MUTATED    17   7
  KRAS WILD-TYPE 164  73
  KRAS MUTATED KRAS WILD-TYPE 
            24            237 
  KRAS MUTATED KRAS WILD-TYPE 
             7             73 
$`KRAS MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6705 TCGA-BR-6802 
        6.97        30.90         6.18         6.61        25.61        30.90 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8366 TCGA-BR-8368 
       24.76        23.93        14.43        12.26         0.95         4.31 
TCGA-BR-8370 TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4QL TCGA-CD-5798 
        3.32        15.81         8.22        22.26        11.57         2.83 
TCGA-CD-8535 TCGA-CD-A4MJ TCGA-CG-5719 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-HU-A4H3 
        0.13        12.62         1.02        79.07        16.24        19.36 

$`KRAS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 
       19.33        39.12        26.10         9.17        32.78        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       19.89         8.98        21.11        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
        9.21        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8371 
        0.26        22.19        17.52        26.33        14.04        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         9.86        15.68        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        13.64         5.13 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.16         0.10         0.10         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
       22.98        30.97         6.97        36.00         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.25        10.19         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  KRAS MUTATED KRAS WILD-TYPE 
          0.13           0.00 
  KRAS MUTATED KRAS WILD-TYPE 
         79.07         105.07 
  KRAS MUTATED KRAS WILD-TYPE 
         12.44          12.66 
[1] "0.1 - 79.1 (12.4)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.2"
D8V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KRAS MUTATED         0        1        5        2         1         1
  KRAS WILD-TYPE       1        8       22       24        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KRAS MUTATED           2          5          4          2        3
  KRAS WILD-TYPE         1         44         32         22       21
D8V3, multiclass
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              5             22
  STAGE II              2             24
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             2              1
  STAGE IIIA            5             44
  STAGE IIIB            4             32
  STAGE IIIC            2             22
  STAGE IV              3             21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KRAS MUTATED     1   7   9  10
  KRAS WILD-TYPE  10  65 113  65
D8V4, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  T1            1             10
  T2            7             65
  T3            9            113
  T4           10             65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  KRAS MUTATED   12  6  4  4
  KRAS WILD-TYPE 81 75 46 49
D8V5, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  N0           12             81
  N1            6             75
  N2            4             46
  N3            4             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                cls
clus               0   1
  KRAS MUTATED    24   2
  KRAS WILD-TYPE 233  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     24    2
  KRAS WILD-TYPE  233   16
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0           24            233
  1            2             16
[1] 2 2
[1] FALSE
D8V7, binary
                cls
clus               0   1
  KRAS MUTATED    15  13
  KRAS WILD-TYPE  95 166
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     15   13
  KRAS WILD-TYPE   95  166
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE           15             95
  MALE             13            166
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KRAS MUTATED                                       2
  KRAS WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KRAS MUTATED                                                       20
  KRAS WILD-TYPE                                                    115
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KRAS MUTATED                                                                   3
  KRAS WILD-TYPE                                                                37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KRAS MUTATED                                                  1
  KRAS WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KRAS MUTATED                                                          1
  KRAS WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KRAS MUTATED                                                           1
  KRAS WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KRAS MUTATED                                          0
  KRAS WILD-TYPE                                        3
D8V8, multiclass
                                                                   clus
vv                                                                  KRAS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      20
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  KRAS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       115
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
                cls
clus               0   1
  KRAS MUTATED     0  28
  KRAS WILD-TYPE   5 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0   28
  KRAS WILD-TYPE    5  256
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO             0              5
  YES           28            256
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  KRAS MUTATED    18   1   0   7
  KRAS WILD-TYPE 209   9  10  17
D8V10, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0           18            209
  R1            1              9
  R2            0             10
  RX            7             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED       5                         0    21
  KRAS WILD-TYPE    71                         4   147
D8V12, multiclass
                           clus
vv                          KRAS MUTATED KRAS WILD-TYPE
  ASIAN                                5             71
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               21            147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MLL2 MUTATION ANALYSIS
D9V1, survival
                sevent
clus2              0   1
  MLL2 MUTATED    42  13
  MLL2 WILD-TYPE 139  67
  MLL2 MUTATED MLL2 WILD-TYPE 
            55            206 
  MLL2 MUTATED MLL2 WILD-TYPE 
            13             67 
$`MLL2 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 
       26.70         6.97        30.90         6.18         6.61        34.68 
TCGA-BR-6455 TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8081 
       13.87        32.78        30.90        23.93        12.26        20.55 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8381 
        6.18        19.50         0.26         4.31        19.17         0.26 
TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-A4QL 
       15.85         1.12        15.81        13.45         7.53        11.57 
TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4306 
        0.10         6.58         0.10        12.62        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 
        8.05        54.08        29.98         6.02       105.07        28.96 
TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6526 TCGA-D7-8570 TCGA-D7-A4YV TCGA-F1-6874 
       65.10        21.07        17.19        24.72         5.92        14.47 
TCGA-F1-A448 TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GN 
       21.27        11.08        26.47        11.41        11.84        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H8 
        0.10         6.51         6.25        10.19        19.36         8.88 
TCGA-HU-A4HD 
       27.42 

$`MLL2 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4279 
       11.70         6.61         4.64         7.43        18.35         9.57 
TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 
       31.20        32.94        12.82         9.21        24.76        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        9.60         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       15.58         7.40        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 
       14.04         3.32        11.80        14.79         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 
       25.18         9.21        20.22        12.79         9.34         6.28 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
        0.16         0.10         0.10         0.13         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 
       11.31        12.43        11.61        12.20        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 
       27.02         7.99         4.01        14.01        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       12.03        79.07         4.01        69.04         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85        13.35        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 
       12.79        10.55        11.31        12.33        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       16.44        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       16.24        72.23         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
       25.81        11.77         8.98         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       23.84        12.30         9.67        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  MLL2 MUTATED MLL2 WILD-TYPE 
           0.1            0.0 
  MLL2 MUTATED MLL2 WILD-TYPE 
        105.07          79.07 
  MLL2 MUTATED MLL2 WILD-TYPE 
        13.450         12.575 
[1] "0.1 - 105.1 (13.4)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.8"
D9V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MLL2 MUTATED         1        2       10        5         8         9
  MLL2 WILD-TYPE       0        7       17       21        23        35
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MLL2 MUTATED           1          6          6          7        4
  MLL2 WILD-TYPE         2         43         30         17       20
D9V3, multiclass
            clus
vv           MLL2 MUTATED MLL2 WILD-TYPE
  STAGE I               1              0
  STAGE IA              2              7
  STAGE IB             10             17
  STAGE II              5             21
  STAGE IIA             8             23
  STAGE IIB             9             35
  STAGE III             1              2
  STAGE IIIA            6             43
  STAGE IIIB            6             30
  STAGE IIIC            7             17
  STAGE IV              4             20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  MLL2 MUTATED    4 17 24 16
  MLL2 WILD-TYPE  7 55 98 59
D9V4, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  T1            4              7
  T2           17             55
  T3           24             98
  T4           16             59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  MLL2 MUTATED   24 19 10  8
  MLL2 WILD-TYPE 69 62 40 45
D9V5, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  N0           24             69
  N1           19             62
  N2           10             40
  N3            8             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                cls
clus               0   1
  MLL2 MUTATED    60   1
  MLL2 WILD-TYPE 197  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     60    1
  MLL2 WILD-TYPE  197   17
   clus
vv  MLL2 MUTATED MLL2 WILD-TYPE
  0           60            197
  1            1             17
[1] 2 2
[1] FALSE
D9V7, binary
                cls
clus               0   1
  MLL2 MUTATED    30  35
  MLL2 WILD-TYPE  80 144
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     30   35
  MLL2 WILD-TYPE   80  144
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  FEMALE           30             80
  MALE             35            144
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MLL2 MUTATED                                       7
  MLL2 WILD-TYPE                                    43
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MLL2 MUTATED                                                       36
  MLL2 WILD-TYPE                                                     99
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MLL2 MUTATED                                                                  11
  MLL2 WILD-TYPE                                                                29
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MLL2 MUTATED                                                  8
  MLL2 WILD-TYPE                                               30
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MLL2 MUTATED                                                          2
  MLL2 WILD-TYPE                                                       14
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MLL2 MUTATED                                                           0
  MLL2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MLL2 MUTATED                                          1
  MLL2 WILD-TYPE                                        2
D9V8, multiclass
                                                                   clus
vv                                                                  MLL2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      36
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  MLL2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         43
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        99
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              30
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, binary
                cls
clus               0   1
  MLL2 MUTATED     1  64
  MLL2 WILD-TYPE   4 220
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      1   64
  MLL2 WILD-TYPE    4  220
     clus
vv    MLL2 MUTATED MLL2 WILD-TYPE
  NO             1              4
  YES           64            220
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MLL2 MUTATED    49   0   1  11
  MLL2 WILD-TYPE 178  10   9  13
D9V10, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  R0           49            178
  R1            0             10
  R2            1              9
  RX           11             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL2 MUTATED      14                         2    37
  MLL2 WILD-TYPE    62                         2   131
D9V12, multiclass
                           clus
vv                          MLL2 MUTATED MLL2 WILD-TYPE
  ASIAN                               14             62
  BLACK OR AFRICAN AMERICAN            2              2
  WHITE                               37            131
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = GNG12 MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2               0   1
  GNG12 MUTATED     6   3
  GNG12 WILD-TYPE 175  77
  GNG12 MUTATED GNG12 WILD-TYPE 
              9             252 
  GNG12 MUTATED GNG12 WILD-TYPE 
              3              77 
$`GNG12 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8363 TCGA-CD-A4MG TCGA-CG-4305 
        6.97        34.68        12.26         0.26         6.58        15.95 
TCGA-CG-5721 TCGA-HU-8602 TCGA-HU-A4GT 
        6.02        11.41         6.51 

$`GNG12 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       19.50        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        5.52        26.47         5.92        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  GNG12 MUTATED GNG12 WILD-TYPE 
           0.26            0.00 
  GNG12 MUTATED GNG12 WILD-TYPE 
          34.68          105.07 
  GNG12 MUTATED GNG12 WILD-TYPE 
          6.970          12.775 
[1] "0.3 - 34.7 (7.0)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.4"
D10V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GNG12 MUTATED         0        0        1        1         3         2
  GNG12 WILD-TYPE       1        9       26       25        28        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GNG12 MUTATED           0          1          0          0        2
  GNG12 WILD-TYPE         3         48         36         24       22
D10V3, multiclass
            clus
vv           GNG12 MUTATED GNG12 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              3              28
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GNG12 MUTATED     0   2   4   4
  GNG12 WILD-TYPE  11  70 118  71
D10V4, multiclass
    clus
vv   GNG12 MUTATED GNG12 WILD-TYPE
  T1             0              11
  T2             2              70
  T3             4             118
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  GNG12 MUTATED    6  4  1  0
  GNG12 WILD-TYPE 87 77 49 53
D10V5, multiclass
    clus
vv   GNG12 MUTATED GNG12 WILD-TYPE
  N0             6              87
  N1             4              77
  N2             1              49
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                 cls
clus                0   1
  GNG12 MUTATED    10   0
  GNG12 WILD-TYPE 247  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNG12 MUTATED     10    0
  GNG12 WILD-TYPE  247   18
   clus
vv  GNG12 MUTATED GNG12 WILD-TYPE
  0            10             247
  1             0              18
[1] 2 2
[1] FALSE
D10V7, binary
                 cls
clus                0   1
  GNG12 MUTATED     7   4
  GNG12 WILD-TYPE 103 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNG12 MUTATED      7    4
  GNG12 WILD-TYPE  103  175
        clus
vv       GNG12 MUTATED GNG12 WILD-TYPE
  FEMALE             7             103
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GNG12 MUTATED                                       2
  GNG12 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GNG12 MUTATED                                                        7
  GNG12 WILD-TYPE                                                    128
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GNG12 MUTATED                                                                   1
  GNG12 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GNG12 MUTATED                                                  1
  GNG12 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GNG12 MUTATED                                                          0
  GNG12 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GNG12 MUTATED                                                           0
  GNG12 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GNG12 MUTATED                                          0
  GNG12 WILD-TYPE                                        3
D10V8, multiclass
                                                                   clus
vv                                                                  GNG12 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  GNG12 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
                 cls
clus                0   1
  GNG12 MUTATED     0  11
  GNG12 WILD-TYPE   5 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNG12 MUTATED      0   11
  GNG12 WILD-TYPE    5  273
     clus
vv    GNG12 MUTATED GNG12 WILD-TYPE
  NO              0               5
  YES            11             273
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GNG12 MUTATED     7   0   0   3
  GNG12 WILD-TYPE 220  10  10  21
D10V10, multiclass
    clus
vv   GNG12 MUTATED GNG12 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GNG12 MUTATED       3                         0     6
  GNG12 WILD-TYPE    73                         4   162
D10V12, multiclass
                           clus
vv                          GNG12 MUTATED GNG12 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = LMAN1 MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2               0   1
  LMAN1 MUTATED    15   4
  LMAN1 WILD-TYPE 166  76
  LMAN1 MUTATED LMAN1 WILD-TYPE 
             19             242 
  LMAN1 MUTATED LMAN1 WILD-TYPE 
              4              76 
$`LMAN1 MUTATED`
TCGA-BR-4201 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8680 
       30.90        12.26        20.55        19.50         4.31        15.81 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-F1-6874 TCGA-F1-A448 
        6.02       105.07        28.96        65.10        14.47        21.27 
TCGA-HJ-7597 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 
       26.47        29.98         0.10         6.51        10.19        19.36 
TCGA-HU-A4H8 
        8.88 

$`LMAN1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 
       17.49        14.43         0.69         9.60         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5730 
        1.02         0.99         0.99        12.03        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        7.99        16.24        72.23         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       11.08         5.52         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        8.98         6.25         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       12.30         9.67        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  LMAN1 MUTATED LMAN1 WILD-TYPE 
            0.1             0.0 
  LMAN1 MUTATED LMAN1 WILD-TYPE 
         105.07           79.07 
  LMAN1 MUTATED LMAN1 WILD-TYPE 
         19.360          12.495 
[1] "0.1 - 105.1 (19.4)" "0.0 - 79.1 (12.5)" 
[1] "hr=" "2.6"
D11V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LMAN1 MUTATED         0        1        6        1         2         2
  LMAN1 WILD-TYPE       1        8       21       25        29        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LMAN1 MUTATED           0          1          1          4        3
  LMAN1 WILD-TYPE         3         48         35         20       21
D11V3, multiclass
            clus
vv           LMAN1 MUTATED LMAN1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               6              21
  STAGE II               1              25
  STAGE IIA              2              29
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             4              20
  STAGE IV               3              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LMAN1 MUTATED     2   8   2  10
  LMAN1 WILD-TYPE   9  64 120  65
D11V4, multiclass
    clus
vv   LMAN1 MUTATED LMAN1 WILD-TYPE
  T1             2               9
  T2             8              64
  T3             2             120
  T4            10              65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  LMAN1 MUTATED   10  4  5  2
  LMAN1 WILD-TYPE 83 77 45 51
D11V5, multiclass
    clus
vv   LMAN1 MUTATED LMAN1 WILD-TYPE
  N0            10              83
  N1             4              77
  N2             5              45
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                 cls
clus                0   1
  LMAN1 MUTATED    20   1
  LMAN1 WILD-TYPE 237  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMAN1 MUTATED     20    1
  LMAN1 WILD-TYPE  237   17
   clus
vv  LMAN1 MUTATED LMAN1 WILD-TYPE
  0            20             237
  1             1              17
[1] 2 2
[1] FALSE
D11V7, binary
                 cls
clus                0   1
  LMAN1 MUTATED    12  10
  LMAN1 WILD-TYPE  98 169
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMAN1 MUTATED     12   10
  LMAN1 WILD-TYPE   98  169
        clus
vv       LMAN1 MUTATED LMAN1 WILD-TYPE
  FEMALE            12              98
  MALE              10             169
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  LMAN1 MUTATED                                       2
  LMAN1 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LMAN1 MUTATED                                                        8
  LMAN1 WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LMAN1 MUTATED                                                                   5
  LMAN1 WILD-TYPE                                                                35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  LMAN1 MUTATED                                                  5
  LMAN1 WILD-TYPE                                               33
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  LMAN1 MUTATED                                                          1
  LMAN1 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  LMAN1 MUTATED                                                           0
  LMAN1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  LMAN1 MUTATED                                          1
  LMAN1 WILD-TYPE                                        2
D11V8, multiclass
                                                                   clus
vv                                                                  LMAN1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  LMAN1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, binary
                 cls
clus                0   1
  LMAN1 MUTATED     0  22
  LMAN1 WILD-TYPE   5 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMAN1 MUTATED      0   22
  LMAN1 WILD-TYPE    5  262
     clus
vv    LMAN1 MUTATED LMAN1 WILD-TYPE
  NO              0               5
  YES            22             262
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LMAN1 MUTATED    19   0   0   3
  LMAN1 WILD-TYPE 208  10  10  21
D11V10, multiclass
    clus
vv   LMAN1 MUTATED LMAN1 WILD-TYPE
  R0            19             208
  R1             0              10
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LMAN1 MUTATED       7                         0    10
  LMAN1 WILD-TYPE    69                         4   158
D11V12, multiclass
                           clus
vv                          LMAN1 MUTATED LMAN1 WILD-TYPE
  ASIAN                                 7              69
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                10             158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = CDH1 MUTATION ANALYSIS
D12V1, survival
                sevent
clus2              0   1
  CDH1 MUTATED    19   8
  CDH1 WILD-TYPE 162  72
  CDH1 MUTATED CDH1 WILD-TYPE 
            27            234 
  CDH1 MUTATED CDH1 WILD-TYPE 
             8             72 
$`CDH1 MUTATED`
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6803 
        4.64         7.43         9.57        34.68        32.78        31.20 
TCGA-BR-8058 TCGA-BR-8364 TCGA-BR-8370 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-A44T 
       17.49        22.19         3.32         6.28         0.49        12.56 
TCGA-BR-A453 TCGA-BR-A4IV TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5813 TCGA-CD-A4MG 
        6.08        13.51         5.13         3.25         0.39         6.58 
TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-A4YU 
       19.13        18.61        17.85        16.80        17.19        16.44 
TCGA-F1-6874 TCGA-FP-8210 TCGA-IN-7808 
       14.47         5.03         3.45 

$`CDH1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4201 
       26.70        11.70         6.61         6.97        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.18         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10         9.17        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 
       19.89         8.98        21.11        30.90        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       18.71        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        19.50         0.26        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31        14.04        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
        8.22        10.68        13.87         7.53        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       13.64        11.57         2.83        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.07         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
        7.99        12.36        12.66        11.93        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.54        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 
       12.79        10.55        11.31        12.33        24.72        19.50 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       18.21        14.66        21.14        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       17.06        59.54        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        8.88        27.42        21.21        18.81         3.39         2.53 

  CDH1 MUTATED CDH1 WILD-TYPE 
          0.39           0.00 
  CDH1 MUTATED CDH1 WILD-TYPE 
         34.68         105.07 
  CDH1 MUTATED CDH1 WILD-TYPE 
         12.56          12.64 
[1] "0.4 - 34.7 (12.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D12V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDH1 MUTATED         0        0        2        4         5         1
  CDH1 WILD-TYPE       1        9       25       22        26        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDH1 MUTATED           1          4          6          1        2
  CDH1 WILD-TYPE         2         45         30         23       22
D12V3, multiclass
            clus
vv           CDH1 MUTATED CDH1 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              4             22
  STAGE IIA             5             26
  STAGE IIB             1             43
  STAGE III             1              2
  STAGE IIIA            4             45
  STAGE IIIB            6             30
  STAGE IIIC            1             23
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CDH1 MUTATED     1   8  12   6
  CDH1 WILD-TYPE  10  64 110  69
D12V4, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  T1            1             10
  T2            8             64
  T3           12            110
  T4            6             69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  CDH1 MUTATED    8  6  6  7
  CDH1 WILD-TYPE 85 75 44 46
D12V5, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  N0            8             85
  N1            6             75
  N2            6             44
  N3            7             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                cls
clus               0   1
  CDH1 MUTATED    26   3
  CDH1 WILD-TYPE 231  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED     26    3
  CDH1 WILD-TYPE  231   15
   clus
vv  CDH1 MUTATED CDH1 WILD-TYPE
  0           26            231
  1            3             15
[1] 2 2
[1] FALSE
D12V7, binary
                cls
clus               0   1
  CDH1 MUTATED    11  18
  CDH1 WILD-TYPE  99 161
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED     11   18
  CDH1 WILD-TYPE   99  161
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  FEMALE           11             99
  MALE             18            161
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CDH1 MUTATED                                      13
  CDH1 WILD-TYPE                                    37
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CDH1 MUTATED                                                       11
  CDH1 WILD-TYPE                                                    124
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CDH1 MUTATED                                                                   2
  CDH1 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CDH1 MUTATED                                                  1
  CDH1 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CDH1 MUTATED                                                          1
  CDH1 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CDH1 MUTATED                                                           0
  CDH1 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CDH1 MUTATED                                          1
  CDH1 WILD-TYPE                                        2
D12V8, multiclass
                                                                   clus
vv                                                                  CDH1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  CDH1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         37
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V9, binary
                cls
clus               0   1
  CDH1 MUTATED     0  29
  CDH1 WILD-TYPE   5 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED      0   29
  CDH1 WILD-TYPE    5  255
     clus
vv    CDH1 MUTATED CDH1 WILD-TYPE
  NO             0              5
  YES           29            255
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CDH1 MUTATED    17   2   1   4
  CDH1 WILD-TYPE 210   8   9  20
D12V10, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  R0           17            210
  R1            2              8
  R2            1              9
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDH1 MUTATED       6                         0    22
  CDH1 WILD-TYPE    70                         4   146
D12V12, multiclass
                           clus
vv                          CDH1 MUTATED CDH1 WILD-TYPE
  ASIAN                                6             70
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               22            146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = PLEKHA6 MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  PLEKHA6 MUTATED    12   6
  PLEKHA6 WILD-TYPE 169  74
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
               18               243 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
                6                74 
$`PLEKHA6 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7715 TCGA-BR-7851 TCGA-BR-8059 
        6.97        34.68        32.78        15.42        12.43        14.43 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-A4QL TCGA-CG-4306 
       19.50         0.26         4.31        15.85        11.57         1.02 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HU-A4GT 
        6.02       105.07        21.07         5.92        11.08         6.51 

$`PLEKHA6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       28.01        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       12.76        18.71        17.49         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       15.58         7.40         6.18        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        0.26         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        13.64         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        1.02         0.99         0.99        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       14.27        16.44        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         0.10         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
             0.26              0.00 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
           105.07             79.07 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
            12.00             12.66 
[1] "0.3 - 105.1 (12.0)" "0.0 - 79.1 (12.7)" 
[1] "hr=" "1.1"
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLEKHA6 MUTATED         0        0        2        1         5         2
  PLEKHA6 WILD-TYPE       1        9       25       25        26        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHA6 MUTATED           1          3          1          2        3
  PLEKHA6 WILD-TYPE         2         46         35         22       21
D13V3, multiclass
            clus
vv           PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 2                25
  STAGE II                 1                25
  STAGE IIA                5                26
  STAGE IIB                2                42
  STAGE III                1                 2
  STAGE IIIA               3                46
  STAGE IIIB               1                35
  STAGE IIIC               2                22
  STAGE IV                 3                21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHA6 MUTATED     0   4   9   7
  PLEKHA6 WILD-TYPE  11  68 113  68
D13V4, multiclass
    clus
vv   PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  T1               0                11
  T2               4                68
  T3               9               113
  T4               7                68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  PLEKHA6 MUTATED    9  5  4  2
  PLEKHA6 WILD-TYPE 84 76 46 51
D13V5, multiclass
    clus
vv   PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  N0               9                84
  N1               5                76
  N2               4                46
  N3               2                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED    18   1
  PLEKHA6 WILD-TYPE 239  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED     18    1
  PLEKHA6 WILD-TYPE  239   17
   clus
vv  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  0              18               239
  1               1                17
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED    12   8
  PLEKHA6 WILD-TYPE  98 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED     12    8
  PLEKHA6 WILD-TYPE   98  171
        clus
vv       PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  FEMALE              12                98
  MALE                 8               171
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PLEKHA6 MUTATED                                       0
  PLEKHA6 WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLEKHA6 MUTATED                                                       14
  PLEKHA6 WILD-TYPE                                                    121
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLEKHA6 MUTATED                                                                   4
  PLEKHA6 WILD-TYPE                                                                36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PLEKHA6 MUTATED                                                  2
  PLEKHA6 WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PLEKHA6 MUTATED                                                          0
  PLEKHA6 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PLEKHA6 MUTATED                                                           0
  PLEKHA6 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PLEKHA6 MUTATED                                          0
  PLEKHA6 WILD-TYPE                                        3
D13V8, multiclass
                                                                   clus
vv                                                                  PLEKHA6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         14
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  PLEKHA6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          121
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V9, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED     0  20
  PLEKHA6 WILD-TYPE   5 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED      0   20
  PLEKHA6 WILD-TYPE    5  264
     clus
vv    PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  NO                0                 5
  YES              20               264
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PLEKHA6 MUTATED    16   0   1   3
  PLEKHA6 WILD-TYPE 211  10   9  21
D13V10, multiclass
    clus
vv   PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  R0              16               211
  R1               0                10
  R2               1                 9
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLEKHA6 MUTATED       1                         1    14
  PLEKHA6 WILD-TYPE    75                         3   154
D13V12, multiclass
                           clus
vv                          PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  ASIAN                                   1                75
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                  14               154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = RHOA MUTATION ANALYSIS
D14V1, survival
                sevent
clus2              0   1
  RHOA MUTATED    12   4
  RHOA WILD-TYPE 169  76
  RHOA MUTATED RHOA WILD-TYPE 
            16            245 
  RHOA MUTATED RHOA WILD-TYPE 
             4             76 
$`RHOA MUTATED`
TCGA-BR-4188 TCGA-BR-6563 TCGA-BR-6802 TCGA-BR-7722 TCGA-BR-8366 TCGA-BR-A4IV 
        7.43        39.12        30.90        15.32         0.95        13.51 
TCGA-BR-A4QM TCGA-CG-4465 TCGA-CG-5720 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        5.13         9.01         0.99        18.84        18.54        18.61 
TCGA-D7-8574 TCGA-D7-A4YU TCGA-F1-A448 TCGA-HU-A4H0 
       17.19        16.44        21.27         2.10 

$`RHOA WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 
       26.70        11.70         6.61         6.97         4.64        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        19.33        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       15.42        28.01        18.15        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
        0.26        22.19        17.52        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
       22.26         1.48        13.41        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64        11.57         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       47.05        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 
       22.98        30.97         6.97        36.00         1.02         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       11.93        19.13        20.55        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 
       12.33        24.72        16.80        19.50        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 
        0.10         6.51         6.25        10.19         0.26        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  RHOA MUTATED RHOA WILD-TYPE 
          0.95           0.00 
  RHOA MUTATED RHOA WILD-TYPE 
         39.12         105.07 
  RHOA MUTATED RHOA WILD-TYPE 
         15.88          12.56 
[1] "0.9 - 39.1 (15.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D14V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RHOA MUTATED         0        0        2        0         1         2
  RHOA WILD-TYPE       1        9       25       26        30        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RHOA MUTATED           0          5          3          1        1
  RHOA WILD-TYPE         3         44         33         23       23
D14V3, multiclass
            clus
vv           RHOA MUTATED RHOA WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              0             26
  STAGE IIA             1             30
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            5             44
  STAGE IIIB            3             33
  STAGE IIIC            1             23
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RHOA MUTATED     0   5   7   3
  RHOA WILD-TYPE  11  67 115  72
D14V4, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  T1            0             11
  T2            5             67
  T3            7            115
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  RHOA MUTATED    3  3  5  5
  RHOA WILD-TYPE 90 78 45 48
D14V5, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  N0            3             90
  N1            3             78
  N2            5             45
  N3            5             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                cls
clus               0   1
  RHOA MUTATED    15   1
  RHOA WILD-TYPE 242  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED     15    1
  RHOA WILD-TYPE  242   17
   clus
vv  RHOA MUTATED RHOA WILD-TYPE
  0           15            242
  1            1             17
[1] 2 2
[1] FALSE
D14V7, binary
                cls
clus               0   1
  RHOA MUTATED     3  13
  RHOA WILD-TYPE 107 166
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      3   13
  RHOA WILD-TYPE  107  166
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  FEMALE            3            107
  MALE             13            166
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RHOA MUTATED                                       5
  RHOA WILD-TYPE                                    45
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RHOA MUTATED                                                        8
  RHOA WILD-TYPE                                                    127
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RHOA MUTATED                                                                   0
  RHOA WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RHOA MUTATED                                                  2
  RHOA WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RHOA MUTATED                                                          1
  RHOA WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RHOA MUTATED                                                           0
  RHOA WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RHOA MUTATED                                          0
  RHOA WILD-TYPE                                        3
D14V8, multiclass
                                                                   clus
vv                                                                  RHOA MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  RHOA WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V9, binary
                cls
clus               0   1
  RHOA MUTATED     0  16
  RHOA WILD-TYPE   5 268
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      0   16
  RHOA WILD-TYPE    5  268
     clus
vv    RHOA MUTATED RHOA WILD-TYPE
  NO             0              5
  YES           16            268
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RHOA MUTATED    14   0   1   1
  RHOA WILD-TYPE 213  10   9  23
D14V10, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  R0           14            213
  R1            0             10
  R2            1              9
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RHOA MUTATED       2                         0    12
  RHOA WILD-TYPE    74                         4   156
D14V12, multiclass
                           clus
vv                          RHOA MUTATED RHOA WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               12            156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = SMAD4 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2               0   1
  SMAD4 MUTATED    16   7
  SMAD4 WILD-TYPE 165  73
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             23             238 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              7              73 
$`SMAD4 MUTATED`
TCGA-BR-4184 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6564 TCGA-BR-7722 TCGA-BR-7958 
        6.97         6.18         9.57        26.10        15.32        12.76 
TCGA-BR-8361 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-A4J6 
       19.50         0.95         3.32        19.17         1.12         0.66 
TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-8529 TCGA-CG-4469 TCGA-CG-5719 TCGA-D7-6815 
        3.25         0.07         0.13         7.07         1.02        15.98 
TCGA-FP-7829 TCGA-HU-8243 TCGA-HU-A4G2 TCGA-HU-A4H4 TCGA-IN-8462 
       19.53         5.92        24.30        23.84        18.81 

$`SMAD4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       30.90         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        19.33        39.12         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       28.01        18.15        28.73        12.43         3.45         9.07 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
       26.33         4.31        14.04        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.72        14.17         0.53        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.15        13.18         0.30         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.10         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 
       12.03         0.00         9.01        18.97        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.22        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       14.47        72.23        21.27         3.48        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.52        26.47        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       10.62         0.76         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       12.95        19.36        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45         3.39         2.53 

  SMAD4 MUTATED SMAD4 WILD-TYPE 
           0.07            0.00 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          26.10          105.07 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          7.070          12.725 
[1] "0.1 - 26.1 (7.1)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.4"
D15V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMAD4 MUTATED         0        0        1        3         3         6
  SMAD4 WILD-TYPE       1        9       26       23        28        38
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMAD4 MUTATED           0          3          2          3        3
  SMAD4 WILD-TYPE         3         46         34         21       21
D15V3, multiclass
            clus
vv           SMAD4 MUTATED SMAD4 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               3              23
  STAGE IIA              3              28
  STAGE IIB              6              38
  STAGE III              0               3
  STAGE IIIA             3              46
  STAGE IIIB             2              34
  STAGE IIIC             3              21
  STAGE IV               3              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SMAD4 MUTATED     0   6  12   6
  SMAD4 WILD-TYPE  11  66 110  69
D15V4, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  T1             0              11
  T2             6              66
  T3            12             110
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  SMAD4 MUTATED    8  8  4  4
  SMAD4 WILD-TYPE 85 73 46 49
D15V5, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  N0             8              85
  N1             8              73
  N2             4              46
  N3             4              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                 cls
clus                0   1
  SMAD4 MUTATED    21   2
  SMAD4 WILD-TYPE 236  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     21    2
  SMAD4 WILD-TYPE  236   16
   clus
vv  SMAD4 MUTATED SMAD4 WILD-TYPE
  0            21             236
  1             2              16
[1] 2 2
[1] FALSE
D15V7, binary
                 cls
clus                0   1
  SMAD4 MUTATED     9  15
  SMAD4 WILD-TYPE 101 164
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      9   15
  SMAD4 WILD-TYPE  101  164
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  FEMALE             9             101
  MALE              15             164
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SMAD4 MUTATED                                       3
  SMAD4 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SMAD4 MUTATED                                                       13
  SMAD4 WILD-TYPE                                                    122
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SMAD4 MUTATED                                                                   3
  SMAD4 WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SMAD4 MUTATED                                                  3
  SMAD4 WILD-TYPE                                               35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SMAD4 MUTATED                                                          2
  SMAD4 WILD-TYPE                                                       14
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SMAD4 MUTATED                                                           0
  SMAD4 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SMAD4 MUTATED                                          0
  SMAD4 WILD-TYPE                                        3
D15V8, multiclass
                                                                   clus
vv                                                                  SMAD4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       13
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  SMAD4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        122
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V9, binary
                 cls
clus                0   1
  SMAD4 MUTATED     0  24
  SMAD4 WILD-TYPE   5 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      0   24
  SMAD4 WILD-TYPE    5  260
     clus
vv    SMAD4 MUTATED SMAD4 WILD-TYPE
  NO              0               5
  YES            24             260
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SMAD4 MUTATED    18   1   0   3
  SMAD4 WILD-TYPE 209   9  10  21
D15V10, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  R0            18             209
  R1             1               9
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMAD4 MUTATED       7                         0    15
  SMAD4 WILD-TYPE    69                         4   153
D15V12, multiclass
                           clus
vv                          SMAD4 MUTATED SMAD4 WILD-TYPE
  ASIAN                                 7              69
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                15             153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = MTG1 MUTATION ANALYSIS
D16V1, survival
                sevent
clus2              0   1
  MTG1 MUTATED     4   5
  MTG1 WILD-TYPE 177  75
  MTG1 MUTATED MTG1 WILD-TYPE 
             9            252 
  MTG1 MUTATED MTG1 WILD-TYPE 
             5             75 
$`MTG1 MUTATED`
TCGA-BR-4184 TCGA-BR-8081 TCGA-CD-A4MG TCGA-CG-4306 TCGA-D7-A4YV TCGA-F1-6874 
        6.97        20.55         6.58         1.02         5.92        14.47 
TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-A4GQ 
       11.08        11.41         0.10 

$`MTG1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       17.49        14.43         0.69        12.26         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       16.44        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       16.24        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        5.52        26.47         5.92        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  MTG1 MUTATED MTG1 WILD-TYPE 
           0.1            0.0 
  MTG1 MUTATED MTG1 WILD-TYPE 
         20.55         105.07 
  MTG1 MUTATED MTG1 WILD-TYPE 
         6.970         12.775 
[1] "0.1 - 20.6 (7.0)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "3.3"
D16V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MTG1 MUTATED         0        0        1        0         2         3
  MTG1 WILD-TYPE       1        9       26       26        29        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MTG1 MUTATED           0          1          0          1        1
  MTG1 WILD-TYPE         3         48         36         23       23
D16V3, multiclass
            clus
vv           MTG1 MUTATED MTG1 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             2             29
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            1             23
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MTG1 MUTATED     0   1   5   3
  MTG1 WILD-TYPE  11  71 117  72
D16V4, multiclass
    clus
vv   MTG1 MUTATED MTG1 WILD-TYPE
  T1            0             11
  T2            1             71
  T3            5            117
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  MTG1 MUTATED    5  2  2  0
  MTG1 WILD-TYPE 88 79 48 53
D16V5, multiclass
    clus
vv   MTG1 MUTATED MTG1 WILD-TYPE
  N0            5             88
  N1            2             79
  N2            2             48
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                cls
clus               0   1
  MTG1 MUTATED     7   1
  MTG1 WILD-TYPE 250  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTG1 MUTATED      7    1
  MTG1 WILD-TYPE  250   17
   clus
vv  MTG1 MUTATED MTG1 WILD-TYPE
  0            7            250
  1            1             17
[1] 2 2
[1] FALSE
D16V7, binary
                cls
clus               0   1
  MTG1 MUTATED     3   6
  MTG1 WILD-TYPE 107 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTG1 MUTATED      3    6
  MTG1 WILD-TYPE  107  173
        clus
vv       MTG1 MUTATED MTG1 WILD-TYPE
  FEMALE            3            107
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MTG1 MUTATED                                       2
  MTG1 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MTG1 MUTATED                                                        4
  MTG1 WILD-TYPE                                                    131
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MTG1 MUTATED                                                                   1
  MTG1 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MTG1 MUTATED                                                  2
  MTG1 WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MTG1 MUTATED                                                          0
  MTG1 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MTG1 MUTATED                                                           0
  MTG1 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MTG1 MUTATED                                          0
  MTG1 WILD-TYPE                                        3
D16V8, multiclass
                                                                   clus
vv                                                                  MTG1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  MTG1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V9, binary
                cls
clus               0   1
  MTG1 MUTATED     0   9
  MTG1 WILD-TYPE   5 275
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTG1 MUTATED      0    9
  MTG1 WILD-TYPE    5  275
     clus
vv    MTG1 MUTATED MTG1 WILD-TYPE
  NO             0              5
  YES            9            275
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MTG1 MUTATED     6   0   1   1
  MTG1 WILD-TYPE 221  10   9  23
D16V10, multiclass
    clus
vv   MTG1 MUTATED MTG1 WILD-TYPE
  R0            6            221
  R1            0             10
  R2            1              9
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MTG1 MUTATED       3                         1     4
  MTG1 WILD-TYPE    73                         3   164
D16V12, multiclass
                           clus
vv                          MTG1 MUTATED MTG1 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                                4            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = KLF3 MUTATION ANALYSIS
D17V1, survival
                sevent
clus2              0   1
  KLF3 MUTATED    12   5
  KLF3 WILD-TYPE 169  75
  KLF3 MUTATED KLF3 WILD-TYPE 
            17            244 
  KLF3 MUTATED KLF3 WILD-TYPE 
             5             75 
$`KLF3 MUTATED`
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-7851 
        6.61        34.68        32.78        32.94        23.93        12.43 
TCGA-BR-8078 TCGA-BR-8289 TCGA-BR-8680 TCGA-BR-8682 TCGA-CD-A4MG TCGA-D7-A4YV 
       12.26         2.66        15.81        16.44         6.58         5.92 
TCGA-HU-8602 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4H2 TCGA-HU-A4H8 
       11.41        29.98         0.10        12.95         8.88 

$`KLF3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
       18.35        30.90         6.18         9.57        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 
       31.20        12.82         9.21        24.76        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        8.05        12.95        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 
       13.45         6.28         7.53         0.49        11.54         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
       19.36        23.84        12.30         9.67        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  KLF3 MUTATED KLF3 WILD-TYPE 
           0.1            0.0 
  KLF3 MUTATED KLF3 WILD-TYPE 
         34.68         105.07 
  KLF3 MUTATED KLF3 WILD-TYPE 
         12.43          12.64 
[1] "0.1 - 34.7 (12.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D17V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KLF3 MUTATED         0        0        2        1         5         5
  KLF3 WILD-TYPE       1        9       25       25        26        39
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KLF3 MUTATED           1          1          1          1        2
  KLF3 WILD-TYPE         2         48         35         23       22
D17V3, multiclass
            clus
vv           KLF3 MUTATED KLF3 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              1             25
  STAGE IIA             5             26
  STAGE IIB             5             39
  STAGE III             1              2
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            1             23
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KLF3 MUTATED     1   4   6   8
  KLF3 WILD-TYPE  10  68 116  67
D17V4, multiclass
    clus
vv   KLF3 MUTATED KLF3 WILD-TYPE
  T1            1             10
  T2            4             68
  T3            6            116
  T4            8             67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  KLF3 MUTATED   10  5  2  2
  KLF3 WILD-TYPE 83 76 48 51
D17V5, multiclass
    clus
vv   KLF3 MUTATED KLF3 WILD-TYPE
  N0           10             83
  N1            5             76
  N2            2             48
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                cls
clus               0   1
  KLF3 MUTATED    17   2
  KLF3 WILD-TYPE 240  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED     17    2
  KLF3 WILD-TYPE  240   16
   clus
vv  KLF3 MUTATED KLF3 WILD-TYPE
  0           17            240
  1            2             16
[1] 2 2
[1] FALSE
D17V7, binary
                cls
clus               0   1
  KLF3 MUTATED    10   9
  KLF3 WILD-TYPE 100 170
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED     10    9
  KLF3 WILD-TYPE  100  170
        clus
vv       KLF3 MUTATED KLF3 WILD-TYPE
  FEMALE           10            100
  MALE              9            170
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KLF3 MUTATED                                       2
  KLF3 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KLF3 MUTATED                                                        7
  KLF3 WILD-TYPE                                                    128
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KLF3 MUTATED                                                                   2
  KLF3 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KLF3 MUTATED                                                  6
  KLF3 WILD-TYPE                                               32
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KLF3 MUTATED                                                          2
  KLF3 WILD-TYPE                                                       14
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KLF3 MUTATED                                                           0
  KLF3 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KLF3 MUTATED                                          0
  KLF3 WILD-TYPE                                        3
D17V8, multiclass
                                                                   clus
vv                                                                  KLF3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  KLF3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V9, binary
                cls
clus               0   1
  KLF3 MUTATED     1  18
  KLF3 WILD-TYPE   4 266
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED      1   18
  KLF3 WILD-TYPE    4  266
     clus
vv    KLF3 MUTATED KLF3 WILD-TYPE
  NO             1              4
  YES           18            266
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  KLF3 MUTATED    16   0   0   2
  KLF3 WILD-TYPE 211  10  10  22
D17V10, multiclass
    clus
vv   KLF3 MUTATED KLF3 WILD-TYPE
  R0           16            211
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KLF3 MUTATED       8                         0    10
  KLF3 WILD-TYPE    68                         4   158
D17V12, multiclass
                           clus
vv                          KLF3 MUTATED KLF3 WILD-TYPE
  ASIAN                                8             68
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               10            158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = CTCF MUTATION ANALYSIS
D18V1, survival
                sevent
clus2              0   1
  CTCF MUTATED    11   4
  CTCF WILD-TYPE 170  76
  CTCF MUTATED CTCF WILD-TYPE 
            15            246 
  CTCF MUTATED CTCF WILD-TYPE 
             4             76 
$`CTCF MUTATED`
TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8372 
       23.93        18.15        12.26        20.55         0.26        19.17 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8592 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-5721 
        1.12        12.79         6.28        15.81        11.57         6.02 
TCGA-CG-5723 TCGA-HJ-7597 TCGA-HU-A4GT 
      105.07        26.47         6.51 

$`CTCF WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
        9.21        24.76        15.42        28.01        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       14.43         0.69         9.60         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 
        5.39        25.18         9.21        20.22        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
       13.45         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        13.64         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
       36.00         1.02         0.99         0.99        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.52         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  CTCF MUTATED CTCF WILD-TYPE 
          0.26           0.00 
  CTCF MUTATED CTCF WILD-TYPE 
        105.07          79.07 
  CTCF MUTATED CTCF WILD-TYPE 
        12.790         12.605 
[1] "0.3 - 105.1 (12.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.4"
D18V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CTCF MUTATED         1        0        3        1         2         3
  CTCF WILD-TYPE       0        9       24       25        29        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTCF MUTATED           0          1          2          1        3
  CTCF WILD-TYPE         3         48         34         23       21
D18V3, multiclass
            clus
vv           CTCF MUTATED CTCF WILD-TYPE
  STAGE I               1              0
  STAGE IA              0              9
  STAGE IB              3             24
  STAGE II              1             25
  STAGE IIA             2             29
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            2             34
  STAGE IIIC            1             23
  STAGE IV              3             21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CTCF MUTATED     1   4   3   9
  CTCF WILD-TYPE  10  68 119  66
D18V4, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  T1            1             10
  T2            4             68
  T3            3            119
  T4            9             66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  CTCF MUTATED    9  6  1  2
  CTCF WILD-TYPE 84 75 49 51
D18V5, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  N0            9             84
  N1            6             75
  N2            1             49
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                cls
clus               0   1
  CTCF MUTATED    15   1
  CTCF WILD-TYPE 242  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED     15    1
  CTCF WILD-TYPE  242   17
   clus
vv  CTCF MUTATED CTCF WILD-TYPE
  0           15            242
  1            1             17
[1] 2 2
[1] FALSE
D18V7, binary
                cls
clus               0   1
  CTCF MUTATED    11   7
  CTCF WILD-TYPE  99 172
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED     11    7
  CTCF WILD-TYPE   99  172
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  FEMALE           11             99
  MALE              7            172
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CTCF MUTATED                                       1
  CTCF WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CTCF MUTATED                                                       13
  CTCF WILD-TYPE                                                    122
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CTCF MUTATED                                                                   1
  CTCF WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CTCF MUTATED                                                  2
  CTCF WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CTCF MUTATED                                                          0
  CTCF WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CTCF MUTATED                                                           0
  CTCF WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CTCF MUTATED                                          1
  CTCF WILD-TYPE                                        2
D18V8, multiclass
                                                                   clus
vv                                                                  CTCF MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      13
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  CTCF WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       122
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V9, binary
                cls
clus               0   1
  CTCF MUTATED     0  18
  CTCF WILD-TYPE   5 266
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED      0   18
  CTCF WILD-TYPE    5  266
     clus
vv    CTCF MUTATED CTCF WILD-TYPE
  NO             0              5
  YES           18            266
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CTCF MUTATED    16   0   0   2
  CTCF WILD-TYPE 211  10  10  22
D18V10, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  R0           16            211
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CTCF MUTATED       2                         1    13
  CTCF WILD-TYPE    74                         3   155
D18V12, multiclass
                           clus
vv                          CTCF MUTATED CTCF WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                               13            155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = ZBTB20 MUTATION ANALYSIS
D19V1, survival
                  sevent
clus2                0   1
  ZBTB20 MUTATED    16   7
  ZBTB20 WILD-TYPE 165  73
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              23              238 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
               7               73 
$`ZBTB20 MUTATED`
TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7958 TCGA-BR-8382 
       30.90         6.61        24.76        23.93        12.76        15.85 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CD-A4MJ 
        1.12        12.79        13.45        11.57         6.58        12.62 
TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5733 
        1.02         9.01         6.02       105.07        28.96        21.07 
TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H8 
       11.84        29.98         6.25        19.36         8.88 

$`ZBTB20 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       18.35         6.18         9.57        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7715 
       30.90        31.20        32.94        12.82         9.21        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
        9.07        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        20.55         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
        3.32        11.80        19.17        14.79         0.26         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 
        5.39        25.18         9.21        20.22        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       47.05        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
        0.99        12.03        79.07        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
       12.95        23.84        12.30         9.67        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
            1.02             0.00 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
          105.07            79.07 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
          12.760           12.575 
[1] "1.0 - 105.1 (12.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.3"
D19V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZBTB20 MUTATED         1        2        4        1         3         3
  ZBTB20 WILD-TYPE       0        7       23       25        28        41
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB20 MUTATED           1          2          2          3        4
  ZBTB20 WILD-TYPE         2         47         34         21       20
D19V3, multiclass
            clus
vv           ZBTB20 MUTATED ZBTB20 WILD-TYPE
  STAGE I                 1                0
  STAGE IA                2                7
  STAGE IB                4               23
  STAGE II                1               25
  STAGE IIA               3               28
  STAGE IIB               3               41
  STAGE III               1                2
  STAGE IIIA              2               47
  STAGE IIIB              2               34
  STAGE IIIC              3               21
  STAGE IV                4               20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZBTB20 MUTATED     4   8   6   9
  ZBTB20 WILD-TYPE   7  64 116  66
D19V4, multiclass
    clus
vv   ZBTB20 MUTATED ZBTB20 WILD-TYPE
  T1              4                7
  T2              8               64
  T3              6              116
  T4              9               66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZBTB20 MUTATED   10  9  3  5
  ZBTB20 WILD-TYPE 83 72 47 48
D19V5, multiclass
    clus
vv   ZBTB20 MUTATED ZBTB20 WILD-TYPE
  N0             10               83
  N1              9               72
  N2              3               47
  N3              5               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED    25   2
  ZBTB20 WILD-TYPE 232  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED     25    2
  ZBTB20 WILD-TYPE  232   16
   clus
vv  ZBTB20 MUTATED ZBTB20 WILD-TYPE
  0             25              232
  1              2               16
[1] 2 2
[1] FALSE
D19V7, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED    14  14
  ZBTB20 WILD-TYPE  96 165
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED     14   14
  ZBTB20 WILD-TYPE   96  165
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  FEMALE             14               96
  MALE               14              165
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZBTB20 MUTATED                                       5
  ZBTB20 WILD-TYPE                                    45
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZBTB20 MUTATED                                                       16
  ZBTB20 WILD-TYPE                                                    119
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZBTB20 MUTATED                                                                   4
  ZBTB20 WILD-TYPE                                                                36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZBTB20 MUTATED                                                  2
  ZBTB20 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZBTB20 MUTATED                                                          0
  ZBTB20 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZBTB20 MUTATED                                                           1
  ZBTB20 WILD-TYPE                                                         5
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZBTB20 MUTATED                                          0
  ZBTB20 WILD-TYPE                                        3
D19V8, multiclass
                                                                   clus
vv                                                                  ZBTB20 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ZBTB20 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         119
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V9, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED     0  28
  ZBTB20 WILD-TYPE   5 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED      0   28
  ZBTB20 WILD-TYPE    5  256
     clus
vv    ZBTB20 MUTATED ZBTB20 WILD-TYPE
  NO               0                5
  YES             28              256
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZBTB20 MUTATED    18   0   2   5
  ZBTB20 WILD-TYPE 209  10   8  19
D19V10, multiclass
    clus
vv   ZBTB20 MUTATED ZBTB20 WILD-TYPE
  R0             18              209
  R1              0               10
  R2              2                8
  RX              5               19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZBTB20 MUTATED       7                         1    13
  ZBTB20 WILD-TYPE    69                         3   155
D19V12, multiclass
                           clus
vv                          ZBTB20 MUTATED ZBTB20 WILD-TYPE
  ASIAN                                  7               69
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                 13              155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = GAS6 MUTATION ANALYSIS
D20V1, survival
                sevent
clus2              0   1
  GAS6 MUTATED    10   4
  GAS6 WILD-TYPE 171  76
  GAS6 MUTATED GAS6 WILD-TYPE 
            14            247 
  GAS6 MUTATED GAS6 WILD-TYPE 
             4             76 
$`GAS6 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8591 TCGA-BR-A4CQ TCGA-BR-A4QL 
        6.97        34.68        19.50        13.45        22.26        11.57 
TCGA-CD-A486 TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-A4YV 
        3.42         6.58         1.02         6.02        65.10         5.92 
TCGA-HU-8245 TCGA-HU-A4G8 
       12.59        11.84 

$`GAS6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
        0.16         0.10         0.10         0.13         0.10         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        28.96        79.07         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8602 
       11.08         5.52        26.47         5.92        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  GAS6 MUTATED GAS6 WILD-TYPE 
          1.02           0.00 
  GAS6 MUTATED GAS6 WILD-TYPE 
         65.10         105.07 
  GAS6 MUTATED GAS6 WILD-TYPE 
        11.705         12.760 
[1] "1.0 - 65.1 (11.7)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.1"
D20V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GAS6 MUTATED         0        0        1        0         4         2
  GAS6 WILD-TYPE       1        9       26       26        27        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GAS6 MUTATED           0          2          1          2        3
  GAS6 WILD-TYPE         3         47         35         22       21
D20V3, multiclass
            clus
vv           GAS6 MUTATED GAS6 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             4             27
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            1             35
  STAGE IIIC            2             22
  STAGE IV              3             21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GAS6 MUTATED     0   1   9   5
  GAS6 WILD-TYPE  11  71 113  70
D20V4, multiclass
    clus
vv   GAS6 MUTATED GAS6 WILD-TYPE
  T1            0             11
  T2            1             71
  T3            9            113
  T4            5             70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  GAS6 MUTATED    5  5  3  2
  GAS6 WILD-TYPE 88 76 47 51
D20V5, multiclass
    clus
vv   GAS6 MUTATED GAS6 WILD-TYPE
  N0            5             88
  N1            5             76
  N2            3             47
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                cls
clus               0   1
  GAS6 MUTATED    14   1
  GAS6 WILD-TYPE 243  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED     14    1
  GAS6 WILD-TYPE  243   17
   clus
vv  GAS6 MUTATED GAS6 WILD-TYPE
  0           14            243
  1            1             17
[1] 2 2
[1] FALSE
D20V7, binary
                cls
clus               0   1
  GAS6 MUTATED     8   8
  GAS6 WILD-TYPE 102 171
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED      8    8
  GAS6 WILD-TYPE  102  171
        clus
vv       GAS6 MUTATED GAS6 WILD-TYPE
  FEMALE            8            102
  MALE              8            171
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GAS6 MUTATED                                       2
  GAS6 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GAS6 MUTATED                                                       10
  GAS6 WILD-TYPE                                                    125
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GAS6 MUTATED                                                                   2
  GAS6 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GAS6 MUTATED                                                  1
  GAS6 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GAS6 MUTATED                                                          0
  GAS6 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GAS6 MUTATED                                                           1
  GAS6 WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GAS6 MUTATED                                          0
  GAS6 WILD-TYPE                                        3
D20V8, multiclass
                                                                   clus
vv                                                                  GAS6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  GAS6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V9, binary
                cls
clus               0   1
  GAS6 MUTATED     0  16
  GAS6 WILD-TYPE   5 268
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED      0   16
  GAS6 WILD-TYPE    5  268
     clus
vv    GAS6 MUTATED GAS6 WILD-TYPE
  NO             0              5
  YES           16            268
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GAS6 MUTATED     9   0   1   3
  GAS6 WILD-TYPE 218  10   9  21
D20V10, multiclass
    clus
vv   GAS6 MUTATED GAS6 WILD-TYPE
  R0            9            218
  R1            0             10
  R2            1              9
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GAS6 MUTATED       4                         0     9
  GAS6 WILD-TYPE    72                         4   159
D20V12, multiclass
                           clus
vv                          GAS6 MUTATED GAS6 WILD-TYPE
  ASIAN                                4             72
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                9            159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = ATP6V1B1 MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  ATP6V1B1 MUTATED    11   7
  ATP6V1B1 WILD-TYPE 170  73
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                18                243 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                 7                 73 
$`ATP6V1B1 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8081 
       26.70         6.97        18.35        23.93        12.26        20.55 
TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5726 
       15.81        11.57         6.58         1.02         6.02        28.96 
TCGA-CG-5733 TCGA-D7-A4YV TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4H4 TCGA-HU-A4H8 
       21.07         5.92        11.84        29.98        23.84         8.88 

$`ATP6V1B1 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 
       11.70         6.61         4.64         7.43        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 
       31.20        32.94        12.82         9.21        24.76        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        9.60         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       12.03        79.07        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        11.77         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       19.36        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
              1.02               0.00 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
             29.98             105.07 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
            14.035             12.620 
[1] "1.0 - 30.0 (14.0)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATP6V1B1 MUTATED         0        1        2        0         2         6
  ATP6V1B1 WILD-TYPE       1        8       25       26        29        38
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP6V1B1 MUTATED           0          2          1          0        3
  ATP6V1B1 WILD-TYPE         3         47         35         24       21
D21V3, multiclass
            clus
vv           ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  1                  8
  STAGE IB                  2                 25
  STAGE II                  0                 26
  STAGE IIA                 2                 29
  STAGE IIB                 6                 38
  STAGE III                 0                  3
  STAGE IIIA                2                 47
  STAGE IIIB                1                 35
  STAGE IIIC                0                 24
  STAGE IV                  3                 21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ATP6V1B1 MUTATED     2   4   6   5
  ATP6V1B1 WILD-TYPE   9  68 116  70
D21V4, multiclass
    clus
vv   ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  T1                2                  9
  T2                4                 68
  T3                6                116
  T4                5                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  ATP6V1B1 MUTATED    6  8  4  1
  ATP6V1B1 WILD-TYPE 87 73 46 52
D21V5, multiclass
    clus
vv   ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  N0                6                 87
  N1                8                 73
  N2                4                 46
  N3                1                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                    cls
clus                   0   1
  ATP6V1B1 MUTATED    17   2
  ATP6V1B1 WILD-TYPE 240  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1B1 MUTATED     17    2
  ATP6V1B1 WILD-TYPE  240   16
   clus
vv  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  0               17                240
  1                2                 16
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  ATP6V1B1 MUTATED    11   9
  ATP6V1B1 WILD-TYPE  99 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1B1 MUTATED     11    9
  ATP6V1B1 WILD-TYPE   99  170
        clus
vv       ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  FEMALE               11                 99
  MALE                  9                170
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ATP6V1B1 MUTATED                                       3
  ATP6V1B1 WILD-TYPE                                    47
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ATP6V1B1 MUTATED                                                        9
  ATP6V1B1 WILD-TYPE                                                    126
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ATP6V1B1 MUTATED                                                                   3
  ATP6V1B1 WILD-TYPE                                                                37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ATP6V1B1 MUTATED                                                  5
  ATP6V1B1 WILD-TYPE                                               33
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ATP6V1B1 MUTATED                                                          0
  ATP6V1B1 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ATP6V1B1 MUTATED                                                           0
  ATP6V1B1 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ATP6V1B1 MUTATED                                          0
  ATP6V1B1 WILD-TYPE                                        3
D21V8, multiclass
                                                                   clus
vv                                                                  ATP6V1B1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  ATP6V1B1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V9, binary
                    cls
clus                   0   1
  ATP6V1B1 MUTATED     0  20
  ATP6V1B1 WILD-TYPE   5 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1B1 MUTATED      0   20
  ATP6V1B1 WILD-TYPE    5  264
     clus
vv    ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  NO                 0                  5
  YES               20                264
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  ATP6V1B1 MUTATED    13   0   1   4
  ATP6V1B1 WILD-TYPE 214  10   9  20
D21V10, multiclass
    clus
vv   ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  R0               13                214
  R1                0                 10
  R2                1                  9
  RX                4                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATP6V1B1 MUTATED       6                         0    10
  ATP6V1B1 WILD-TYPE    70                         4   158
D21V12, multiclass
                           clus
vv                          ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  ASIAN                                    6                 70
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                   10                158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = PTEN MUTATION ANALYSIS
D22V1, survival
                sevent
clus2              0   1
  PTEN MUTATED    14   5
  PTEN WILD-TYPE 167  75
  PTEN MUTATED PTEN WILD-TYPE 
            19            242 
  PTEN MUTATED PTEN WILD-TYPE 
             5             75 
$`PTEN MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6707 TCGA-BR-7851 
       26.70        30.90         6.61        34.68        19.89        12.43 
TCGA-BR-8284 TCGA-BR-8368 TCGA-BR-8381 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-8531 
        8.05         4.31         0.26         1.12        13.45         0.10 
TCGA-CG-4305 TCGA-CG-5728 TCGA-D7-5577 TCGA-FP-7735 TCGA-FP-8211 TCGA-FP-A4BE 
       15.95        65.10        12.36         3.48        13.58        11.08 
TCGA-HU-A4GT 
        6.51 

$`PTEN WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       18.05         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       12.82         9.21        24.76        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
       20.55        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79        15.81         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.13         0.16         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
        0.10        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 
       79.07         4.01        69.04        21.07         7.99        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         0.10         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  PTEN MUTATED PTEN WILD-TYPE 
           0.1            0.0 
  PTEN MUTATED PTEN WILD-TYPE 
         65.10         105.07 
  PTEN MUTATED PTEN WILD-TYPE 
         12.36          12.71 
[1] "0.1 - 65.1 (12.4)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.2"
D22V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTEN MUTATED         0        0        3        1         5         4
  PTEN WILD-TYPE       1        9       24       25        26        40
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTEN MUTATED           1          3          0          2        0
  PTEN WILD-TYPE         2         46         36         22       24
D22V3, multiclass
            clus
vv           PTEN MUTATED PTEN WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              3             24
  STAGE II              1             25
  STAGE IIA             5             26
  STAGE IIB             4             40
  STAGE III             1              2
  STAGE IIIA            3             46
  STAGE IIIB            0             36
  STAGE IIIC            2             22
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PTEN MUTATED     0   7   9   4
  PTEN WILD-TYPE  11  65 113  71
D22V4, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T1            0             11
  T2            7             65
  T3            9            113
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  PTEN MUTATED   10  8  0  3
  PTEN WILD-TYPE 83 73 50 50
D22V5, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  N0           10             83
  N1            8             73
  N2            0             50
  N3            3             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                cls
clus               0   1
  PTEN MUTATED    21   0
  PTEN WILD-TYPE 236  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     21    0
  PTEN WILD-TYPE  236   18
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0           21            236
  1            0             18
[1] 2 2
[1] FALSE
D22V7, binary
                cls
clus               0   1
  PTEN MUTATED    14   9
  PTEN WILD-TYPE  96 170
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     14    9
  PTEN WILD-TYPE   96  170
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE           14             96
  MALE              9            170
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PTEN MUTATED                                       2
  PTEN WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PTEN MUTATED                                                       16
  PTEN WILD-TYPE                                                    119
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PTEN MUTATED                                                                   3
  PTEN WILD-TYPE                                                                37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PTEN MUTATED                                                  2
  PTEN WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PTEN MUTATED                                                          0
  PTEN WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PTEN MUTATED                                                           0
  PTEN WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PTEN MUTATED                                          0
  PTEN WILD-TYPE                                        3
D22V8, multiclass
                                                                   clus
vv                                                                  PTEN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  PTEN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       119
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V9, binary
                cls
clus               0   1
  PTEN MUTATED     0  23
  PTEN WILD-TYPE   5 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0   23
  PTEN WILD-TYPE    5  261
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             0              5
  YES           23            261
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PTEN MUTATED    16   1   0   6
  PTEN WILD-TYPE 211   9  10  18
D22V10, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0           16            211
  R1            1              9
  R2            0             10
  RX            6             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       2                         2    17
  PTEN WILD-TYPE    74                         2   151
D22V12, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            2              2
  WHITE                               17            151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = HLA-A MUTATION ANALYSIS
D23V1, survival
                 sevent
clus2               0   1
  HLA-A MUTATED     9   2
  HLA-A WILD-TYPE 172  78
  HLA-A MUTATED HLA-A WILD-TYPE 
             11             250 
  HLA-A MUTATED HLA-A WILD-TYPE 
              2              78 
$`HLA-A MUTATED`
TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8372 TCGA-CD-8536 TCGA-CD-A4MG 
       32.94        12.26        20.55        19.17         0.10         6.58 
TCGA-CG-4438 TCGA-CG-5718 TCGA-F1-6874 TCGA-HU-A4G8 TCGA-HU-A4GT 
       54.08        36.00        14.47        11.84         6.51 

$`HLA-A WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        30.90        31.20        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 
       17.49        14.43         0.69         9.60         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99         8.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
        7.07        22.98        30.97         6.97         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 
       14.76         0.62         7.99        16.24        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  HLA-A MUTATED HLA-A WILD-TYPE 
            0.1             0.0 
  HLA-A MUTATED HLA-A WILD-TYPE 
          54.08          105.07 
  HLA-A MUTATED HLA-A WILD-TYPE 
         14.470          12.605 
[1] "0.1 - 54.1 (14.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.4"
D23V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HLA-A MUTATED         0        0        1        2         3         3
  HLA-A WILD-TYPE       1        9       26       24        28        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HLA-A MUTATED           0          1          0          1        1
  HLA-A WILD-TYPE         3         48         36         23       23
D23V3, multiclass
            clus
vv           HLA-A MUTATED HLA-A WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               2              24
  STAGE IIA              3              28
  STAGE IIB              3              41
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HLA-A MUTATED     0   2   5   5
  HLA-A WILD-TYPE  11  70 117  70
D23V4, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  T1             0              11
  T2             2              70
  T3             5             117
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  HLA-A MUTATED    8  3  1  1
  HLA-A WILD-TYPE 85 78 49 52
D23V5, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  N0             8              85
  N1             3              78
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                 cls
clus                0   1
  HLA-A MUTATED    15   0
  HLA-A WILD-TYPE 242  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED     15    0
  HLA-A WILD-TYPE  242   18
   clus
vv  HLA-A MUTATED HLA-A WILD-TYPE
  0            15             242
  1             0              18
[1] 2 2
[1] FALSE
D23V7, binary
                 cls
clus                0   1
  HLA-A MUTATED    10   5
  HLA-A WILD-TYPE 100 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED     10    5
  HLA-A WILD-TYPE  100  174
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  FEMALE            10             100
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  HLA-A MUTATED                                       2
  HLA-A WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HLA-A MUTATED                                                        9
  HLA-A WILD-TYPE                                                    126
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HLA-A MUTATED                                                                   3
  HLA-A WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  HLA-A MUTATED                                                  1
  HLA-A WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  HLA-A MUTATED                                                          0
  HLA-A WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  HLA-A MUTATED                                                           0
  HLA-A WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  HLA-A MUTATED                                          0
  HLA-A WILD-TYPE                                        3
D23V8, multiclass
                                                                   clus
vv                                                                  HLA-A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  HLA-A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V9, binary
                 cls
clus                0   1
  HLA-A MUTATED     0  15
  HLA-A WILD-TYPE   5 269
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      0   15
  HLA-A WILD-TYPE    5  269
     clus
vv    HLA-A MUTATED HLA-A WILD-TYPE
  NO              0               5
  YES            15             269
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HLA-A MUTATED     9   0   0   4
  HLA-A WILD-TYPE 218  10  10  20
D23V10, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  R0             9             218
  R1             0              10
  R2             0              10
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HLA-A MUTATED       4                         0     9
  HLA-A WILD-TYPE    72                         4   159
D23V12, multiclass
                           clus
vv                          HLA-A MUTATED HLA-A WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 9             159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = FBXW7 MUTATION ANALYSIS
D24V1, survival
                 sevent
clus2               0   1
  FBXW7 MUTATED    19   3
  FBXW7 WILD-TYPE 162  77
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             22             239 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              3              77 
$`FBXW7 MUTATED`
TCGA-BR-4201 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-8360 TCGA-BR-8361 
       30.90        32.94        23.93        12.43         6.18        19.50 
TCGA-BR-8372 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-A4QL 
       19.17         9.21         1.12        11.54        15.81        11.57 
TCGA-CD-8536 TCGA-CD-A4MJ TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 
        0.10        12.62         6.02       105.07        65.10        21.07 
TCGA-D7-A4YV TCGA-F1-A448 TCGA-HU-8602 TCGA-HU-A4GN 
        5.92        21.27        11.41        29.98 

$`FBXW7 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       15.42        28.01        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8364 
       16.31         2.20        15.58         7.40         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        6.28         7.53         0.49        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
        0.16         0.10         0.10         0.13         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
        0.99        12.03        28.96        79.07         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       26.47         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        11.77         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
            0.1             0.0 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         105.07           79.07 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         14.215          12.590 
[1] "0.1 - 105.1 (14.2)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "3.6"
D24V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FBXW7 MUTATED         0        0        4        3         4         3
  FBXW7 WILD-TYPE       1        9       23       23        27        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXW7 MUTATED           0          1          2          4        2
  FBXW7 WILD-TYPE         3         48         34         20       22
D24V3, multiclass
            clus
vv           FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               4              23
  STAGE II               3              23
  STAGE IIA              4              27
  STAGE IIB              3              41
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             2              34
  STAGE IIIC             4              20
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FBXW7 MUTATED     0  10   7   8
  FBXW7 WILD-TYPE  11  62 115  67
D24V4, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  T1             0              11
  T2            10              62
  T3             7             115
  T4             8              67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  FBXW7 MUTATED   10  7  3  5
  FBXW7 WILD-TYPE 83 74 47 48
D24V5, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  N0            10              83
  N1             7              74
  N2             3              47
  N3             5              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                 cls
clus                0   1
  FBXW7 MUTATED    26   1
  FBXW7 WILD-TYPE 231  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     26    1
  FBXW7 WILD-TYPE  231   17
   clus
vv  FBXW7 MUTATED FBXW7 WILD-TYPE
  0            26             231
  1             1              17
[1] 2 2
[1] FALSE
D24V7, binary
                 cls
clus                0   1
  FBXW7 MUTATED    13  14
  FBXW7 WILD-TYPE  97 165
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     13   14
  FBXW7 WILD-TYPE   97  165
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE            13              97
  MALE              14             165
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FBXW7 MUTATED                                       1
  FBXW7 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FBXW7 MUTATED                                                       16
  FBXW7 WILD-TYPE                                                    119
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FBXW7 MUTATED                                                                   5
  FBXW7 WILD-TYPE                                                                35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FBXW7 MUTATED                                                  3
  FBXW7 WILD-TYPE                                               35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FBXW7 MUTATED                                                          2
  FBXW7 WILD-TYPE                                                       14
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FBXW7 MUTATED                                                           0
  FBXW7 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FBXW7 MUTATED                                          0
  FBXW7 WILD-TYPE                                        3
D24V8, multiclass
                                                                   clus
vv                                                                  FBXW7 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  FBXW7 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        119
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V9, binary
                 cls
clus                0   1
  FBXW7 MUTATED     1  26
  FBXW7 WILD-TYPE   4 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      1   26
  FBXW7 WILD-TYPE    4  258
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  NO              1               4
  YES            26             258
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FBXW7 MUTATED    21   1   0   4
  FBXW7 WILD-TYPE 206   9  10  20
D24V10, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  R0            21             206
  R1             1               9
  R2             0              10
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FBXW7 MUTATED       5                         0    17
  FBXW7 WILD-TYPE    71                         4   151
D24V12, multiclass
                           clus
vv                          FBXW7 MUTATED FBXW7 WILD-TYPE
  ASIAN                                 5              71
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                17             151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = MVK MUTATION ANALYSIS
D25V1, survival
               sevent
clus2             0   1
  MVK MUTATED     7   4
  MVK WILD-TYPE 174  76
  MVK MUTATED MVK WILD-TYPE 
           11           250 
  MVK MUTATED MVK WILD-TYPE 
            4            76 
$`MVK MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-7707 TCGA-BR-8361 TCGA-BR-8589 TCGA-CD-A4MG 
        6.97         6.61        23.93        19.50        15.81         6.58 
TCGA-CD-A4MI TCGA-CG-5733 TCGA-HU-A4G8 TCGA-HU-A4GU TCGA-HU-A4H3 
        0.10        21.07        11.84         6.25        19.36 

$`MVK WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10         4.01        69.04         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  MVK MUTATED MVK WILD-TYPE 
          0.1           0.0 
  MVK MUTATED MVK WILD-TYPE 
        23.93        105.07 
  MVK MUTATED MVK WILD-TYPE 
        11.84         12.64 
[1] "0.1 - 23.9 (11.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D25V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MVK MUTATED         0        0        2        0         1         2
  MVK WILD-TYPE       1        9       25       26        30        42
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MVK MUTATED           1          2          2          2        0
  MVK WILD-TYPE         2         47         34         22       24
D25V3, multiclass
            clus
vv           MVK MUTATED MVK WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             9
  STAGE IB             2            25
  STAGE II             0            26
  STAGE IIA            1            30
  STAGE IIB            2            42
  STAGE III            1             2
  STAGE IIIA           2            47
  STAGE IIIB           2            34
  STAGE IIIC           2            22
  STAGE IV             0            24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MVK MUTATED     1   4   5   3
  MVK WILD-TYPE  10  68 117  72
D25V4, multiclass
    clus
vv   MVK MUTATED MVK WILD-TYPE
  T1           1            10
  T2           4            68
  T3           5           117
  T4           3            72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  MVK MUTATED    3  6  2  1
  MVK WILD-TYPE 90 75 48 52
D25V5, multiclass
    clus
vv   MVK MUTATED MVK WILD-TYPE
  N0           3            90
  N1           6            75
  N2           2            48
  N3           1            52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
               cls
clus              0   1
  MVK MUTATED    12   0
  MVK WILD-TYPE 245  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED     12    0
  MVK WILD-TYPE  245   18
   clus
vv  MVK MUTATED MVK WILD-TYPE
  0          12           245
  1           0            18
[1] 2 2
[1] FALSE
D25V7, binary
               cls
clus              0   1
  MVK MUTATED     7   6
  MVK WILD-TYPE 103 173
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED      7    6
  MVK WILD-TYPE  103  173
        clus
vv       MVK MUTATED MVK WILD-TYPE
  FEMALE           7           103
  MALE             6           173
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MVK MUTATED                                       4
  MVK WILD-TYPE                                    46
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MVK MUTATED                                                        7
  MVK WILD-TYPE                                                    128
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MVK MUTATED                                                                   2
  MVK WILD-TYPE                                                                38
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MVK MUTATED                                                  0
  MVK WILD-TYPE                                               38
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MVK MUTATED                                                          0
  MVK WILD-TYPE                                                       16
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MVK MUTATED                                                           0
  MVK WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MVK MUTATED                                          0
  MVK WILD-TYPE                                        3
D25V8, multiclass
                                                                   clus
vv                                                                  MVK MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  MVK WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V9, binary
               cls
clus              0   1
  MVK MUTATED     0  13
  MVK WILD-TYPE   5 271
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED      0   13
  MVK WILD-TYPE    5  271
     clus
vv    MVK MUTATED MVK WILD-TYPE
  NO            0             5
  YES          13           271
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  MVK MUTATED     7   0   0   3
  MVK WILD-TYPE 220  10  10  21
D25V10, multiclass
    clus
vv   MVK MUTATED MVK WILD-TYPE
  R0           7           220
  R1           0            10
  R2           0            10
  RX           3            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MVK MUTATED       5                         0     6
  MVK WILD-TYPE    71                         4   162
D25V12, multiclass
                           clus
vv                          MVK MUTATED MVK WILD-TYPE
  ASIAN                               5            71
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                               6           162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = FRMD4A MUTATION ANALYSIS
D26V1, survival
                  sevent
clus2                0   1
  FRMD4A MUTATED    12   3
  FRMD4A WILD-TYPE 169  77
  FRMD4A MUTATED FRMD4A WILD-TYPE 
              15              246 
  FRMD4A MUTATED FRMD4A WILD-TYPE 
               3               77 
$`FRMD4A MUTATED`
TCGA-B7-5816 TCGA-BR-7707 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 
       26.70        23.93        19.50         1.12        13.45        15.81 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-6822 TCGA-D7-A4YY TCGA-F1-6874 
        6.58         6.02        28.96        12.33        13.78        14.47 
TCGA-FP-A4BE TCGA-HU-A4GQ TCGA-HU-A4H8 
       11.08         0.10         8.88 

$`FRMD4A WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79        15.81         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 
        0.99         0.99       105.07        12.03        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        10.55        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       16.44         5.92        15.16        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       16.24        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  FRMD4A MUTATED FRMD4A WILD-TYPE 
             0.1              0.0 
  FRMD4A MUTATED FRMD4A WILD-TYPE 
           28.96           105.07 
  FRMD4A MUTATED FRMD4A WILD-TYPE 
          13.450           12.605 
[1] "0.1 - 29.0 (13.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.5"
D26V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FRMD4A MUTATED         0        1        4        1         3         1
  FRMD4A WILD-TYPE       1        8       23       25        28        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FRMD4A MUTATED           0          0          1          3        2
  FRMD4A WILD-TYPE         3         49         35         21       22
D26V3, multiclass
            clus
vv           FRMD4A MUTATED FRMD4A WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                4               23
  STAGE II                1               25
  STAGE IIA               3               28
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              1               35
  STAGE IIIC              3               21
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FRMD4A MUTATED     2   4   4   6
  FRMD4A WILD-TYPE   9  68 118  69
D26V4, multiclass
    clus
vv   FRMD4A MUTATED FRMD4A WILD-TYPE
  T1              2                9
  T2              4               68
  T3              4              118
  T4              6               69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  FRMD4A MUTATED    8  5  3  2
  FRMD4A WILD-TYPE 85 76 47 51
D26V5, multiclass
    clus
vv   FRMD4A MUTATED FRMD4A WILD-TYPE
  N0              8               85
  N1              5               76
  N2              3               47
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                  cls
clus                 0   1
  FRMD4A MUTATED    17   1
  FRMD4A WILD-TYPE 240  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMD4A MUTATED     17    1
  FRMD4A WILD-TYPE  240   17
   clus
vv  FRMD4A MUTATED FRMD4A WILD-TYPE
  0             17              240
  1              1               17
[1] 2 2
[1] FALSE
D26V7, binary
                  cls
clus                 0   1
  FRMD4A MUTATED     5  13
  FRMD4A WILD-TYPE 105 166
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMD4A MUTATED      5   13
  FRMD4A WILD-TYPE  105  166
        clus
vv       FRMD4A MUTATED FRMD4A WILD-TYPE
  FEMALE              5              105
  MALE               13              166
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FRMD4A MUTATED                                       2
  FRMD4A WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FRMD4A MUTATED                                                        8
  FRMD4A WILD-TYPE                                                    127
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FRMD4A MUTATED                                                                   3
  FRMD4A WILD-TYPE                                                                37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FRMD4A MUTATED                                                  4
  FRMD4A WILD-TYPE                                               34
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FRMD4A MUTATED                                                          1
  FRMD4A WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FRMD4A MUTATED                                                           0
  FRMD4A WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FRMD4A MUTATED                                          0
  FRMD4A WILD-TYPE                                        3
D26V8, multiclass
                                                                   clus
vv                                                                  FRMD4A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  FRMD4A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V9, binary
                  cls
clus                 0   1
  FRMD4A MUTATED     1  17
  FRMD4A WILD-TYPE   4 267
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMD4A MUTATED      1   17
  FRMD4A WILD-TYPE    4  267
     clus
vv    FRMD4A MUTATED FRMD4A WILD-TYPE
  NO               1                4
  YES             17              267
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FRMD4A MUTATED    15   0   0   2
  FRMD4A WILD-TYPE 212  10  10  22
D26V10, multiclass
    clus
vv   FRMD4A MUTATED FRMD4A WILD-TYPE
  R0             15              212
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FRMD4A MUTATED       4                         1    10
  FRMD4A WILD-TYPE    72                         3   158
D26V12, multiclass
                           clus
vv                          FRMD4A MUTATED FRMD4A WILD-TYPE
  ASIAN                                  4               72
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                 10              158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = MBD6 MUTATION ANALYSIS
D27V1, survival
                sevent
clus2              0   1
  MBD6 MUTATED    14   4
  MBD6 WILD-TYPE 167  76
  MBD6 MUTATED MBD6 WILD-TYPE 
            18            243 
  MBD6 MUTATED MBD6 WILD-TYPE 
             4             76 
$`MBD6 MUTATED`
TCGA-BR-4201 TCGA-BR-6801 TCGA-BR-8360 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-A4QL 
       30.90        21.11         6.18         1.12        13.45        11.57 
TCGA-CD-A4MG TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-6524 TCGA-D7-A4YV TCGA-F1-6874 
        6.58       105.07        65.10        17.85         5.92        14.47 
TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-A4GU TCGA-HU-A4H3 
       11.08        26.47        14.17        11.41         6.25        19.36 

$`MBD6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79        15.81         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         6.02         0.99        12.03        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       16.44        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       16.24        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.52         5.92        12.59        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.51        10.19         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  MBD6 MUTATED MBD6 WILD-TYPE 
          1.12           0.00 
  MBD6 MUTATED MBD6 WILD-TYPE 
        105.07          79.07 
  MBD6 MUTATED MBD6 WILD-TYPE 
         13.81          12.59 
[1] "1.1 - 105.1 (13.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "2"  
D27V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MBD6 MUTATED         0        0        4        2         5         3
  MBD6 WILD-TYPE       1        9       23       24        26        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MBD6 MUTATED           0          2          1          2        0
  MBD6 WILD-TYPE         3         47         35         22       24
D27V3, multiclass
            clus
vv           MBD6 MUTATED MBD6 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              4             23
  STAGE II              2             24
  STAGE IIA             5             26
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            1             35
  STAGE IIIC            2             22
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MBD6 MUTATED     1   7   9   4
  MBD6 WILD-TYPE  10  65 113  71
D27V4, multiclass
    clus
vv   MBD6 MUTATED MBD6 WILD-TYPE
  T1            1             10
  T2            7             65
  T3            9            113
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  MBD6 MUTATED   11  5  1  3
  MBD6 WILD-TYPE 82 76 49 50
D27V5, multiclass
    clus
vv   MBD6 MUTATED MBD6 WILD-TYPE
  N0           11             82
  N1            5             76
  N2            1             49
  N3            3             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                cls
clus               0   1
  MBD6 MUTATED    22   0
  MBD6 WILD-TYPE 235  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED     22    0
  MBD6 WILD-TYPE  235   18
   clus
vv  MBD6 MUTATED MBD6 WILD-TYPE
  0           22            235
  1            0             18
[1] 2 2
[1] FALSE
D27V7, binary
                cls
clus               0   1
  MBD6 MUTATED    12  11
  MBD6 WILD-TYPE  98 168
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED     12   11
  MBD6 WILD-TYPE   98  168
        clus
vv       MBD6 MUTATED MBD6 WILD-TYPE
  FEMALE           12             98
  MALE             11            168
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MBD6 MUTATED                                       5
  MBD6 WILD-TYPE                                    45
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MBD6 MUTATED                                                       11
  MBD6 WILD-TYPE                                                    124
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MBD6 MUTATED                                                                   4
  MBD6 WILD-TYPE                                                                36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MBD6 MUTATED                                                  2
  MBD6 WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MBD6 MUTATED                                                          0
  MBD6 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MBD6 MUTATED                                                           0
  MBD6 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MBD6 MUTATED                                          1
  MBD6 WILD-TYPE                                        2
D27V8, multiclass
                                                                   clus
vv                                                                  MBD6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  MBD6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V9, binary
                cls
clus               0   1
  MBD6 MUTATED     0  23
  MBD6 WILD-TYPE   5 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED      0   23
  MBD6 WILD-TYPE    5  261
     clus
vv    MBD6 MUTATED MBD6 WILD-TYPE
  NO             0              5
  YES           23            261
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MBD6 MUTATED    16   1   0   5
  MBD6 WILD-TYPE 211   9  10  19
D27V10, multiclass
    clus
vv   MBD6 MUTATED MBD6 WILD-TYPE
  R0           16            211
  R1            1              9
  R2            0             10
  RX            5             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MBD6 MUTATED       5                         1    14
  MBD6 WILD-TYPE    71                         3   154
D27V12, multiclass
                           clus
vv                          MBD6 MUTATED MBD6 WILD-TYPE
  ASIAN                                5             71
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                               14            154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = ZBTB7C MUTATION ANALYSIS
D28V1, survival
                  sevent
clus2                0   1
  ZBTB7C MUTATED    10   3
  ZBTB7C WILD-TYPE 171  77
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
              13              248 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
               3               77 
$`ZBTB7C MUTATED`
TCGA-BR-6452 TCGA-BR-7851 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8368 TCGA-BR-8487 
       34.68        12.43        12.26         6.18         4.31         1.12 
TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4449 TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-A4YV 
       11.57         6.58        19.07        28.96        65.10         5.92 
TCGA-HU-A4G8 
       11.84 

$`ZBTB7C WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        2.66        16.31         2.20        15.58         7.40        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
        0.99       105.07        12.03        79.07         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
            1.12             0.00 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
           65.10           105.07 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
          11.840           12.775 
[1] "1.1 - 65.1 (11.8)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.5"
D28V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZBTB7C MUTATED         1        1        2        1         4         4
  ZBTB7C WILD-TYPE       0        8       25       25        27        40
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB7C MUTATED           0          0          1          0        0
  ZBTB7C WILD-TYPE         3         49         35         24       24
D28V3, multiclass
            clus
vv           ZBTB7C MUTATED ZBTB7C WILD-TYPE
  STAGE I                 1                0
  STAGE IA                1                8
  STAGE IB                2               25
  STAGE II                1               25
  STAGE IIA               4               27
  STAGE IIB               4               40
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              1               35
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZBTB7C MUTATED     3   3   7   2
  ZBTB7C WILD-TYPE   8  69 115  73
D28V4, multiclass
    clus
vv   ZBTB7C MUTATED ZBTB7C WILD-TYPE
  T1              3                8
  T2              3               69
  T3              7              115
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZBTB7C MUTATED    9  4  0  1
  ZBTB7C WILD-TYPE 84 77 50 52
D28V5, multiclass
    clus
vv   ZBTB7C MUTATED ZBTB7C WILD-TYPE
  N0              9               84
  N1              4               77
  N2              0               50
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                  cls
clus                 0   1
  ZBTB7C MUTATED    14   0
  ZBTB7C WILD-TYPE 243  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7C MUTATED     14    0
  ZBTB7C WILD-TYPE  243   18
   clus
vv  ZBTB7C MUTATED ZBTB7C WILD-TYPE
  0             14              243
  1              0               18
[1] 2 2
[1] FALSE
D28V7, binary
                  cls
clus                 0   1
  ZBTB7C MUTATED     9   6
  ZBTB7C WILD-TYPE 101 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7C MUTATED      9    6
  ZBTB7C WILD-TYPE  101  173
        clus
vv       ZBTB7C MUTATED ZBTB7C WILD-TYPE
  FEMALE              9              101
  MALE                6              173
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZBTB7C MUTATED                                       2
  ZBTB7C WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZBTB7C MUTATED                                                        7
  ZBTB7C WILD-TYPE                                                    128
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZBTB7C MUTATED                                                                   4
  ZBTB7C WILD-TYPE                                                                36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZBTB7C MUTATED                                                  1
  ZBTB7C WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZBTB7C MUTATED                                                          1
  ZBTB7C WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZBTB7C MUTATED                                                           0
  ZBTB7C WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZBTB7C MUTATED                                          0
  ZBTB7C WILD-TYPE                                        3
D28V8, multiclass
                                                                   clus
vv                                                                  ZBTB7C MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ZBTB7C WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V9, binary
                  cls
clus                 0   1
  ZBTB7C MUTATED     0  15
  ZBTB7C WILD-TYPE   5 269
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7C MUTATED      0   15
  ZBTB7C WILD-TYPE    5  269
     clus
vv    ZBTB7C MUTATED ZBTB7C WILD-TYPE
  NO               0                5
  YES             15              269
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZBTB7C MUTATED    12   0   0   1
  ZBTB7C WILD-TYPE 215  10  10  23
D28V10, multiclass
    clus
vv   ZBTB7C MUTATED ZBTB7C WILD-TYPE
  R0             12              215
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZBTB7C MUTATED       2                         1     9
  ZBTB7C WILD-TYPE    74                         3   159
D28V12, multiclass
                           clus
vv                          ZBTB7C MUTATED ZBTB7C WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  9              159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = JARID2 MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2                0   1
  JARID2 MUTATED    19   4
  JARID2 WILD-TYPE 162  76
  JARID2 MUTATED JARID2 WILD-TYPE 
              23              238 
  JARID2 MUTATED JARID2 WILD-TYPE 
               4               76 
$`JARID2 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8487 
       34.68        32.94        14.43        12.26         4.31         1.12 
TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4306 
       13.45        15.81         0.10         6.58        12.62         1.02 
TCGA-CG-4455 TCGA-CG-5723 TCGA-D7-5578 TCGA-F1-6874 TCGA-HU-8602 TCGA-HU-A4G8 
       12.03       105.07        12.66        14.47        11.41        11.84 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-HU-A4H8 
       29.98         0.10         6.51        19.36         8.88 

$`JARID2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       15.81         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       11.61        12.20         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        47.05        19.07         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         6.02         0.99        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        0.62         7.99        16.24        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       11.77         8.98         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
       12.95        23.84        12.30         9.67        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  JARID2 MUTATED JARID2 WILD-TYPE 
             0.1              0.0 
  JARID2 MUTATED JARID2 WILD-TYPE 
          105.07            79.07 
  JARID2 MUTATED JARID2 WILD-TYPE 
          12.260           12.775 
[1] "0.1 - 105.1 (12.3)" "0.0 - 79.1 (12.8)" 
[1] "hr=" "2.1"
D29V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  JARID2 MUTATED         0        0        5        3         6         3
  JARID2 WILD-TYPE       1        9       22       23        25        41
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  JARID2 MUTATED           1          2          0          3        2
  JARID2 WILD-TYPE         2         47         36         21       22
D29V3, multiclass
            clus
vv           JARID2 MUTATED JARID2 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                5               22
  STAGE II                3               23
  STAGE IIA               6               25
  STAGE IIB               3               41
  STAGE III               1                2
  STAGE IIIA              2               47
  STAGE IIIB              0               36
  STAGE IIIC              3               21
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  JARID2 MUTATED     2   7  10   8
  JARID2 WILD-TYPE   9  65 112  67
D29V4, multiclass
    clus
vv   JARID2 MUTATED JARID2 WILD-TYPE
  T1              2                9
  T2              7               65
  T3             10              112
  T4              8               67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  JARID2 MUTATED   13  6  4  2
  JARID2 WILD-TYPE 80 75 46 51
D29V5, multiclass
    clus
vv   JARID2 MUTATED JARID2 WILD-TYPE
  N0             13               80
  N1              6               75
  N2              4               46
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                  cls
clus                 0   1
  JARID2 MUTATED    25   2
  JARID2 WILD-TYPE 232  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JARID2 MUTATED     25    2
  JARID2 WILD-TYPE  232   16
   clus
vv  JARID2 MUTATED JARID2 WILD-TYPE
  0             25              232
  1              2               16
[1] 2 2
[1] FALSE
D29V7, binary
                  cls
clus                 0   1
  JARID2 MUTATED    13  15
  JARID2 WILD-TYPE  97 164
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JARID2 MUTATED     13   15
  JARID2 WILD-TYPE   97  164
        clus
vv       JARID2 MUTATED JARID2 WILD-TYPE
  FEMALE             13               97
  MALE               15              164
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  JARID2 MUTATED                                       4
  JARID2 WILD-TYPE                                    46
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  JARID2 MUTATED                                                       14
  JARID2 WILD-TYPE                                                    121
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  JARID2 MUTATED                                                                   3
  JARID2 WILD-TYPE                                                                37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  JARID2 MUTATED                                                  6
  JARID2 WILD-TYPE                                               32
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  JARID2 MUTATED                                                          1
  JARID2 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  JARID2 MUTATED                                                           0
  JARID2 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  JARID2 MUTATED                                          0
  JARID2 WILD-TYPE                                        3
D29V8, multiclass
                                                                   clus
vv                                                                  JARID2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        14
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  JARID2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         121
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V9, binary
                  cls
clus                 0   1
  JARID2 MUTATED     0  28
  JARID2 WILD-TYPE   5 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JARID2 MUTATED      0   28
  JARID2 WILD-TYPE    5  256
     clus
vv    JARID2 MUTATED JARID2 WILD-TYPE
  NO               0                5
  YES             28              256
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  JARID2 MUTATED    20   0   1   4
  JARID2 WILD-TYPE 207  10   9  20
D29V10, multiclass
    clus
vv   JARID2 MUTATED JARID2 WILD-TYPE
  R0             20              207
  R1              0               10
  R2              1                9
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  JARID2 MUTATED      11                         0    13
  JARID2 WILD-TYPE    65                         4   155
D29V12, multiclass
                           clus
vv                          JARID2 MUTATED JARID2 WILD-TYPE
  ASIAN                                 11               65
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                 13              155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = PAX6 MUTATION ANALYSIS
D30V1, survival
                sevent
clus2              0   1
  PAX6 MUTATED    13   2
  PAX6 WILD-TYPE 168  78
  PAX6 MUTATED PAX6 WILD-TYPE 
            15            246 
  PAX6 MUTATED PAX6 WILD-TYPE 
             2             78 
$`PAX6 MUTATED`
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-A4CQ 
       24.76        23.93        12.26        19.50        19.17        22.26 
TCGA-CD-8529 TCGA-CG-5721 TCGA-CG-5733 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7916 
        0.13         6.02        21.07        14.47        21.27        14.07 
TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-HU-A4GU 
       11.84         6.51         6.25 

$`PAX6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
        9.21        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
        0.07         0.07         0.07         0.07         0.10         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        0.62         7.99        16.24        72.23         3.48        19.53 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         0.10        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  PAX6 MUTATED PAX6 WILD-TYPE 
          0.13           0.00 
  PAX6 MUTATED PAX6 WILD-TYPE 
         24.76         105.07 
  PAX6 MUTATED PAX6 WILD-TYPE 
        14.470         12.575 
[1] "0.1 - 24.8 (14.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.5"
D30V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PAX6 MUTATED         0        1        3        0         1         3
  PAX6 WILD-TYPE       1        8       24       26        30        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PAX6 MUTATED           0          2          1          3        2
  PAX6 WILD-TYPE         3         47         35         21       22
D30V3, multiclass
            clus
vv           PAX6 MUTATED PAX6 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              3             24
  STAGE II              0             26
  STAGE IIA             1             30
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            1             35
  STAGE IIIC            3             21
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PAX6 MUTATED     1   4   5   7
  PAX6 WILD-TYPE  10  68 117  68
D30V4, multiclass
    clus
vv   PAX6 MUTATED PAX6 WILD-TYPE
  T1            1             10
  T2            4             68
  T3            5            117
  T4            7             68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  PAX6 MUTATED    7  4  2  3
  PAX6 WILD-TYPE 86 77 48 50
D30V5, multiclass
    clus
vv   PAX6 MUTATED PAX6 WILD-TYPE
  N0            7             86
  N1            4             77
  N2            2             48
  N3            3             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                cls
clus               0   1
  PAX6 MUTATED    15   1
  PAX6 WILD-TYPE 242  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX6 MUTATED     15    1
  PAX6 WILD-TYPE  242   17
   clus
vv  PAX6 MUTATED PAX6 WILD-TYPE
  0           15            242
  1            1             17
[1] 2 2
[1] FALSE
D30V7, binary
                cls
clus               0   1
  PAX6 MUTATED     8  10
  PAX6 WILD-TYPE 102 169
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX6 MUTATED      8   10
  PAX6 WILD-TYPE  102  169
        clus
vv       PAX6 MUTATED PAX6 WILD-TYPE
  FEMALE            8            102
  MALE             10            169
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PAX6 MUTATED                                       3
  PAX6 WILD-TYPE                                    47
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PAX6 MUTATED                                                        7
  PAX6 WILD-TYPE                                                    128
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PAX6 MUTATED                                                                   4
  PAX6 WILD-TYPE                                                                36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PAX6 MUTATED                                                  1
  PAX6 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PAX6 MUTATED                                                          2
  PAX6 WILD-TYPE                                                       14
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PAX6 MUTATED                                                           1
  PAX6 WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PAX6 MUTATED                                          0
  PAX6 WILD-TYPE                                        3
D30V8, multiclass
                                                                   clus
vv                                                                  PAX6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  PAX6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V9, binary
                cls
clus               0   1
  PAX6 MUTATED     0  18
  PAX6 WILD-TYPE   5 266
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX6 MUTATED      0   18
  PAX6 WILD-TYPE    5  266
     clus
vv    PAX6 MUTATED PAX6 WILD-TYPE
  NO             0              5
  YES           18            266
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PAX6 MUTATED    14   0   0   2
  PAX6 WILD-TYPE 213  10  10  22
D30V10, multiclass
    clus
vv   PAX6 MUTATED PAX6 WILD-TYPE
  R0           14            213
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PAX6 MUTATED       5                         0    10
  PAX6 WILD-TYPE    71                         4   158
D30V12, multiclass
                           clus
vv                          PAX6 MUTATED PAX6 WILD-TYPE
  ASIAN                                5             71
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               10            158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = PIK3CA MUTATION ANALYSIS
D31V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED    38  11
  PIK3CA WILD-TYPE 143  69
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              49              212 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              11               69 
$`PIK3CA MUTATED`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6706 TCGA-BR-6707 
       26.70        11.70        34.68        13.87        18.05        19.89 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7851 TCGA-BR-8081 TCGA-BR-8284 
       30.90        32.94        12.82        12.43        20.55         8.05 
TCGA-BR-8360 TCGA-BR-8366 TCGA-BR-8381 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        6.18         0.95         0.26         1.12        12.79        15.81 
TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A4IV TCGA-CD-5801 
       13.45         7.53        15.81        15.68        13.51        13.18 
TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-4305 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        0.10         0.10        15.95         0.99         6.02         0.99 
TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6815 TCGA-D7-A4YV 
       65.10        21.07        12.36        12.66        15.98         5.92 
TCGA-D7-A4YX TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-HU-8602 TCGA-HU-8608 
       15.16         3.48        14.07        22.29        11.41        10.62 
TCGA-HU-A4G2 TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H3 
       24.30         0.10         6.25        10.19         2.10        19.36 
TCGA-HU-A4H4 
       23.84 

$`PIK3CA WILD-TYPE`
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57         6.61        15.95        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
        8.98        21.11        31.20         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       15.42        28.01        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       12.26         9.60        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40        19.50         0.26        22.19        17.52 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       20.22         9.34         6.28         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        9.86         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08        22.26         1.48        13.41        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        2.83         3.25        13.15         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
        0.16         0.10         0.10         0.13         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5723 TCGA-CG-5724 
       30.97         6.97        36.00         1.02       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5579 
       28.96        79.07         4.01        69.04         7.99        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       13.35        17.19        10.26        15.22        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       72.23        21.27        19.53        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.59        14.17        12.10         0.76         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H5 
       29.98         8.98         6.51         0.26        12.95        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
             0.1              0.0 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           65.10           105.07 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          12.820           12.495 
[1] "0.1 - 65.1 (12.8)"  "0.0 - 105.1 (12.5)"
[1] "hr=" "1.4"
D31V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIK3CA MUTATED         1        0        5        3         7        13
  PIK3CA WILD-TYPE       0        9       22       23        24        31
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3CA MUTATED           0          8          6          8        5
  PIK3CA WILD-TYPE         3         41         30         16       19
D31V3, multiclass
            clus
vv           PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                 1                0
  STAGE IA                0                9
  STAGE IB                5               22
  STAGE II                3               23
  STAGE IIA               7               24
  STAGE IIB              13               31
  STAGE III               0                3
  STAGE IIIA              8               41
  STAGE IIIB              6               30
  STAGE IIIC              8               16
  STAGE IV                5               19
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  PIK3CA MUTATED    1 12 23 21
  PIK3CA WILD-TYPE 10 60 99 54
D31V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              1               10
  T2             12               60
  T3             23               99
  T4             21               54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  PIK3CA MUTATED   19 16 12  9
  PIK3CA WILD-TYPE 74 65 38 44
D31V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0             19               74
  N1             16               65
  N2             12               38
  N3              9               44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    49   4
  PIK3CA WILD-TYPE 208  14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     49    4
  PIK3CA WILD-TYPE  208   14
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0             49              208
  1              4               14
[1] 2 2
[1] FALSE
D31V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    22  35
  PIK3CA WILD-TYPE  88 144
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     22   35
  PIK3CA WILD-TYPE   88  144
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             22               88
  MALE               35              144
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PIK3CA MUTATED                                      13
  PIK3CA WILD-TYPE                                    37
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIK3CA MUTATED                                                       26
  PIK3CA WILD-TYPE                                                    109
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIK3CA MUTATED                                                                   9
  PIK3CA WILD-TYPE                                                                31
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PIK3CA MUTATED                                                  8
  PIK3CA WILD-TYPE                                               30
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PIK3CA MUTATED                                                          1
  PIK3CA WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PIK3CA MUTATED                                                           0
  PIK3CA WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PIK3CA MUTATED                                          0
  PIK3CA WILD-TYPE                                        3
D31V8, multiclass
                                                                   clus
vv                                                                  PIK3CA MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        26
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  PIK3CA WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           37
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         109
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                30
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V9, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     1  56
  PIK3CA WILD-TYPE   4 228
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1   56
  PIK3CA WILD-TYPE    4  228
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO               1                4
  YES             56              228
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PIK3CA MUTATED    50   0   2   3
  PIK3CA WILD-TYPE 177  10   8  21
D31V10, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0             50              177
  R1              0               10
  R2              2                8
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED      16                         2    30
  PIK3CA WILD-TYPE    60                         2   138
D31V12, multiclass
                           clus
vv                          PIK3CA MUTATED PIK3CA WILD-TYPE
  ASIAN                                 16               60
  BLACK OR AFRICAN AMERICAN              2                2
  WHITE                                 30              138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = APC MUTATION ANALYSIS
D32V1, survival
               sevent
clus2             0   1
  APC MUTATED    20  17
  APC WILD-TYPE 161  63
  APC MUTATED APC WILD-TYPE 
           37           224 
  APC MUTATED APC WILD-TYPE 
           17            63 
$`APC MUTATED`
TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6563 TCGA-BR-6565 
        6.97        18.35         6.18        34.68        39.12         9.17 
TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-8081 TCGA-BR-8363 
       32.78        30.90         9.21        24.76        20.55         0.26 
TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A452 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A4MG 
        1.12        15.81         7.53         0.13         0.10         6.58 
TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-5718 TCGA-CG-5721 
       12.62         1.02         9.01         7.07        36.00         6.02 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5733 TCGA-D7-6528 TCGA-D7-A4YV TCGA-F1-6875 
      105.07        28.96        21.07        15.22         5.92        72.23 
TCGA-FP-7735 TCGA-FP-8211 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-A4GU 
        3.48        13.58         5.92        12.59        12.10         6.25 
TCGA-HU-A4H3 
       19.36 

$`APC WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
       26.70        11.70         6.61         4.64         7.43        30.90 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       19.33        26.10        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-7715 
       21.11        31.20        32.94        12.82        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       12.26         9.60         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
        2.20        15.58         7.40         6.18        19.50        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
        0.10        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 
       19.07        12.03         0.00        18.97        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 
        6.97         1.02         0.99         0.99        12.03        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        10.26        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       16.44        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       16.24        14.47        21.27        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       17.06        59.54         5.03         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       26.47        14.17        11.41        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  APC MUTATED APC WILD-TYPE 
          0.1           0.0 
  APC MUTATED APC WILD-TYPE 
       105.07         79.07 
  APC MUTATED APC WILD-TYPE 
       12.100        12.775 
[1] "0.1 - 105.1 (12.1)" "0.0 - 79.1 (12.8)" 
[1] "hr=" "1.3"
D32V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  APC MUTATED         0        3        6        4         6         6
  APC WILD-TYPE       1        6       21       22        25        38
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  APC MUTATED           0          6          0          3        5
  APC WILD-TYPE         3         43         36         21       19
D32V3, multiclass
            clus
vv           APC MUTATED APC WILD-TYPE
  STAGE I              0             1
  STAGE IA             3             6
  STAGE IB             6            21
  STAGE II             4            22
  STAGE IIA            6            25
  STAGE IIB            6            38
  STAGE III            0             3
  STAGE IIIA           6            43
  STAGE IIIB           0            36
  STAGE IIIC           3            21
  STAGE IV             5            19
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  APC MUTATED     2  10  17  10
  APC WILD-TYPE   9  62 105  65
D32V4, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  T1           2             9
  T2          10            62
  T3          17           105
  T4          10            65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  APC MUTATED   20 12  4  5
  APC WILD-TYPE 73 69 46 48
D32V5, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  N0          20            73
  N1          12            69
  N2           4            46
  N3           5            48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
               cls
clus              0   1
  APC MUTATED    36   3
  APC WILD-TYPE 221  15
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     36    3
  APC WILD-TYPE  221   15
   clus
vv  APC MUTATED APC WILD-TYPE
  0          36           221
  1           3            15
[1] 2 2
[1] FALSE
D32V7, binary
               cls
clus              0   1
  APC MUTATED    14  28
  APC WILD-TYPE  96 151
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     14   28
  APC WILD-TYPE   96  151
        clus
vv       APC MUTATED APC WILD-TYPE
  FEMALE          14            96
  MALE            28           151
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  APC MUTATED                                       5
  APC WILD-TYPE                                    45
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  APC MUTATED                                                       23
  APC WILD-TYPE                                                    112
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  APC MUTATED                                                                   6
  APC WILD-TYPE                                                                34
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  APC MUTATED                                                  6
  APC WILD-TYPE                                               32
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  APC MUTATED                                                          0
  APC WILD-TYPE                                                       16
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  APC MUTATED                                                           2
  APC WILD-TYPE                                                         4
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  APC MUTATED                                          0
  APC WILD-TYPE                                        3
D32V8, multiclass
                                                                   clus
vv                                                                  APC MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                     23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  APC WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      112
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V9, binary
               cls
clus              0   1
  APC MUTATED     0  42
  APC WILD-TYPE   5 242
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED      0   42
  APC WILD-TYPE    5  242
     clus
vv    APC MUTATED APC WILD-TYPE
  NO            0             5
  YES          42           242
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  APC MUTATED    30   2   2   6
  APC WILD-TYPE 197   8   8  18
D32V10, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  R0          30           197
  R1           2             8
  R2           2             8
  RX           6            18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  APC MUTATED      11                         2    19
  APC WILD-TYPE    65                         2   149
D32V12, multiclass
                           clus
vv                          APC MUTATED APC WILD-TYPE
  ASIAN                              11            65
  BLACK OR AFRICAN AMERICAN           2             2
  WHITE                              19           149
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = NLK MUTATION ANALYSIS
D33V1, survival
               sevent
clus2             0   1
  NLK MUTATED     7   3
  NLK WILD-TYPE 174  77
  NLK MUTATED NLK WILD-TYPE 
           10           251 
  NLK MUTATED NLK WILD-TYPE 
            3            77 
$`NLK MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7715 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8368 
        6.97        34.68        15.42         6.18         0.26         4.31 
TCGA-BR-8372 TCGA-CD-A4MG TCGA-HU-A4G8 TCGA-HU-A4GN 
       19.17         6.58        11.84        29.98 

$`NLK WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       23.93        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        2.66        16.31         2.20        15.58         7.40        19.50 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        11.77         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  NLK MUTATED NLK WILD-TYPE 
         0.26          0.00 
  NLK MUTATED NLK WILD-TYPE 
        34.68        105.07 
  NLK MUTATED NLK WILD-TYPE 
        9.405        12.660 
[1] "0.3 - 34.7 (9.4)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1"  
D33V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NLK MUTATED         0        0        2        0         5         1
  NLK WILD-TYPE       1        9       25       26        26        43
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NLK MUTATED           0          2          0          1        0
  NLK WILD-TYPE         3         47         36         23       24
D33V3, multiclass
            clus
vv           NLK MUTATED NLK WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             9
  STAGE IB             2            25
  STAGE II             0            26
  STAGE IIA            5            26
  STAGE IIB            1            43
  STAGE III            0             3
  STAGE IIIA           2            47
  STAGE IIIB           0            36
  STAGE IIIC           1            23
  STAGE IV             0            24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NLK MUTATED     0   3   7   2
  NLK WILD-TYPE  11  69 115  73
D33V4, multiclass
    clus
vv   NLK MUTATED NLK WILD-TYPE
  T1           0            11
  T2           3            69
  T3           7           115
  T4           2            73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  NLK MUTATED    7  3  0  1
  NLK WILD-TYPE 86 78 50 52
D33V5, multiclass
    clus
vv   NLK MUTATED NLK WILD-TYPE
  N0           7            86
  N1           3            78
  N2           0            50
  N3           1            52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
               cls
clus              0   1
  NLK MUTATED    10   0
  NLK WILD-TYPE 247  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED     10    0
  NLK WILD-TYPE  247   18
   clus
vv  NLK MUTATED NLK WILD-TYPE
  0          10           247
  1           0            18
[1] 2 2
[1] FALSE
D33V7, binary
               cls
clus              0   1
  NLK MUTATED     6   6
  NLK WILD-TYPE 104 173
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED      6    6
  NLK WILD-TYPE  104  173
        clus
vv       NLK MUTATED NLK WILD-TYPE
  FEMALE           6           104
  MALE             6           173
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NLK MUTATED                                       2
  NLK WILD-TYPE                                    48
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NLK MUTATED                                                        8
  NLK WILD-TYPE                                                    127
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NLK MUTATED                                                                   1
  NLK WILD-TYPE                                                                39
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NLK MUTATED                                                  1
  NLK WILD-TYPE                                               37
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NLK MUTATED                                                          0
  NLK WILD-TYPE                                                       16
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NLK MUTATED                                                           0
  NLK WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NLK MUTATED                                          0
  NLK WILD-TYPE                                        3
D33V8, multiclass
                                                                   clus
vv                                                                  NLK MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  NLK WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V9, binary
               cls
clus              0   1
  NLK MUTATED     0  12
  NLK WILD-TYPE   5 272
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED      0   12
  NLK WILD-TYPE    5  272
     clus
vv    NLK MUTATED NLK WILD-TYPE
  NO            0             5
  YES          12           272
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  NLK MUTATED     7   0   0   3
  NLK WILD-TYPE 220  10  10  21
D33V10, multiclass
    clus
vv   NLK MUTATED NLK WILD-TYPE
  R0           7           220
  R1           0            10
  R2           0            10
  RX           3            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NLK MUTATED       3                         0     9
  NLK WILD-TYPE    73                         4   159
D33V12, multiclass
                           clus
vv                          NLK MUTATED NLK WILD-TYPE
  ASIAN                               3            73
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                               9           159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = POLM MUTATION ANALYSIS
D34V1, survival
                sevent
clus2              0   1
  POLM MUTATED     6   1
  POLM WILD-TYPE 175  79
  POLM MUTATED POLM WILD-TYPE 
             7            254 
  POLM MUTATED POLM WILD-TYPE 
             1             79 
$`POLM MUTATED`
TCGA-BR-6452 TCGA-BR-7851 TCGA-BR-8487 TCGA-CD-A4MJ TCGA-CG-5723 TCGA-F1-6875 
       34.68        12.43         1.12        12.62       105.07        72.23 
TCGA-HU-A4G9 
       24.20 

$`POLM WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       16.24        14.47        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        11.84         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  POLM MUTATED POLM WILD-TYPE 
          1.12           0.00 
  POLM MUTATED POLM WILD-TYPE 
        105.07          79.07 
  POLM MUTATED POLM WILD-TYPE 
        24.200         12.575 
[1] "1.1 - 105.1 (24.2)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "6.9"
D34V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  POLM MUTATED         1        2        2        1         2         1
  POLM WILD-TYPE       0        7       25       25        29        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  POLM MUTATED           0          0          0          0        0
  POLM WILD-TYPE         3         49         36         24       24
D34V3, multiclass
            clus
vv           POLM MUTATED POLM WILD-TYPE
  STAGE I               1              0
  STAGE IA              2              7
  STAGE IB              2             25
  STAGE II              1             25
  STAGE IIA             2             29
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  POLM MUTATED     2   4   2   1
  POLM WILD-TYPE   9  68 120  74
D34V4, multiclass
    clus
vv   POLM MUTATED POLM WILD-TYPE
  T1            2              9
  T2            4             68
  T3            2            120
  T4            1             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  POLM MUTATED    7  2  0  0
  POLM WILD-TYPE 86 79 50 53
D34V5, multiclass
    clus
vv   POLM MUTATED POLM WILD-TYPE
  N0            7             86
  N1            2             79
  N2            0             50
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                cls
clus               0   1
  POLM MUTATED     9   0
  POLM WILD-TYPE 248  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLM MUTATED      9    0
  POLM WILD-TYPE  248   18
   clus
vv  POLM MUTATED POLM WILD-TYPE
  0            9            248
  1            0             18
[1] 2 2
[1] FALSE
D34V7, binary
                cls
clus               0   1
  POLM MUTATED     4   6
  POLM WILD-TYPE 106 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLM MUTATED      4    6
  POLM WILD-TYPE  106  173
        clus
vv       POLM MUTATED POLM WILD-TYPE
  FEMALE            4            106
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  POLM MUTATED                                       0
  POLM WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  POLM MUTATED                                                        7
  POLM WILD-TYPE                                                    128
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  POLM MUTATED                                                                   2
  POLM WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  POLM MUTATED                                                  1
  POLM WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  POLM MUTATED                                                          0
  POLM WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  POLM MUTATED                                                           0
  POLM WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  POLM MUTATED                                          0
  POLM WILD-TYPE                                        3
D34V8, multiclass
                                                                   clus
vv                                                                  POLM MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  POLM WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V9, binary
                cls
clus               0   1
  POLM MUTATED     0  10
  POLM WILD-TYPE   5 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLM MUTATED      0   10
  POLM WILD-TYPE    5  274
     clus
vv    POLM MUTATED POLM WILD-TYPE
  NO             0              5
  YES           10            274
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  POLM MUTATED     8   0   0   1
  POLM WILD-TYPE 219  10  10  23
D34V10, multiclass
    clus
vv   POLM MUTATED POLM WILD-TYPE
  R0            8            219
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  POLM MUTATED       2                         2     4
  POLM WILD-TYPE    74                         2   164
D34V12, multiclass
                           clus
vv                          POLM MUTATED POLM WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            2              2
  WHITE                                4            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = TMEM41A MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                 0   1
  TMEM41A MUTATED     3   2
  TMEM41A WILD-TYPE 178  78
  TMEM41A MUTATED TMEM41A WILD-TYPE 
                5               256 
  TMEM41A MUTATED TMEM41A WILD-TYPE 
                2                78 
$`TMEM41A MUTATED`
TCGA-BR-8078 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-5726 
       12.26         1.12         6.58         0.10        28.96 

$`TMEM41A WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       12.43        11.61        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  TMEM41A MUTATED TMEM41A WILD-TYPE 
              0.1               0.0 
  TMEM41A MUTATED TMEM41A WILD-TYPE 
            28.96            105.07 
  TMEM41A MUTATED TMEM41A WILD-TYPE 
             6.58             12.71 
[1] "0.1 - 29.0 (6.6)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.7"
D35V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEM41A MUTATED         0        1        0        0         2         1
  TMEM41A WILD-TYPE       1        8       27       26        29        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM41A MUTATED           0          1          1          0        0
  TMEM41A WILD-TYPE         3         48         35         24       24
D35V3, multiclass
            clus
vv           TMEM41A MUTATED TMEM41A WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 1                 8
  STAGE IB                 0                27
  STAGE II                 0                26
  STAGE IIA                2                29
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               1                35
  STAGE IIIC               0                24
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM41A MUTATED     1   0   3   2
  TMEM41A WILD-TYPE  10  72 119  73
D35V4, multiclass
    clus
vv   TMEM41A MUTATED TMEM41A WILD-TYPE
  T1               1                10
  T2               0                72
  T3               3               119
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  TMEM41A MUTATED    5  1  0  0
  TMEM41A WILD-TYPE 88 80 50 53
D35V5, multiclass
    clus
vv   TMEM41A MUTATED TMEM41A WILD-TYPE
  N0               5                88
  N1               1                80
  N2               0                50
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                   cls
clus                  0   1
  TMEM41A MUTATED     6   0
  TMEM41A WILD-TYPE 251  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41A MUTATED      6    0
  TMEM41A WILD-TYPE  251   18
   clus
vv  TMEM41A MUTATED TMEM41A WILD-TYPE
  0               6               251
  1               0                18
[1] 2 2
[1] FALSE
D35V7, binary
                   cls
clus                  0   1
  TMEM41A MUTATED     3   3
  TMEM41A WILD-TYPE 107 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41A MUTATED      3    3
  TMEM41A WILD-TYPE  107  176
        clus
vv       TMEM41A MUTATED TMEM41A WILD-TYPE
  FEMALE               3               107
  MALE                 3               176
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TMEM41A MUTATED                                       1
  TMEM41A WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TMEM41A MUTATED                                                        4
  TMEM41A WILD-TYPE                                                    131
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TMEM41A MUTATED                                                                   1
  TMEM41A WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TMEM41A MUTATED                                                  0
  TMEM41A WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TMEM41A MUTATED                                                          0
  TMEM41A WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TMEM41A MUTATED                                                           0
  TMEM41A WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TMEM41A MUTATED                                          0
  TMEM41A WILD-TYPE                                        3
D35V8, multiclass
                                                                   clus
vv                                                                  TMEM41A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  TMEM41A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V9, binary
                   cls
clus                  0   1
  TMEM41A MUTATED     0   6
  TMEM41A WILD-TYPE   5 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41A MUTATED      0    6
  TMEM41A WILD-TYPE    5  278
     clus
vv    TMEM41A MUTATED TMEM41A WILD-TYPE
  NO                0                 5
  YES               6               278
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TMEM41A MUTATED     3   0   0   1
  TMEM41A WILD-TYPE 224  10  10  23
D35V10, multiclass
    clus
vv   TMEM41A MUTATED TMEM41A WILD-TYPE
  R0               3               224
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMEM41A MUTATED       2                         0     3
  TMEM41A WILD-TYPE    74                         4   165
D35V12, multiclass
                           clus
vv                          TMEM41A MUTATED TMEM41A WILD-TYPE
  ASIAN                                   2                74
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   3               165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = WBP1 MUTATION ANALYSIS
D36V1, survival
                sevent
clus2              0   1
  WBP1 MUTATED     5   2
  WBP1 WILD-TYPE 176  78
  WBP1 MUTATED WBP1 WILD-TYPE 
             7            254 
  WBP1 MUTATED WBP1 WILD-TYPE 
             2             78 
$`WBP1 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8286 TCGA-CD-A4MG TCGA-CG-5721 TCGA-HJ-7597 
       26.70        34.68        12.95         6.58         6.02        26.47 
TCGA-HU-A4GT 
        6.51 

$`WBP1 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56        11.08         5.52         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         0.10         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  WBP1 MUTATED WBP1 WILD-TYPE 
          6.02           0.00 
  WBP1 MUTATED WBP1 WILD-TYPE 
         34.68         105.07 
  WBP1 MUTATED WBP1 WILD-TYPE 
        12.950         12.605 
[1] "6.0 - 34.7 (12.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D36V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WBP1 MUTATED         1        0        1        1         3         1
  WBP1 WILD-TYPE       0        9       26       25        28        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WBP1 MUTATED           0          0          0          0        1
  WBP1 WILD-TYPE         3         49         36         24       23
D36V3, multiclass
            clus
vv           WBP1 MUTATED WBP1 WILD-TYPE
  STAGE I               1              0
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              1             25
  STAGE IIA             3             28
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WBP1 MUTATED     1   1   4   2
  WBP1 WILD-TYPE  10  71 118  73
D36V4, multiclass
    clus
vv   WBP1 MUTATED WBP1 WILD-TYPE
  T1            1             10
  T2            1             71
  T3            4            118
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  WBP1 MUTATED    6  2  0  0
  WBP1 WILD-TYPE 87 79 50 53
D36V5, multiclass
    clus
vv   WBP1 MUTATED WBP1 WILD-TYPE
  N0            6             87
  N1            2             79
  N2            0             50
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                cls
clus               0   1
  WBP1 MUTATED     6   0
  WBP1 WILD-TYPE 251  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  WBP1 MUTATED      6    0
  WBP1 WILD-TYPE  251   18
   clus
vv  WBP1 MUTATED WBP1 WILD-TYPE
  0            6            251
  1            0             18
[1] 2 2
[1] FALSE
D36V7, binary
                cls
clus               0   1
  WBP1 MUTATED     4   4
  WBP1 WILD-TYPE 106 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  WBP1 MUTATED      4    4
  WBP1 WILD-TYPE  106  175
        clus
vv       WBP1 MUTATED WBP1 WILD-TYPE
  FEMALE            4            106
  MALE              4            175
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  WBP1 MUTATED                                       2
  WBP1 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WBP1 MUTATED                                                        3
  WBP1 WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WBP1 MUTATED                                                                   1
  WBP1 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  WBP1 MUTATED                                                  1
  WBP1 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  WBP1 MUTATED                                                          0
  WBP1 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  WBP1 MUTATED                                                           0
  WBP1 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  WBP1 MUTATED                                          1
  WBP1 WILD-TYPE                                        2
D36V8, multiclass
                                                                   clus
vv                                                                  WBP1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  WBP1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V9, binary
                cls
clus               0   1
  WBP1 MUTATED     0   8
  WBP1 WILD-TYPE   5 276
[1] "tbl2"
                cls
clus             [,1] [,2]
  WBP1 MUTATED      0    8
  WBP1 WILD-TYPE    5  276
     clus
vv    WBP1 MUTATED WBP1 WILD-TYPE
  NO             0              5
  YES            8            276
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  WBP1 MUTATED     7   0   0   0
  WBP1 WILD-TYPE 220  10  10  24
D36V10, multiclass
    clus
vv   WBP1 MUTATED WBP1 WILD-TYPE
  R0            7            220
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WBP1 MUTATED       2                         1     4
  WBP1 WILD-TYPE    74                         3   164
D36V12, multiclass
                           clus
vv                          WBP1 MUTATED WBP1 WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                                4            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = KIAA0182 MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  KIAA0182 MUTATED    12   3
  KIAA0182 WILD-TYPE 169  77
  KIAA0182 MUTATED KIAA0182 WILD-TYPE 
                15                246 
  KIAA0182 MUTATED KIAA0182 WILD-TYPE 
                 3                 77 
$`KIAA0182 MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-7707 TCGA-BR-8361 TCGA-BR-8373 TCGA-BR-8382 
        6.97         6.61        23.93        19.50        14.79        15.85 
TCGA-BR-A4QL TCGA-CD-8527 TCGA-CD-8536 TCGA-CD-A4MJ TCGA-HJ-7597 TCGA-HU-8602 
       11.57         0.07         0.10        12.62        26.47        11.41 
TCGA-HU-A4GN TCGA-HU-A4GX TCGA-HU-A4H3 
       29.98        10.19        19.36 

$`KIAA0182 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8384 
       14.04         3.32        11.80        19.17         0.26         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56        11.08         5.52         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       11.77         8.98         0.10         6.51         6.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  KIAA0182 MUTATED KIAA0182 WILD-TYPE 
              0.07               0.00 
  KIAA0182 MUTATED KIAA0182 WILD-TYPE 
             29.98             105.07 
  KIAA0182 MUTATED KIAA0182 WILD-TYPE 
            12.620             12.625 
[1] "0.1 - 30.0 (12.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.6"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0182 MUTATED         1        0        3        2         1         1
  KIAA0182 WILD-TYPE       0        9       24       24        30        43
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0182 MUTATED           1          3          1          4        0
  KIAA0182 WILD-TYPE         2         46         35         20       24
D37V3, multiclass
            clus
vv           KIAA0182 MUTATED KIAA0182 WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                  0                  9
  STAGE IB                  3                 24
  STAGE II                  2                 24
  STAGE IIA                 1                 30
  STAGE IIB                 1                 43
  STAGE III                 1                  2
  STAGE IIIA                3                 46
  STAGE IIIB                1                 35
  STAGE IIIC                4                 20
  STAGE IV                  0                 24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0182 MUTATED     2   6   4   7
  KIAA0182 WILD-TYPE   9  66 118  68
D37V4, multiclass
    clus
vv   KIAA0182 MUTATED KIAA0182 WILD-TYPE
  T1                2                  9
  T2                6                 66
  T3                4                118
  T4                7                 68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  KIAA0182 MUTATED    6  6  2  3
  KIAA0182 WILD-TYPE 87 75 48 50
D37V5, multiclass
    clus
vv   KIAA0182 MUTATED KIAA0182 WILD-TYPE
  N0                6                 87
  N1                6                 75
  N2                2                 48
  N3                3                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                    cls
clus                   0   1
  KIAA0182 MUTATED    16   0
  KIAA0182 WILD-TYPE 241  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0182 MUTATED     16    0
  KIAA0182 WILD-TYPE  241   18
   clus
vv  KIAA0182 MUTATED KIAA0182 WILD-TYPE
  0               16                241
  1                0                 18
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  KIAA0182 MUTATED    15   5
  KIAA0182 WILD-TYPE  95 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0182 MUTATED     15    5
  KIAA0182 WILD-TYPE   95  174
        clus
vv       KIAA0182 MUTATED KIAA0182 WILD-TYPE
  FEMALE               15                 95
  MALE                  5                174
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KIAA0182 MUTATED                                       3
  KIAA0182 WILD-TYPE                                    47
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA0182 MUTATED                                                       13
  KIAA0182 WILD-TYPE                                                    122
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA0182 MUTATED                                                                   2
  KIAA0182 WILD-TYPE                                                                38
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KIAA0182 MUTATED                                                  1
  KIAA0182 WILD-TYPE                                               37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KIAA0182 MUTATED                                                          0
  KIAA0182 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KIAA0182 MUTATED                                                           0
  KIAA0182 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KIAA0182 MUTATED                                          1
  KIAA0182 WILD-TYPE                                        2
D37V8, multiclass
                                                                   clus
vv                                                                  KIAA0182 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          13
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  KIAA0182 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           122
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V9, binary
                    cls
clus                   0   1
  KIAA0182 MUTATED     0  20
  KIAA0182 WILD-TYPE   5 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0182 MUTATED      0   20
  KIAA0182 WILD-TYPE    5  264
     clus
vv    KIAA0182 MUTATED KIAA0182 WILD-TYPE
  NO                 0                  5
  YES               20                264
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0182 MUTATED    13   0   0   6
  KIAA0182 WILD-TYPE 214  10  10  18
D37V10, multiclass
    clus
vv   KIAA0182 MUTATED KIAA0182 WILD-TYPE
  R0               13                214
  R1                0                 10
  R2                0                 10
  RX                6                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA0182 MUTATED       7                         1    12
  KIAA0182 WILD-TYPE    69                         3   156
D37V12, multiclass
                           clus
vv                          KIAA0182 MUTATED KIAA0182 WILD-TYPE
  ASIAN                                    7                 69
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                   12                156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = SNAPC2 MUTATION ANALYSIS
D38V1, survival
                  sevent
clus2                0   1
  SNAPC2 MUTATED     9   2
  SNAPC2 WILD-TYPE 172  78
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
              11              250 
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               2               78 
$`SNAPC2 MUTATED`
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8078 TCGA-BR-8361 TCGA-CG-5721 
        6.61        34.68        24.76        12.26        19.50         6.02 
TCGA-D7-A4YY TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H8 
       13.78        29.98         0.10         6.25         8.88 

$`SNAPC2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
       18.35        30.90         6.18         9.57        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 
       30.90        31.20        32.94        12.82         9.21        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
       16.31         2.20        15.58         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       15.16        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
       19.36        23.84        12.30         9.67        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
             0.1              0.0 
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
           34.68           105.07 
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
           12.26            12.64 
[1] "0.1 - 34.7 (12.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.8"
D38V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SNAPC2 MUTATED         0        1        1        0         2         2
  SNAPC2 WILD-TYPE       1        8       26       26        29        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SNAPC2 MUTATED           1          0          1          2        1
  SNAPC2 WILD-TYPE         2         49         35         22       23
D38V3, multiclass
            clus
vv           SNAPC2 MUTATED SNAPC2 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               2               29
  STAGE IIB               2               42
  STAGE III               1                2
  STAGE IIIA              0               49
  STAGE IIIB              1               35
  STAGE IIIC              2               22
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SNAPC2 MUTATED     2   2   3   4
  SNAPC2 WILD-TYPE   9  70 119  71
D38V4, multiclass
    clus
vv   SNAPC2 MUTATED SNAPC2 WILD-TYPE
  T1              2                9
  T2              2               70
  T3              3              119
  T4              4               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  SNAPC2 MUTATED    3  5  2  1
  SNAPC2 WILD-TYPE 90 76 48 52
D38V5, multiclass
    clus
vv   SNAPC2 MUTATED SNAPC2 WILD-TYPE
  N0              3               90
  N1              5               76
  N2              2               48
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                  cls
clus                 0   1
  SNAPC2 MUTATED    11   0
  SNAPC2 WILD-TYPE 246  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC2 MUTATED     11    0
  SNAPC2 WILD-TYPE  246   18
   clus
vv  SNAPC2 MUTATED SNAPC2 WILD-TYPE
  0             11              246
  1              0               18
[1] 2 2
[1] FALSE
D38V7, binary
                  cls
clus                 0   1
  SNAPC2 MUTATED     4   7
  SNAPC2 WILD-TYPE 106 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC2 MUTATED      4    7
  SNAPC2 WILD-TYPE  106  172
        clus
vv       SNAPC2 MUTATED SNAPC2 WILD-TYPE
  FEMALE              4              106
  MALE                7              172
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SNAPC2 MUTATED                                       1
  SNAPC2 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SNAPC2 MUTATED                                                        5
  SNAPC2 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SNAPC2 MUTATED                                                                   1
  SNAPC2 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SNAPC2 MUTATED                                                  3
  SNAPC2 WILD-TYPE                                               35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SNAPC2 MUTATED                                                          0
  SNAPC2 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SNAPC2 MUTATED                                                           1
  SNAPC2 WILD-TYPE                                                         5
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SNAPC2 MUTATED                                          0
  SNAPC2 WILD-TYPE                                        3
D38V8, multiclass
                                                                   clus
vv                                                                  SNAPC2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  SNAPC2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V9, binary
                  cls
clus                 0   1
  SNAPC2 MUTATED     0  11
  SNAPC2 WILD-TYPE   5 273
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC2 MUTATED      0   11
  SNAPC2 WILD-TYPE    5  273
     clus
vv    SNAPC2 MUTATED SNAPC2 WILD-TYPE
  NO               0                5
  YES             11              273
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SNAPC2 MUTATED    10   0   0   1
  SNAPC2 WILD-TYPE 217  10  10  23
D38V10, multiclass
    clus
vv   SNAPC2 MUTATED SNAPC2 WILD-TYPE
  R0             10              217
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SNAPC2 MUTATED       4                         0     6
  SNAPC2 WILD-TYPE    72                         4   162
D38V12, multiclass
                           clus
vv                          SNAPC2 MUTATED SNAPC2 WILD-TYPE
  ASIAN                                  4               72
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = C1QTNF5 MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                 0   1
  C1QTNF5 MUTATED     3   3
  C1QTNF5 WILD-TYPE 178  77
  C1QTNF5 MUTATED C1QTNF5 WILD-TYPE 
                6               255 
  C1QTNF5 MUTATED C1QTNF5 WILD-TYPE 
                3                77 
$`C1QTNF5 MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-F1-6874 TCGA-HU-A4GQ 
       11.70         6.97         6.58        12.62        14.47         0.10 

$`C1QTNF5 WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       26.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       12.43        11.61        12.20         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.99        16.24        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  C1QTNF5 MUTATED C1QTNF5 WILD-TYPE 
              0.1               0.0 
  C1QTNF5 MUTATED C1QTNF5 WILD-TYPE 
            14.47            105.07 
  C1QTNF5 MUTATED C1QTNF5 WILD-TYPE 
            9.335            12.760 
[1] "0.1 - 14.5 (9.3)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "3"  
D39V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C1QTNF5 MUTATED         0        0        3        0         1         0
  C1QTNF5 WILD-TYPE       1        9       24       26        30        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1QTNF5 MUTATED           0          2          0          1        0
  C1QTNF5 WILD-TYPE         3         47         36         23       24
D39V3, multiclass
            clus
vv           C1QTNF5 MUTATED C1QTNF5 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 3                24
  STAGE II                 0                26
  STAGE IIA                1                30
  STAGE IIB                0                44
  STAGE III                0                 3
  STAGE IIIA               2                47
  STAGE IIIB               0                36
  STAGE IIIC               1                23
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C1QTNF5 MUTATED     0   3   2   2
  C1QTNF5 WILD-TYPE  11  69 120  73
D39V4, multiclass
    clus
vv   C1QTNF5 MUTATED C1QTNF5 WILD-TYPE
  T1               0                11
  T2               3                69
  T3               2               120
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  C1QTNF5 MUTATED    5  2  1  0
  C1QTNF5 WILD-TYPE 88 79 49 53
D39V5, multiclass
    clus
vv   C1QTNF5 MUTATED C1QTNF5 WILD-TYPE
  N0               5                88
  N1               2                79
  N2               1                49
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                   cls
clus                  0   1
  C1QTNF5 MUTATED     7   0
  C1QTNF5 WILD-TYPE 250  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF5 MUTATED      7    0
  C1QTNF5 WILD-TYPE  250   18
   clus
vv  C1QTNF5 MUTATED C1QTNF5 WILD-TYPE
  0               7               250
  1               0                18
[1] 2 2
[1] FALSE
D39V7, binary
                   cls
clus                  0   1
  C1QTNF5 MUTATED     2   6
  C1QTNF5 WILD-TYPE 108 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF5 MUTATED      2    6
  C1QTNF5 WILD-TYPE  108  173
        clus
vv       C1QTNF5 MUTATED C1QTNF5 WILD-TYPE
  FEMALE               2               108
  MALE                 6               173
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C1QTNF5 MUTATED                                       2
  C1QTNF5 WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C1QTNF5 MUTATED                                                        4
  C1QTNF5 WILD-TYPE                                                    131
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C1QTNF5 MUTATED                                                                   1
  C1QTNF5 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C1QTNF5 MUTATED                                                  1
  C1QTNF5 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C1QTNF5 MUTATED                                                          0
  C1QTNF5 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C1QTNF5 MUTATED                                                           0
  C1QTNF5 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C1QTNF5 MUTATED                                          0
  C1QTNF5 WILD-TYPE                                        3
D39V8, multiclass
                                                                   clus
vv                                                                  C1QTNF5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  C1QTNF5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V9, binary
                   cls
clus                  0   1
  C1QTNF5 MUTATED     0   8
  C1QTNF5 WILD-TYPE   5 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF5 MUTATED      0    8
  C1QTNF5 WILD-TYPE    5  276
     clus
vv    C1QTNF5 MUTATED C1QTNF5 WILD-TYPE
  NO                0                 5
  YES               8               276
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C1QTNF5 MUTATED     3   0   0   3
  C1QTNF5 WILD-TYPE 224  10  10  21
D39V10, multiclass
    clus
vv   C1QTNF5 MUTATED C1QTNF5 WILD-TYPE
  R0               3               224
  R1               0                10
  R2               0                10
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C1QTNF5 MUTATED       3                         0     5
  C1QTNF5 WILD-TYPE    73                         4   163
D39V12, multiclass
                           clus
vv                          C1QTNF5 MUTATED C1QTNF5 WILD-TYPE
  ASIAN                                   3                73
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   5               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = AOC3 MUTATION ANALYSIS
D40V1, survival
                sevent
clus2              0   1
  AOC3 MUTATED    10   1
  AOC3 WILD-TYPE 171  79
  AOC3 MUTATED AOC3 WILD-TYPE 
            11            250 
  AOC3 MUTATED AOC3 WILD-TYPE 
             1             79 
$`AOC3 MUTATED`
TCGA-BR-6452 TCGA-BR-7197 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8373 TCGA-BR-8487 
       34.68         9.21         0.95         4.31        14.79         1.12 
TCGA-BR-A4QL TCGA-CG-4306 TCGA-D7-A4YY TCGA-HU-A4G6 TCGA-HU-A4GH 
       11.57         1.02        13.78        12.30        11.77 

$`AOC3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       21.11        30.90        31.20        32.94        12.82        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 
        6.18        19.50         0.26        22.19        17.52        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        19.17         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 
       20.91        14.27        16.44         5.92        15.16        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       22.75        25.81        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  AOC3 MUTATED AOC3 WILD-TYPE 
          0.95           0.00 
  AOC3 MUTATED AOC3 WILD-TYPE 
         34.68         105.07 
  AOC3 MUTATED AOC3 WILD-TYPE 
        11.570         12.775 
[1] "0.9 - 34.7 (11.6)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "2.5"
D40V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AOC3 MUTATED         0        2        1        2         3         0
  AOC3 WILD-TYPE       1        7       26       24        28        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AOC3 MUTATED           0          1          2          0        1
  AOC3 WILD-TYPE         3         48         34         24       23
D40V3, multiclass
            clus
vv           AOC3 MUTATED AOC3 WILD-TYPE
  STAGE I               0              1
  STAGE IA              2              7
  STAGE IB              1             26
  STAGE II              2             24
  STAGE IIA             3             28
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            2             34
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AOC3 MUTATED     3   1   8   1
  AOC3 WILD-TYPE   8  71 114  74
D40V4, multiclass
    clus
vv   AOC3 MUTATED AOC3 WILD-TYPE
  T1            3              8
  T2            1             71
  T3            8            114
  T4            1             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  AOC3 MUTATED    8  1  1  2
  AOC3 WILD-TYPE 85 80 49 51
D40V5, multiclass
    clus
vv   AOC3 MUTATED AOC3 WILD-TYPE
  N0            8             85
  N1            1             80
  N2            1             49
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                cls
clus               0   1
  AOC3 MUTATED    12   1
  AOC3 WILD-TYPE 245  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  AOC3 MUTATED     12    1
  AOC3 WILD-TYPE  245   17
   clus
vv  AOC3 MUTATED AOC3 WILD-TYPE
  0           12            245
  1            1             17
[1] 2 2
[1] FALSE
D40V7, binary
                cls
clus               0   1
  AOC3 MUTATED     7   6
  AOC3 WILD-TYPE 103 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  AOC3 MUTATED      7    6
  AOC3 WILD-TYPE  103  173
        clus
vv       AOC3 MUTATED AOC3 WILD-TYPE
  FEMALE            7            103
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AOC3 MUTATED                                       1
  AOC3 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AOC3 MUTATED                                                        9
  AOC3 WILD-TYPE                                                    126
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AOC3 MUTATED                                                                   1
  AOC3 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AOC3 MUTATED                                                  1
  AOC3 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AOC3 MUTATED                                                          0
  AOC3 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AOC3 MUTATED                                                           1
  AOC3 WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AOC3 MUTATED                                          0
  AOC3 WILD-TYPE                                        3
D40V8, multiclass
                                                                   clus
vv                                                                  AOC3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  AOC3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V9, binary
                cls
clus               0   1
  AOC3 MUTATED     0  13
  AOC3 WILD-TYPE   5 271
[1] "tbl2"
                cls
clus             [,1] [,2]
  AOC3 MUTATED      0   13
  AOC3 WILD-TYPE    5  271
     clus
vv    AOC3 MUTATED AOC3 WILD-TYPE
  NO             0              5
  YES           13            271
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  AOC3 MUTATED    11   0   1   1
  AOC3 WILD-TYPE 216  10   9  23
D40V10, multiclass
    clus
vv   AOC3 MUTATED AOC3 WILD-TYPE
  R0           11            216
  R1            0             10
  R2            1              9
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AOC3 MUTATED       3                         0     9
  AOC3 WILD-TYPE    73                         4   159
D40V12, multiclass
                           clus
vv                          AOC3 MUTATED AOC3 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                9            159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = CIC MUTATION ANALYSIS
D41V1, survival
               sevent
clus2             0   1
  CIC MUTATED    16   5
  CIC WILD-TYPE 165  75
  CIC MUTATED CIC WILD-TYPE 
           21           240 
  CIC MUTATED CIC WILD-TYPE 
            5            75 
$`CIC MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8372 TCGA-BR-8487 
        6.97        30.90        34.68        32.94        19.17         1.12 
TCGA-BR-A4QL TCGA-CD-8532 TCGA-CD-A4MI TCGA-CG-4465 TCGA-CG-5723 TCGA-CG-5728 
       11.57         0.10         0.10         9.01       105.07        65.10 
TCGA-CG-5733 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4G8 
       21.07        16.24        14.47        26.47        11.41        11.84 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H3 
        6.51         6.25        19.36 

$`CIC WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       31.20        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
       12.03         0.00        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       12.03        28.96        79.07         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 
       13.78        14.76         0.62         7.99        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 
        5.03        13.58         0.56        11.08         5.52         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY 
       11.77        29.98         8.98         0.10        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  CIC MUTATED CIC WILD-TYPE 
          0.1           0.0 
  CIC MUTATED CIC WILD-TYPE 
       105.07         79.07 
  CIC MUTATED CIC WILD-TYPE 
       14.470        12.605 
[1] "0.1 - 105.1 (14.5)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "2"  
D41V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CIC MUTATED         1        0        4        2         4         3
  CIC WILD-TYPE       0        9       23       24        27        41
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CIC MUTATED           0          2          3          2        2
  CIC WILD-TYPE         3         47         33         22       22
D41V3, multiclass
            clus
vv           CIC MUTATED CIC WILD-TYPE
  STAGE I              1             0
  STAGE IA             0             9
  STAGE IB             4            23
  STAGE II             2            24
  STAGE IIA            4            27
  STAGE IIB            3            41
  STAGE III            0             3
  STAGE IIIA           2            47
  STAGE IIIB           3            33
  STAGE IIIC           2            22
  STAGE IV             2            22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CIC MUTATED     1   7  11   6
  CIC WILD-TYPE  10  65 111  69
D41V4, multiclass
    clus
vv   CIC MUTATED CIC WILD-TYPE
  T1           1            10
  T2           7            65
  T3          11           111
  T4           6            69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  CIC MUTATED   10  8  2  4
  CIC WILD-TYPE 83 73 48 49
D41V5, multiclass
    clus
vv   CIC MUTATED CIC WILD-TYPE
  N0          10            83
  N1           8            73
  N2           2            48
  N3           4            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
               cls
clus              0   1
  CIC MUTATED    20   1
  CIC WILD-TYPE 237  17
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED     20    1
  CIC WILD-TYPE  237   17
   clus
vv  CIC MUTATED CIC WILD-TYPE
  0          20           237
  1           1            17
[1] 2 2
[1] FALSE
D41V7, binary
               cls
clus              0   1
  CIC MUTATED    15  11
  CIC WILD-TYPE  95 168
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED     15   11
  CIC WILD-TYPE   95  168
        clus
vv       CIC MUTATED CIC WILD-TYPE
  FEMALE          15            95
  MALE            11           168
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CIC MUTATED                                       5
  CIC WILD-TYPE                                    45
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CIC MUTATED                                                       15
  CIC WILD-TYPE                                                    120
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CIC MUTATED                                                                   4
  CIC WILD-TYPE                                                                36
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CIC MUTATED                                                  1
  CIC WILD-TYPE                                               37
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CIC MUTATED                                                          0
  CIC WILD-TYPE                                                       16
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CIC MUTATED                                                           0
  CIC WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CIC MUTATED                                          1
  CIC WILD-TYPE                                        2
D41V8, multiclass
                                                                   clus
vv                                                                  CIC MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                     15
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    1
                                                                   clus
vv                                                                  CIC WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      120
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V9, binary
               cls
clus              0   1
  CIC MUTATED     0  26
  CIC WILD-TYPE   5 258
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED      0   26
  CIC WILD-TYPE    5  258
     clus
vv    CIC MUTATED CIC WILD-TYPE
  NO            0             5
  YES          26           258
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  CIC MUTATED    18   0   1   5
  CIC WILD-TYPE 209  10   9  19
D41V10, multiclass
    clus
vv   CIC MUTATED CIC WILD-TYPE
  R0          18           209
  R1           0            10
  R2           1             9
  RX           5            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CIC MUTATED       7                         1    13
  CIC WILD-TYPE    69                         3   155
D41V12, multiclass
                           clus
vv                          CIC MUTATED CIC WILD-TYPE
  ASIAN                               7            69
  BLACK OR AFRICAN AMERICAN           1             3
  WHITE                              13           155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = HLA-B MUTATION ANALYSIS
D42V1, survival
                 sevent
clus2               0   1
  HLA-B MUTATED     8   4
  HLA-B WILD-TYPE 173  76
  HLA-B MUTATED HLA-B WILD-TYPE 
             12             249 
  HLA-B MUTATED HLA-B WILD-TYPE 
              4              76 
$`HLA-B MUTATED`
TCGA-B7-5816 TCGA-BR-4280 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8589 TCGA-CD-8531 
       26.70         6.61        32.94        12.26        15.81         0.10 
TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-5726 TCGA-CG-5728 TCGA-F1-6874 TCGA-HU-A4GQ 
        6.58        12.62        28.96        65.10        14.47         0.10 

$`HLA-B WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.13         0.16         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5730 
        6.02         0.99       105.07        12.03        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.99        16.24        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  HLA-B MUTATED HLA-B WILD-TYPE 
            0.1             0.0 
  HLA-B MUTATED HLA-B WILD-TYPE 
          65.10          105.07 
  HLA-B MUTATED HLA-B WILD-TYPE 
         13.545          12.590 
[1] "0.1 - 65.1 (13.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D42V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HLA-B MUTATED         0        1        3        0         2         2
  HLA-B WILD-TYPE       1        8       24       26        29        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HLA-B MUTATED           1          2          1          1        0
  HLA-B WILD-TYPE         2         47         35         23       24
D42V3, multiclass
            clus
vv           HLA-B MUTATED HLA-B WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               3              24
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              2              42
  STAGE III              1               2
  STAGE IIIA             2              47
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HLA-B MUTATED     1   4   4   5
  HLA-B WILD-TYPE  10  68 118  70
D42V4, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  T1             1              10
  T2             4              68
  T3             4             118
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  HLA-B MUTATED    9  3  1  0
  HLA-B WILD-TYPE 84 78 49 53
D42V5, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  N0             9              84
  N1             3              78
  N2             1              49
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                 cls
clus                0   1
  HLA-B MUTATED    13   0
  HLA-B WILD-TYPE 244  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED     13    0
  HLA-B WILD-TYPE  244   18
   clus
vv  HLA-B MUTATED HLA-B WILD-TYPE
  0            13             244
  1             0              18
[1] 2 2
[1] FALSE
D42V7, binary
                 cls
clus                0   1
  HLA-B MUTATED     8   6
  HLA-B WILD-TYPE 102 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      8    6
  HLA-B WILD-TYPE  102  173
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  FEMALE             8             102
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  HLA-B MUTATED                                       3
  HLA-B WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HLA-B MUTATED                                                        7
  HLA-B WILD-TYPE                                                    128
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HLA-B MUTATED                                                                   3
  HLA-B WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  HLA-B MUTATED                                                  1
  HLA-B WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  HLA-B MUTATED                                                          0
  HLA-B WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  HLA-B MUTATED                                                           0
  HLA-B WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  HLA-B MUTATED                                          0
  HLA-B WILD-TYPE                                        3
D42V8, multiclass
                                                                   clus
vv                                                                  HLA-B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  HLA-B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V9, binary
                 cls
clus                0   1
  HLA-B MUTATED     0  14
  HLA-B WILD-TYPE   5 270
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      0   14
  HLA-B WILD-TYPE    5  270
     clus
vv    HLA-B MUTATED HLA-B WILD-TYPE
  NO              0               5
  YES            14             270
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HLA-B MUTATED     9   0   0   3
  HLA-B WILD-TYPE 218  10  10  21
D42V10, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  R0             9             218
  R1             0              10
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HLA-B MUTATED       4                         0     8
  HLA-B WILD-TYPE    72                         4   160
D42V12, multiclass
                           clus
vv                          HLA-B MUTATED HLA-B WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 8             160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = CD4 MUTATION ANALYSIS
D43V1, survival
               sevent
clus2             0   1
  CD4 MUTATED    13   2
  CD4 WILD-TYPE 168  78
  CD4 MUTATED CD4 WILD-TYPE 
           15           246 
  CD4 MUTATED CD4 WILD-TYPE 
            2            78 
$`CD4 MUTATED`
TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8680 TCGA-CD-A4MI 
       34.68        30.90         4.31        19.17        15.81         0.10 
TCGA-CG-4449 TCGA-D7-A4YV TCGA-F1-A448 TCGA-HJ-7597 TCGA-HU-A4G8 TCGA-HU-A4GT 
       19.07         5.92        21.27        26.47        11.84         6.51 
TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H8 
       10.19        19.36         8.88 

$`CD4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
       26.33        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        47.05        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 
        5.03        13.58         0.56        11.08         5.52         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         0.10         6.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  CD4 MUTATED CD4 WILD-TYPE 
          0.1           0.0 
  CD4 MUTATED CD4 WILD-TYPE 
        34.68        105.07 
  CD4 MUTATED CD4 WILD-TYPE 
       15.810        12.605 
[1] "0.1 - 34.7 (15.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.8"
D43V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CD4 MUTATED         0        0        3        1         2         2
  CD4 WILD-TYPE       1        9       24       25        29        42
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CD4 MUTATED           0          1          2          3        1
  CD4 WILD-TYPE         3         48         34         21       23
D43V3, multiclass
            clus
vv           CD4 MUTATED CD4 WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             9
  STAGE IB             3            24
  STAGE II             1            25
  STAGE IIA            2            29
  STAGE IIB            2            42
  STAGE III            0             3
  STAGE IIIA           1            48
  STAGE IIIB           2            34
  STAGE IIIC           3            21
  STAGE IV             1            23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CD4 MUTATED     1   3   7   4
  CD4 WILD-TYPE  10  69 115  71
D43V4, multiclass
    clus
vv   CD4 MUTATED CD4 WILD-TYPE
  T1           1            10
  T2           3            69
  T3           7           115
  T4           4            71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  CD4 MUTATED    4  5  3  3
  CD4 WILD-TYPE 89 76 47 50
D43V5, multiclass
    clus
vv   CD4 MUTATED CD4 WILD-TYPE
  N0           4            89
  N1           5            76
  N2           3            47
  N3           3            50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
               cls
clus              0   1
  CD4 MUTATED    13   1
  CD4 WILD-TYPE 244  17
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD4 MUTATED     13    1
  CD4 WILD-TYPE  244   17
   clus
vv  CD4 MUTATED CD4 WILD-TYPE
  0          13           244
  1           1            17
[1] 2 2
[1] FALSE
D43V7, binary
               cls
clus              0   1
  CD4 MUTATED     8   7
  CD4 WILD-TYPE 102 172
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD4 MUTATED      8    7
  CD4 WILD-TYPE  102  172
        clus
vv       CD4 MUTATED CD4 WILD-TYPE
  FEMALE           8           102
  MALE             7           172
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CD4 MUTATED                                       3
  CD4 WILD-TYPE                                    47
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CD4 MUTATED                                                        5
  CD4 WILD-TYPE                                                    130
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CD4 MUTATED                                                                   0
  CD4 WILD-TYPE                                                                40
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CD4 MUTATED                                                  4
  CD4 WILD-TYPE                                               34
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CD4 MUTATED                                                          2
  CD4 WILD-TYPE                                                       14
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CD4 MUTATED                                                           0
  CD4 WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CD4 MUTATED                                          1
  CD4 WILD-TYPE                                        2
D43V8, multiclass
                                                                   clus
vv                                                                  CD4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    1
                                                                   clus
vv                                                                  CD4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V9, binary
               cls
clus              0   1
  CD4 MUTATED     0  15
  CD4 WILD-TYPE   5 269
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD4 MUTATED      0   15
  CD4 WILD-TYPE    5  269
     clus
vv    CD4 MUTATED CD4 WILD-TYPE
  NO            0             5
  YES          15           269
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  CD4 MUTATED    13   0   0   0
  CD4 WILD-TYPE 214  10  10  24
D43V10, multiclass
    clus
vv   CD4 MUTATED CD4 WILD-TYPE
  R0          13           214
  R1           0            10
  R2           0            10
  RX           0            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD4 MUTATED       7                         0     7
  CD4 WILD-TYPE    69                         4   161
D43V12, multiclass
                           clus
vv                          CD4 MUTATED CD4 WILD-TYPE
  ASIAN                               7            69
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                               7           161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = ZMYM4 MUTATION ANALYSIS
D44V1, survival
                 sevent
clus2               0   1
  ZMYM4 MUTATED    11   4
  ZMYM4 WILD-TYPE 170  76
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
             15             246 
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
              4              76 
$`ZMYM4 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-8382 TCGA-BR-8589 
       26.70         6.97        23.93        12.43        15.85        15.81 
TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-4466 TCGA-CG-5721 
       13.45        15.81         6.58        15.95        18.97         6.02 
TCGA-CG-5726 TCGA-HU-A4GQ TCGA-HU-A4GX 
       28.96         0.10        10.19 

$`ZMYM4 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       15.42        28.01        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       12.79         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         6.51         6.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
            0.1             0.0 
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
          28.96          105.07 
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
         15.810          12.575 
[1] "0.1 - 29.0 (15.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D44V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZMYM4 MUTATED         0        1        2        1         1         2
  ZMYM4 WILD-TYPE       1        8       25       25        30        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZMYM4 MUTATED           0          2          1          4        3
  ZMYM4 WILD-TYPE         3         47         35         20       21
D44V3, multiclass
            clus
vv           ZMYM4 MUTATED ZMYM4 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               2              25
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             1              35
  STAGE IIIC             4              20
  STAGE IV               3              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZMYM4 MUTATED     1   3   2  11
  ZMYM4 WILD-TYPE  10  69 120  64
D44V4, multiclass
    clus
vv   ZMYM4 MUTATED ZMYM4 WILD-TYPE
  T1             1              10
  T2             3              69
  T3             2             120
  T4            11              64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ZMYM4 MUTATED    7  4  4  2
  ZMYM4 WILD-TYPE 86 77 46 51
D44V5, multiclass
    clus
vv   ZMYM4 MUTATED ZMYM4 WILD-TYPE
  N0             7              86
  N1             4              77
  N2             4              46
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                 cls
clus                0   1
  ZMYM4 MUTATED    15   1
  ZMYM4 WILD-TYPE 242  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM4 MUTATED     15    1
  ZMYM4 WILD-TYPE  242   17
   clus
vv  ZMYM4 MUTATED ZMYM4 WILD-TYPE
  0            15             242
  1             1              17
[1] 2 2
[1] FALSE
D44V7, binary
                 cls
clus                0   1
  ZMYM4 MUTATED     7  10
  ZMYM4 WILD-TYPE 103 169
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM4 MUTATED      7   10
  ZMYM4 WILD-TYPE  103  169
        clus
vv       ZMYM4 MUTATED ZMYM4 WILD-TYPE
  FEMALE             7             103
  MALE              10             169
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZMYM4 MUTATED                                       3
  ZMYM4 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZMYM4 MUTATED                                                        8
  ZMYM4 WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZMYM4 MUTATED                                                                   4
  ZMYM4 WILD-TYPE                                                                36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZMYM4 MUTATED                                                  2
  ZMYM4 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZMYM4 MUTATED                                                          0
  ZMYM4 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZMYM4 MUTATED                                                           0
  ZMYM4 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZMYM4 MUTATED                                          0
  ZMYM4 WILD-TYPE                                        3
D44V8, multiclass
                                                                   clus
vv                                                                  ZMYM4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ZMYM4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V9, binary
                 cls
clus                0   1
  ZMYM4 MUTATED     0  17
  ZMYM4 WILD-TYPE   5 267
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM4 MUTATED      0   17
  ZMYM4 WILD-TYPE    5  267
     clus
vv    ZMYM4 MUTATED ZMYM4 WILD-TYPE
  NO              0               5
  YES            17             267
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ZMYM4 MUTATED    13   0   0   3
  ZMYM4 WILD-TYPE 214  10  10  21
D44V10, multiclass
    clus
vv   ZMYM4 MUTATED ZMYM4 WILD-TYPE
  R0            13             214
  R1             0              10
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZMYM4 MUTATED       4                         0     9
  ZMYM4 WILD-TYPE    72                         4   159
D44V12, multiclass
                           clus
vv                          ZMYM4 MUTATED ZMYM4 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 9             159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = ZNF43 MUTATION ANALYSIS
D45V1, survival
                 sevent
clus2               0   1
  ZNF43 MUTATED    23   7
  ZNF43 WILD-TYPE 158  73
  ZNF43 MUTATED ZNF43 WILD-TYPE 
             30             231 
  ZNF43 MUTATED ZNF43 WILD-TYPE 
              7              73 
$`ZNF43 MUTATED`
TCGA-BR-4183 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6458 TCGA-BR-6566 
        6.61        30.90        34.68        15.95        19.33        32.78 
TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8361 
       32.94         9.21        23.93        12.26        20.55        19.50 
TCGA-BR-8363 TCGA-BR-8382 TCGA-BR-8589 TCGA-BR-8680 TCGA-CD-5801 TCGA-CD-8536 
        0.26        15.85        15.81        15.81        13.18         0.10 
TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-5578 
        6.58        12.62        15.95         6.02        65.10        12.66 
TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-HU-A4G8 TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H8 
        5.92        14.76        11.84         6.25        10.19         8.88 

$`ZNF43 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57         6.61        13.87        17.29        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7703 
        8.98        21.11        30.90        31.20        12.82        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        0.69         9.60         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 
        2.20        15.58         7.40         6.18        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       19.17        14.79         0.26         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22         1.12        12.79         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.15         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 
        0.13         0.16         0.10         0.10         0.13         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        28.96        79.07         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        12.36        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        15.16 
TCGA-D7-A4YY TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       13.78         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10         6.51         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  ZNF43 MUTATED ZNF43 WILD-TYPE 
            0.1             0.0 
  ZNF43 MUTATED ZNF43 WILD-TYPE 
          65.10          105.07 
  ZNF43 MUTATED ZNF43 WILD-TYPE 
          13.97           12.43 
[1] "0.1 - 65.1 (14.0)"  "0.0 - 105.1 (12.4)"
[1] "hr=" "1.6"
D45V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF43 MUTATED         1        0        5        3         5         7
  ZNF43 WILD-TYPE       0        9       22       23        26        37
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF43 MUTATED           0          4          1          3        2
  ZNF43 WILD-TYPE         3         45         35         21       22
D45V3, multiclass
            clus
vv           ZNF43 MUTATED ZNF43 WILD-TYPE
  STAGE I                1               0
  STAGE IA               0               9
  STAGE IB               5              22
  STAGE II               3              23
  STAGE IIA              5              26
  STAGE IIB              7              37
  STAGE III              0               3
  STAGE IIIA             4              45
  STAGE IIIB             1              35
  STAGE IIIC             3              21
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZNF43 MUTATED     2   8  13   9
  ZNF43 WILD-TYPE   9  64 109  66
D45V4, multiclass
    clus
vv   ZNF43 MUTATED ZNF43 WILD-TYPE
  T1             2               9
  T2             8              64
  T3            13             109
  T4             9              66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ZNF43 MUTATED   13 14  5  1
  ZNF43 WILD-TYPE 80 67 45 52
D45V5, multiclass
    clus
vv   ZNF43 MUTATED ZNF43 WILD-TYPE
  N0            13              80
  N1            14              67
  N2             5              45
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                 cls
clus                0   1
  ZNF43 MUTATED    32   1
  ZNF43 WILD-TYPE 225  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF43 MUTATED     32    1
  ZNF43 WILD-TYPE  225   17
   clus
vv  ZNF43 MUTATED ZNF43 WILD-TYPE
  0            32             225
  1             1              17
[1] 2 2
[1] FALSE
D45V7, binary
                 cls
clus                0   1
  ZNF43 MUTATED    19  15
  ZNF43 WILD-TYPE  91 164
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF43 MUTATED     19   15
  ZNF43 WILD-TYPE   91  164
        clus
vv       ZNF43 MUTATED ZNF43 WILD-TYPE
  FEMALE            19              91
  MALE              15             164
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZNF43 MUTATED                                       4
  ZNF43 WILD-TYPE                                    46
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF43 MUTATED                                                       23
  ZNF43 WILD-TYPE                                                    112
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF43 MUTATED                                                                   2
  ZNF43 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZNF43 MUTATED                                                  4
  ZNF43 WILD-TYPE                                               34
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZNF43 MUTATED                                                          1
  ZNF43 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZNF43 MUTATED                                                           0
  ZNF43 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZNF43 MUTATED                                          0
  ZNF43 WILD-TYPE                                        3
D45V8, multiclass
                                                                   clus
vv                                                                  ZNF43 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ZNF43 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        112
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V9, binary
                 cls
clus                0   1
  ZNF43 MUTATED     0  34
  ZNF43 WILD-TYPE   5 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF43 MUTATED      0   34
  ZNF43 WILD-TYPE    5  250
     clus
vv    ZNF43 MUTATED ZNF43 WILD-TYPE
  NO              0               5
  YES            34             250
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ZNF43 MUTATED    26   0   0   5
  ZNF43 WILD-TYPE 201  10  10  19
D45V10, multiclass
    clus
vv   ZNF43 MUTATED ZNF43 WILD-TYPE
  R0            26             201
  R1             0              10
  R2             0              10
  RX             5              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF43 MUTATED       9                         1    21
  ZNF43 WILD-TYPE    67                         3   147
D45V12, multiclass
                           clus
vv                          ZNF43 MUTATED ZNF43 WILD-TYPE
  ASIAN                                 9              67
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                21             147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = NT5M MUTATION ANALYSIS
D46V1, survival
                sevent
clus2              0   1
  NT5M MUTATED     3   0
  NT5M WILD-TYPE 178  80
  NT5M MUTATED NT5M WILD-TYPE 
             3            258 
  NT5M MUTATED NT5M WILD-TYPE 
             0             80 
$`NT5M MUTATED`
TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-A4QL 
       12.26         1.12        11.57 

$`NT5M WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  NT5M MUTATED NT5M WILD-TYPE 
          1.12           0.00 
  NT5M MUTATED NT5M WILD-TYPE 
         12.26         105.07 
  NT5M MUTATED NT5M WILD-TYPE 
         11.57          12.71 
[1] "1.1 - 12.3 (11.6)"  "0.0 - 105.1 (12.7)"
[1] "hr="     "3300000"
D46V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NT5M MUTATED         0        0        0        0         1         1
  NT5M WILD-TYPE       1        9       27       26        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NT5M MUTATED           0          1          1          0        1
  NT5M WILD-TYPE         3         48         35         24       23
D46V3, multiclass
            clus
vv           NT5M MUTATED NT5M WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              0             26
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NT5M MUTATED     0   0   2   3
  NT5M WILD-TYPE  11  72 120  72
D46V4, multiclass
    clus
vv   NT5M MUTATED NT5M WILD-TYPE
  T1            0             11
  T2            0             72
  T3            2            120
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  NT5M MUTATED    3  0  1  1
  NT5M WILD-TYPE 90 81 49 52
D46V5, multiclass
    clus
vv   NT5M MUTATED NT5M WILD-TYPE
  N0            3             90
  N1            0             81
  N2            1             49
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                cls
clus               0   1
  NT5M MUTATED     5   0
  NT5M WILD-TYPE 252  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  NT5M MUTATED      5    0
  NT5M WILD-TYPE  252   18
   clus
vv  NT5M MUTATED NT5M WILD-TYPE
  0            5            252
  1            0             18
[1] 2 2
[1] FALSE
D46V7, binary
                cls
clus               0   1
  NT5M MUTATED     5   0
  NT5M WILD-TYPE 105 179
[1] "tbl2"
                cls
clus             [,1] [,2]
  NT5M MUTATED      5    0
  NT5M WILD-TYPE  105  179
        clus
vv       NT5M MUTATED NT5M WILD-TYPE
  FEMALE            5            105
  MALE              0            179
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NT5M MUTATED                                       0
  NT5M WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NT5M MUTATED                                                        5
  NT5M WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NT5M MUTATED                                                                   0
  NT5M WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NT5M MUTATED                                                  0
  NT5M WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NT5M MUTATED                                                          0
  NT5M WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NT5M MUTATED                                                           0
  NT5M WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NT5M MUTATED                                          0
  NT5M WILD-TYPE                                        3
D46V8, multiclass
                                                                   clus
vv                                                                  NT5M MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  NT5M WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V9, binary
                cls
clus               0   1
  NT5M MUTATED     0   5
  NT5M WILD-TYPE   5 279
[1] "tbl2"
                cls
clus             [,1] [,2]
  NT5M MUTATED      0    5
  NT5M WILD-TYPE    5  279
     clus
vv    NT5M MUTATED NT5M WILD-TYPE
  NO             0              5
  YES            5            279
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NT5M MUTATED     3   0   0   2
  NT5M WILD-TYPE 224  10  10  22
D46V10, multiclass
    clus
vv   NT5M MUTATED NT5M WILD-TYPE
  R0            3            224
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NT5M MUTATED       0                         0     5
  NT5M WILD-TYPE    76                         4   163
D46V12, multiclass
                           clus
vv                          NT5M MUTATED NT5M WILD-TYPE
  ASIAN                                0             76
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                5            163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = GBP7 MUTATION ANALYSIS
D47V1, survival
                sevent
clus2              0   1
  GBP7 MUTATED     5   4
  GBP7 WILD-TYPE 176  76
  GBP7 MUTATED GBP7 WILD-TYPE 
             9            252 
  GBP7 MUTATED GBP7 WILD-TYPE 
             4             76 
$`GBP7 MUTATED`
TCGA-BR-4201 TCGA-BR-6566 TCGA-BR-8591 TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-4465 
       30.90        32.78        13.45         0.10         1.02         9.01 
TCGA-CG-5728 TCGA-HU-A4GQ TCGA-HU-A4GX 
       65.10         0.10        10.19 

$`GBP7 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         6.51         6.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  GBP7 MUTATED GBP7 WILD-TYPE 
           0.1            0.0 
  GBP7 MUTATED GBP7 WILD-TYPE 
         65.10         105.07 
  GBP7 MUTATED GBP7 WILD-TYPE 
         10.19          12.64 
[1] "0.1 - 65.1 (10.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D47V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GBP7 MUTATED         0        0        1        0         1         0
  GBP7 WILD-TYPE       1        9       26       26        30        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GBP7 MUTATED           0          0          1          3        2
  GBP7 WILD-TYPE         3         49         35         21       22
D47V3, multiclass
            clus
vv           GBP7 MUTATED GBP7 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             1             30
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            1             35
  STAGE IIIC            3             21
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GBP7 MUTATED     0   2   3   4
  GBP7 WILD-TYPE  11  70 119  71
D47V4, multiclass
    clus
vv   GBP7 MUTATED GBP7 WILD-TYPE
  T1            0             11
  T2            2             70
  T3            3            119
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  GBP7 MUTATED    2  1  3  2
  GBP7 WILD-TYPE 91 80 47 51
D47V5, multiclass
    clus
vv   GBP7 MUTATED GBP7 WILD-TYPE
  N0            2             91
  N1            1             80
  N2            3             47
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                cls
clus               0   1
  GBP7 MUTATED     7   2
  GBP7 WILD-TYPE 250  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  GBP7 MUTATED      7    2
  GBP7 WILD-TYPE  250   16
   clus
vv  GBP7 MUTATED GBP7 WILD-TYPE
  0            7            250
  1            2             16
[1] 2 2
[1] FALSE
D47V7, binary
                cls
clus               0   1
  GBP7 MUTATED     5   4
  GBP7 WILD-TYPE 105 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  GBP7 MUTATED      5    4
  GBP7 WILD-TYPE  105  175
        clus
vv       GBP7 MUTATED GBP7 WILD-TYPE
  FEMALE            5            105
  MALE              4            175
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GBP7 MUTATED                                       2
  GBP7 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GBP7 MUTATED                                                        5
  GBP7 WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GBP7 MUTATED                                                                   1
  GBP7 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GBP7 MUTATED                                                  1
  GBP7 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GBP7 MUTATED                                                          0
  GBP7 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GBP7 MUTATED                                                           0
  GBP7 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GBP7 MUTATED                                          0
  GBP7 WILD-TYPE                                        3
D47V8, multiclass
                                                                   clus
vv                                                                  GBP7 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  GBP7 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V9, binary
                cls
clus               0   1
  GBP7 MUTATED     0   9
  GBP7 WILD-TYPE   5 275
[1] "tbl2"
                cls
clus             [,1] [,2]
  GBP7 MUTATED      0    9
  GBP7 WILD-TYPE    5  275
     clus
vv    GBP7 MUTATED GBP7 WILD-TYPE
  NO             0              5
  YES            9            275
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GBP7 MUTATED     5   0   2   1
  GBP7 WILD-TYPE 222  10   8  23
D47V10, multiclass
    clus
vv   GBP7 MUTATED GBP7 WILD-TYPE
  R0            5            222
  R1            0             10
  R2            2              8
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GBP7 MUTATED       3                         0     3
  GBP7 WILD-TYPE    73                         4   165
D47V12, multiclass
                           clus
vv                          GBP7 MUTATED GBP7 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                3            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = BCL9L MUTATION ANALYSIS
D48V1, survival
                 sevent
clus2               0   1
  BCL9L MUTATED    18   3
  BCL9L WILD-TYPE 163  77
  BCL9L MUTATED BCL9L WILD-TYPE 
             21             240 
  BCL9L MUTATED BCL9L WILD-TYPE 
              3              77 
$`BCL9L MUTATED`
TCGA-BR-4280 TCGA-BR-6801 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8382 TCGA-BR-8591 
        6.61        21.11        12.26        19.50        15.85        13.45 
TCGA-BR-8680 TCGA-CD-A4MJ TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5730 TCGA-D7-6818 
       15.81        12.62         6.02        28.96         4.01        10.55 
TCGA-D7-8570 TCGA-D7-A4YY TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-A4BE TCGA-HU-8602 
       24.72        13.78        14.47        21.27        11.08        11.41 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
        0.10         6.51         6.25 

$`BCL9L WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        15.81         9.34         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 
        0.99       105.07        12.03        79.07        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 
       17.19        10.26        15.22        15.98        12.79        11.31 
TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.33        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7735 
       14.76         0.62         7.99        16.24        72.23         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       11.77        29.98         8.98        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  BCL9L MUTATED BCL9L WILD-TYPE 
            0.1             0.0 
  BCL9L MUTATED BCL9L WILD-TYPE 
          28.96          105.07 
  BCL9L MUTATED BCL9L WILD-TYPE 
         12.620          12.625 
[1] "0.1 - 29.0 (12.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.1"
D48V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BCL9L MUTATED         0        1        3        0         3         3
  BCL9L WILD-TYPE       1        8       24       26        28        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BCL9L MUTATED           1          2          3          4        3
  BCL9L WILD-TYPE         2         47         33         20       21
D48V3, multiclass
            clus
vv           BCL9L MUTATED BCL9L WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               3              24
  STAGE II               0              26
  STAGE IIA              3              28
  STAGE IIB              3              41
  STAGE III              1               2
  STAGE IIIA             2              47
  STAGE IIIB             3              33
  STAGE IIIC             4              20
  STAGE IV               3              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BCL9L MUTATED     1   6   7   9
  BCL9L WILD-TYPE  10  66 115  66
D48V4, multiclass
    clus
vv   BCL9L MUTATED BCL9L WILD-TYPE
  T1             1              10
  T2             6              66
  T3             7             115
  T4             9              66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  BCL9L MUTATED   10  4  3  6
  BCL9L WILD-TYPE 83 77 47 47
D48V5, multiclass
    clus
vv   BCL9L MUTATED BCL9L WILD-TYPE
  N0            10              83
  N1             4              77
  N2             3              47
  N3             6              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                 cls
clus                0   1
  BCL9L MUTATED    22   2
  BCL9L WILD-TYPE 235  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED     22    2
  BCL9L WILD-TYPE  235   16
   clus
vv  BCL9L MUTATED BCL9L WILD-TYPE
  0            22             235
  1             2              16
[1] 2 2
[1] FALSE
D48V7, binary
                 cls
clus                0   1
  BCL9L MUTATED     9  15
  BCL9L WILD-TYPE 101 164
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED      9   15
  BCL9L WILD-TYPE  101  164
        clus
vv       BCL9L MUTATED BCL9L WILD-TYPE
  FEMALE             9             101
  MALE              15             164
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  BCL9L MUTATED                                       3
  BCL9L WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BCL9L MUTATED                                                       11
  BCL9L WILD-TYPE                                                    124
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BCL9L MUTATED                                                                   5
  BCL9L WILD-TYPE                                                                35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  BCL9L MUTATED                                                  4
  BCL9L WILD-TYPE                                               34
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  BCL9L MUTATED                                                          1
  BCL9L WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  BCL9L MUTATED                                                           0
  BCL9L WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  BCL9L MUTATED                                          0
  BCL9L WILD-TYPE                                        3
D48V8, multiclass
                                                                   clus
vv                                                                  BCL9L MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  BCL9L WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V9, binary
                 cls
clus                0   1
  BCL9L MUTATED     1  23
  BCL9L WILD-TYPE   4 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED      1   23
  BCL9L WILD-TYPE    4  261
     clus
vv    BCL9L MUTATED BCL9L WILD-TYPE
  NO              1               4
  YES            23             261
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BCL9L MUTATED    19   0   1   3
  BCL9L WILD-TYPE 208  10   9  21
D48V10, multiclass
    clus
vv   BCL9L MUTATED BCL9L WILD-TYPE
  R0            19             208
  R1             0              10
  R2             1               9
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCL9L MUTATED       6                         1    13
  BCL9L WILD-TYPE    70                         3   155
D48V12, multiclass
                           clus
vv                          BCL9L MUTATED BCL9L WILD-TYPE
  ASIAN                                 6              70
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                13             155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = TBX4 MUTATION ANALYSIS
D49V1, survival
                sevent
clus2              0   1
  TBX4 MUTATED     9   2
  TBX4 WILD-TYPE 172  78
  TBX4 MUTATED TBX4 WILD-TYPE 
            11            250 
  TBX4 MUTATED TBX4 WILD-TYPE 
             2             78 
$`TBX4 MUTATED`
TCGA-BR-4184 TCGA-BR-8078 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-A4MJ TCGA-CG-4465 
        6.97        12.26        13.45        11.57        12.62         9.01 
TCGA-CG-5721 TCGA-CG-5728 TCGA-F1-6874 TCGA-HU-A4GU TCGA-HU-A4H8 
        6.02        65.10        14.47         6.25         8.88 

$`TBX4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 
       14.76         0.62         7.99        16.24        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
       19.36        23.84        12.30         9.67        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  TBX4 MUTATED TBX4 WILD-TYPE 
          6.02           0.00 
  TBX4 MUTATED TBX4 WILD-TYPE 
         65.10         105.07 
  TBX4 MUTATED TBX4 WILD-TYPE 
        11.570         12.775 
[1] "6.0 - 65.1 (11.6)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.6"
D49V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TBX4 MUTATED         0        0        4        0         0         2
  TBX4 WILD-TYPE       1        9       23       26        31        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBX4 MUTATED           0          1          1          1        2
  TBX4 WILD-TYPE         3         48         35         23       22
D49V3, multiclass
            clus
vv           TBX4 MUTATED TBX4 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              4             23
  STAGE II              0             26
  STAGE IIA             0             31
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            1             23
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TBX4 MUTATED     1   3   3   4
  TBX4 WILD-TYPE  10  69 119  71
D49V4, multiclass
    clus
vv   TBX4 MUTATED TBX4 WILD-TYPE
  T1            1             10
  T2            3             69
  T3            3            119
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  TBX4 MUTATED    4  4  0  3
  TBX4 WILD-TYPE 89 77 50 50
D49V5, multiclass
    clus
vv   TBX4 MUTATED TBX4 WILD-TYPE
  N0            4             89
  N1            4             77
  N2            0             50
  N3            3             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                cls
clus               0   1
  TBX4 MUTATED     9   1
  TBX4 WILD-TYPE 248  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBX4 MUTATED      9    1
  TBX4 WILD-TYPE  248   17
   clus
vv  TBX4 MUTATED TBX4 WILD-TYPE
  0            9            248
  1            1             17
[1] 2 2
[1] FALSE
D49V7, binary
                cls
clus               0   1
  TBX4 MUTATED     4   7
  TBX4 WILD-TYPE 106 172
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBX4 MUTATED      4    7
  TBX4 WILD-TYPE  106  172
        clus
vv       TBX4 MUTATED TBX4 WILD-TYPE
  FEMALE            4            106
  MALE              7            172
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TBX4 MUTATED                                       2
  TBX4 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TBX4 MUTATED                                                        5
  TBX4 WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TBX4 MUTATED                                                                   3
  TBX4 WILD-TYPE                                                                37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TBX4 MUTATED                                                  1
  TBX4 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TBX4 MUTATED                                                          0
  TBX4 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TBX4 MUTATED                                                           0
  TBX4 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TBX4 MUTATED                                          0
  TBX4 WILD-TYPE                                        3
D49V8, multiclass
                                                                   clus
vv                                                                  TBX4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  TBX4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V9, binary
                cls
clus               0   1
  TBX4 MUTATED     0  11
  TBX4 WILD-TYPE   5 273
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBX4 MUTATED      0   11
  TBX4 WILD-TYPE    5  273
     clus
vv    TBX4 MUTATED TBX4 WILD-TYPE
  NO             0              5
  YES           11            273
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TBX4 MUTATED     8   0   1   1
  TBX4 WILD-TYPE 219  10   9  23
D49V10, multiclass
    clus
vv   TBX4 MUTATED TBX4 WILD-TYPE
  R0            8            219
  R1            0             10
  R2            1              9
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TBX4 MUTATED       3                         0     5
  TBX4 WILD-TYPE    73                         4   163
D49V12, multiclass
                           clus
vv                          TBX4 MUTATED TBX4 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                5            163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = C7ORF50 MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  C7ORF50 MUTATED     8   2
  C7ORF50 WILD-TYPE 173  78
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
               10               251 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
                2                78 
$`C7ORF50 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-A4QL 
       34.68        32.94         6.18        19.50         1.12        11.57 
TCGA-CG-5726 TCGA-D7-A4YY TCGA-HU-A4G8 TCGA-HU-A4GQ 
       28.96        13.78        11.84         0.10 

$`C7ORF50 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
              0.1               0.0 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
            34.68            105.07 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
            12.81             12.62 
[1] "0.1 - 34.7 (12.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.9"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C7ORF50 MUTATED         0        1        0        0         4         1
  C7ORF50 WILD-TYPE       1        8       27       26        27        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C7ORF50 MUTATED           0          0          2          2        0
  C7ORF50 WILD-TYPE         3         49         34         22       24
D50V3, multiclass
            clus
vv           C7ORF50 MUTATED C7ORF50 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 1                 8
  STAGE IB                 0                27
  STAGE II                 0                26
  STAGE IIA                4                27
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               2                34
  STAGE IIIC               2                22
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C7ORF50 MUTATED     1   0   7   2
  C7ORF50 WILD-TYPE  10  72 115  73
D50V4, multiclass
    clus
vv   C7ORF50 MUTATED C7ORF50 WILD-TYPE
  T1               1                10
  T2               0                72
  T3               7               115
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  C7ORF50 MUTATED    5  1  2  2
  C7ORF50 WILD-TYPE 88 80 48 51
D50V5, multiclass
    clus
vv   C7ORF50 MUTATED C7ORF50 WILD-TYPE
  N0               5                88
  N1               1                80
  N2               2                48
  N3               2                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                   cls
clus                  0   1
  C7ORF50 MUTATED    10   0
  C7ORF50 WILD-TYPE 247  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF50 MUTATED     10    0
  C7ORF50 WILD-TYPE  247   18
   clus
vv  C7ORF50 MUTATED C7ORF50 WILD-TYPE
  0              10               247
  1               0                18
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  C7ORF50 MUTATED     6   4
  C7ORF50 WILD-TYPE 104 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF50 MUTATED      6    4
  C7ORF50 WILD-TYPE  104  175
        clus
vv       C7ORF50 MUTATED C7ORF50 WILD-TYPE
  FEMALE               6               104
  MALE                 4               175
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C7ORF50 MUTATED                                       1
  C7ORF50 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C7ORF50 MUTATED                                                        6
  C7ORF50 WILD-TYPE                                                    129
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C7ORF50 MUTATED                                                                   2
  C7ORF50 WILD-TYPE                                                                38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C7ORF50 MUTATED                                                  1
  C7ORF50 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C7ORF50 MUTATED                                                          0
  C7ORF50 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C7ORF50 MUTATED                                                           0
  C7ORF50 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C7ORF50 MUTATED                                          0
  C7ORF50 WILD-TYPE                                        3
D50V8, multiclass
                                                                   clus
vv                                                                  C7ORF50 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  C7ORF50 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V9, binary
                   cls
clus                  0   1
  C7ORF50 MUTATED     0  10
  C7ORF50 WILD-TYPE   5 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF50 MUTATED      0   10
  C7ORF50 WILD-TYPE    5  274
     clus
vv    C7ORF50 MUTATED C7ORF50 WILD-TYPE
  NO                0                 5
  YES              10               274
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C7ORF50 MUTATED     9   0   0   0
  C7ORF50 WILD-TYPE 218  10  10  24
D50V10, multiclass
    clus
vv   C7ORF50 MUTATED C7ORF50 WILD-TYPE
  R0               9               218
  R1               0                10
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C7ORF50 MUTATED       2                         0     7
  C7ORF50 WILD-TYPE    74                         4   161
D50V12, multiclass
                           clus
vv                          C7ORF50 MUTATED C7ORF50 WILD-TYPE
  ASIAN                                   2                74
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   7               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = DDC MUTATION ANALYSIS
D51V1, survival
               sevent
clus2             0   1
  DDC MUTATED     7   2
  DDC WILD-TYPE 174  78
  DDC MUTATED DDC WILD-TYPE 
            9           252 
  DDC MUTATED DDC WILD-TYPE 
            2            78 
$`DDC MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8363 TCGA-CD-8531 TCGA-CG-4305 
        6.97        34.68        23.93         0.26         0.10        15.95 
TCGA-CG-4455 TCGA-CG-5721 TCGA-HU-A4GX 
       12.03         6.02        10.19 

$`DDC WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       19.50        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.10         0.13         0.16         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        47.05        19.07         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  DDC MUTATED DDC WILD-TYPE 
          0.1           0.0 
  DDC MUTATED DDC WILD-TYPE 
        34.68        105.07 
  DDC MUTATED DDC WILD-TYPE 
        10.19         12.71 
[1] "0.1 - 34.7 (10.2)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.2"
D51V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDC MUTATED         0        0        2        2         1         0
  DDC WILD-TYPE       1        9       25       24        30        44
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DDC MUTATED           0          2          0          1        1
  DDC WILD-TYPE         3         47         36         23       23
D51V3, multiclass
            clus
vv           DDC MUTATED DDC WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             9
  STAGE IB             2            25
  STAGE II             2            24
  STAGE IIA            1            30
  STAGE IIB            0            44
  STAGE III            0             3
  STAGE IIIA           2            47
  STAGE IIIB           0            36
  STAGE IIIC           1            23
  STAGE IV             1            23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  DDC MUTATED     0   4   3   2
  DDC WILD-TYPE  11  68 119  73
D51V4, multiclass
    clus
vv   DDC MUTATED DDC WILD-TYPE
  T1           0            11
  T2           4            68
  T3           3           119
  T4           2            73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  DDC MUTATED    3  5  1  0
  DDC WILD-TYPE 90 76 49 53
D51V5, multiclass
    clus
vv   DDC MUTATED DDC WILD-TYPE
  N0           3            90
  N1           5            76
  N2           1            49
  N3           0            53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
               cls
clus              0   1
  DDC MUTATED     8   0
  DDC WILD-TYPE 249  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  DDC MUTATED      8    0
  DDC WILD-TYPE  249   18
   clus
vv  DDC MUTATED DDC WILD-TYPE
  0           8           249
  1           0            18
[1] 2 2
[1] FALSE
D51V7, binary
               cls
clus              0   1
  DDC MUTATED     5   4
  DDC WILD-TYPE 105 175
[1] "tbl2"
               cls
clus            [,1] [,2]
  DDC MUTATED      5    4
  DDC WILD-TYPE  105  175
        clus
vv       DDC MUTATED DDC WILD-TYPE
  FEMALE           5           105
  MALE             4           175
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DDC MUTATED                                       2
  DDC WILD-TYPE                                    48
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DDC MUTATED                                                        5
  DDC WILD-TYPE                                                    130
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DDC MUTATED                                                                   1
  DDC WILD-TYPE                                                                39
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DDC MUTATED                                                  0
  DDC WILD-TYPE                                               38
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DDC MUTATED                                                          1
  DDC WILD-TYPE                                                       15
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DDC MUTATED                                                           0
  DDC WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DDC MUTATED                                          0
  DDC WILD-TYPE                                        3
D51V8, multiclass
                                                                   clus
vv                                                                  DDC MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  DDC WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V9, binary
               cls
clus              0   1
  DDC MUTATED     0   9
  DDC WILD-TYPE   5 275
[1] "tbl2"
               cls
clus            [,1] [,2]
  DDC MUTATED      0    9
  DDC WILD-TYPE    5  275
     clus
vv    DDC MUTATED DDC WILD-TYPE
  NO            0             5
  YES           9           275
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  DDC MUTATED     8   0   0   1
  DDC WILD-TYPE 219  10  10  23
D51V10, multiclass
    clus
vv   DDC MUTATED DDC WILD-TYPE
  R0           8           219
  R1           0            10
  R2           0            10
  RX           1            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDC MUTATED       2                         0     4
  DDC WILD-TYPE    74                         4   164
D51V12, multiclass
                           clus
vv                          DDC MUTATED DDC WILD-TYPE
  ASIAN                               2            74
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                               4           164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = ADAM28 MUTATION ANALYSIS
D52V1, survival
                  sevent
clus2                0   1
  ADAM28 MUTATED     9   3
  ADAM28 WILD-TYPE 172  77
  ADAM28 MUTATED ADAM28 WILD-TYPE 
              12              249 
  ADAM28 MUTATED ADAM28 WILD-TYPE 
               3               77 
$`ADAM28 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8372 TCGA-BR-8487 TCGA-CG-4306 
        6.97        34.68        32.78        19.17         1.12         1.02 
TCGA-CG-5728 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-HU-A4G8 TCGA-HU-A4G9 
       65.10        16.24        72.23        21.27        11.84        24.20 

$`ADAM28 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-FP-7735 
       13.78        14.76         0.62         7.99        14.47         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.30         5.59        12.30         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  ADAM28 MUTATED ADAM28 WILD-TYPE 
            1.02             0.00 
  ADAM28 MUTATED ADAM28 WILD-TYPE 
           72.23           105.07 
  ADAM28 MUTATED ADAM28 WILD-TYPE 
           20.22            12.56 
[1] "1.0 - 72.2 (20.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.4"
D52V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ADAM28 MUTATED         0        2        1        0         3         1
  ADAM28 WILD-TYPE       1        7       26       26        28        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAM28 MUTATED           0          2          2          1        2
  ADAM28 WILD-TYPE         3         47         34         23       22
D52V3, multiclass
            clus
vv           ADAM28 MUTATED ADAM28 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                2                7
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               3               28
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              2               34
  STAGE IIIC              1               23
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ADAM28 MUTATED     1   2   7   4
  ADAM28 WILD-TYPE  10  70 115  71
D52V4, multiclass
    clus
vv   ADAM28 MUTATED ADAM28 WILD-TYPE
  T1              1               10
  T2              2               70
  T3              7              115
  T4              4               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ADAM28 MUTATED    7  3  2  2
  ADAM28 WILD-TYPE 86 78 48 51
D52V5, multiclass
    clus
vv   ADAM28 MUTATED ADAM28 WILD-TYPE
  N0              7               86
  N1              3               78
  N2              2               48
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                  cls
clus                 0   1
  ADAM28 MUTATED    11   1
  ADAM28 WILD-TYPE 246  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM28 MUTATED     11    1
  ADAM28 WILD-TYPE  246   17
   clus
vv  ADAM28 MUTATED ADAM28 WILD-TYPE
  0             11              246
  1              1               17
[1] 2 2
[1] FALSE
D52V7, binary
                  cls
clus                 0   1
  ADAM28 MUTATED     8   6
  ADAM28 WILD-TYPE 102 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM28 MUTATED      8    6
  ADAM28 WILD-TYPE  102  173
        clus
vv       ADAM28 MUTATED ADAM28 WILD-TYPE
  FEMALE              8              102
  MALE                6              173
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ADAM28 MUTATED                                       1
  ADAM28 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ADAM28 MUTATED                                                       10
  ADAM28 WILD-TYPE                                                    125
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ADAM28 MUTATED                                                                   1
  ADAM28 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ADAM28 MUTATED                                                  1
  ADAM28 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ADAM28 MUTATED                                                          1
  ADAM28 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ADAM28 MUTATED                                                           0
  ADAM28 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ADAM28 MUTATED                                          0
  ADAM28 WILD-TYPE                                        3
D52V8, multiclass
                                                                   clus
vv                                                                  ADAM28 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ADAM28 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V9, binary
                  cls
clus                 0   1
  ADAM28 MUTATED     0  14
  ADAM28 WILD-TYPE   5 270
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM28 MUTATED      0   14
  ADAM28 WILD-TYPE    5  270
     clus
vv    ADAM28 MUTATED ADAM28 WILD-TYPE
  NO               0                5
  YES             14              270
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ADAM28 MUTATED     9   0   1   3
  ADAM28 WILD-TYPE 218  10   9  21
D52V10, multiclass
    clus
vv   ADAM28 MUTATED ADAM28 WILD-TYPE
  R0              9              218
  R1              0               10
  R2              1                9
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ADAM28 MUTATED       2                         1     9
  ADAM28 WILD-TYPE    74                         3   159
D52V12, multiclass
                           clus
vv                          ADAM28 MUTATED ADAM28 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  9              159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = IWS1 MUTATION ANALYSIS
D53V1, survival
                sevent
clus2              0   1
  IWS1 MUTATED     7   2
  IWS1 WILD-TYPE 174  78
  IWS1 MUTATED IWS1 WILD-TYPE 
             9            252 
  IWS1 MUTATED IWS1 WILD-TYPE 
             2             78 
$`IWS1 MUTATED`
TCGA-BR-4184 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8487 TCGA-CG-4465 TCGA-CG-5723 
        6.97        12.26         6.18         1.12         9.01       105.07 
TCGA-D7-A4YX TCGA-HU-A4GU TCGA-HU-A4H3 
       15.16         6.25        19.36 

$`IWS1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  IWS1 MUTATED IWS1 WILD-TYPE 
          1.12           0.00 
  IWS1 MUTATED IWS1 WILD-TYPE 
        105.07          79.07 
  IWS1 MUTATED IWS1 WILD-TYPE 
          9.01          12.71 
[1] "1.1 - 105.1 (9.0)" "0.0 - 79.1 (12.7)"
[1] "hr=" "1.7"
D53V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IWS1 MUTATED         0        0        0        2         2         3
  IWS1 WILD-TYPE       1        9       27       24        29        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IWS1 MUTATED           0          2          0          1        1
  IWS1 WILD-TYPE         3         47         36         23       23
D53V3, multiclass
            clus
vv           IWS1 MUTATED IWS1 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              2             24
  STAGE IIA             2             29
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            0             36
  STAGE IIIC            1             23
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IWS1 MUTATED     1   1   6   4
  IWS1 WILD-TYPE  10  71 116  71
D53V4, multiclass
    clus
vv   IWS1 MUTATED IWS1 WILD-TYPE
  T1            1             10
  T2            1             71
  T3            6            116
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  IWS1 MUTATED    5  4  0  2
  IWS1 WILD-TYPE 88 77 50 51
D53V5, multiclass
    clus
vv   IWS1 MUTATED IWS1 WILD-TYPE
  N0            5             88
  N1            4             77
  N2            0             50
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                cls
clus               0   1
  IWS1 MUTATED    10   1
  IWS1 WILD-TYPE 247  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  IWS1 MUTATED     10    1
  IWS1 WILD-TYPE  247   17
   clus
vv  IWS1 MUTATED IWS1 WILD-TYPE
  0           10            247
  1            1             17
[1] 2 2
[1] FALSE
D53V7, binary
                cls
clus               0   1
  IWS1 MUTATED     6   6
  IWS1 WILD-TYPE 104 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  IWS1 MUTATED      6    6
  IWS1 WILD-TYPE  104  173
        clus
vv       IWS1 MUTATED IWS1 WILD-TYPE
  FEMALE            6            104
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  IWS1 MUTATED                                       4
  IWS1 WILD-TYPE                                    46
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IWS1 MUTATED                                                        7
  IWS1 WILD-TYPE                                                    128
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IWS1 MUTATED                                                                   1
  IWS1 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  IWS1 MUTATED                                                  0
  IWS1 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  IWS1 MUTATED                                                          0
  IWS1 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  IWS1 MUTATED                                                           0
  IWS1 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  IWS1 MUTATED                                          0
  IWS1 WILD-TYPE                                        3
D53V8, multiclass
                                                                   clus
vv                                                                  IWS1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  IWS1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V9, binary
                cls
clus               0   1
  IWS1 MUTATED     0  12
  IWS1 WILD-TYPE   5 272
[1] "tbl2"
                cls
clus             [,1] [,2]
  IWS1 MUTATED      0   12
  IWS1 WILD-TYPE    5  272
     clus
vv    IWS1 MUTATED IWS1 WILD-TYPE
  NO             0              5
  YES           12            272
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IWS1 MUTATED     8   0   1   3
  IWS1 WILD-TYPE 219  10   9  21
D53V10, multiclass
    clus
vv   IWS1 MUTATED IWS1 WILD-TYPE
  R0            8            219
  R1            0             10
  R2            1              9
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IWS1 MUTATED       3                         0     7
  IWS1 WILD-TYPE    73                         4   161
D53V12, multiclass
                           clus
vv                          IWS1 MUTATED IWS1 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                7            161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = MUC6 MUTATION ANALYSIS
D54V1, survival
                sevent
clus2              0   1
  MUC6 MUTATED    26   6
  MUC6 WILD-TYPE 155  74
  MUC6 MUTATED MUC6 WILD-TYPE 
            32            229 
  MUC6 MUTATED MUC6 WILD-TYPE 
             6             74 
$`MUC6 MUTATED`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6801 TCGA-BR-7703 
       26.70         6.61         6.97        34.68        21.11        24.76 
TCGA-BR-7723 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8382 TCGA-BR-8487 
       28.73        12.26        20.55        19.50        15.85         1.12 
TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-CD-8525 TCGA-CD-8536 
       13.45        15.81        20.42        11.57         0.07         0.10 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-4475 TCGA-CG-5721 
        6.58        12.20         0.10         1.02        22.98         6.02 
TCGA-CG-5723 TCGA-D7-6526 TCGA-D7-8578 TCGA-FP-8211 TCGA-FP-8631 TCGA-HU-A4G2 
      105.07        17.19        21.14        13.58         0.56        24.30 
TCGA-HU-A4H3 TCGA-IN-8663 
       19.36         3.39 

$`MUC6 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
       11.70         4.64         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       18.05        19.89         8.98        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       12.82         9.21        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 
       17.49        14.43         0.69         9.60         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       15.81         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        19.36        13.51        20.65         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.07         0.39         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 
        0.13         0.16         0.10         0.10         0.13         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MJ TCGA-CG-4300 
        9.34        11.31        12.43        11.61        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
       36.00         1.02         0.99         0.99        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 
       18.54        18.61        17.85        13.35        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 
       16.80        19.50        17.19        18.21        14.66        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        5.03        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 
       14.17        11.41        12.10        10.62         0.76         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IP-7968 
        2.53 

  MUC6 MUTATED MUC6 WILD-TYPE 
          0.07           0.00 
  MUC6 MUTATED MUC6 WILD-TYPE 
        105.07          79.07 
  MUC6 MUTATED MUC6 WILD-TYPE 
        14.695         12.560 
[1] "0.1 - 105.1 (14.7)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "2"  
D54V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MUC6 MUTATED         0        1        2        2         5         7
  MUC6 WILD-TYPE       1        8       25       24        26        37
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MUC6 MUTATED           0          6          3          4        3
  MUC6 WILD-TYPE         3         43         33         20       21
D54V3, multiclass
            clus
vv           MUC6 MUTATED MUC6 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              2             25
  STAGE II              2             24
  STAGE IIA             5             26
  STAGE IIB             7             37
  STAGE III             0              3
  STAGE IIIA            6             43
  STAGE IIIB            3             33
  STAGE IIIC            4             20
  STAGE IV              3             21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MUC6 MUTATED     1   4  18  10
  MUC6 WILD-TYPE  10  68 104  65
D54V4, multiclass
    clus
vv   MUC6 MUTATED MUC6 WILD-TYPE
  T1            1             10
  T2            4             68
  T3           18            104
  T4           10             65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  MUC6 MUTATED   13 10  6  5
  MUC6 WILD-TYPE 80 71 44 48
D54V5, multiclass
    clus
vv   MUC6 MUTATED MUC6 WILD-TYPE
  N0           13             80
  N1           10             71
  N2            6             44
  N3            5             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                cls
clus               0   1
  MUC6 MUTATED    29   2
  MUC6 WILD-TYPE 228  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED     29    2
  MUC6 WILD-TYPE  228   16
   clus
vv  MUC6 MUTATED MUC6 WILD-TYPE
  0           29            228
  1            2             16
[1] 2 2
[1] FALSE
D54V7, binary
                cls
clus               0   1
  MUC6 MUTATED    16  18
  MUC6 WILD-TYPE  94 161
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED     16   18
  MUC6 WILD-TYPE   94  161
        clus
vv       MUC6 MUTATED MUC6 WILD-TYPE
  FEMALE           16             94
  MALE             18            161
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MUC6 MUTATED                                       4
  MUC6 WILD-TYPE                                    46
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MUC6 MUTATED                                                       23
  MUC6 WILD-TYPE                                                    112
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MUC6 MUTATED                                                                   2
  MUC6 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MUC6 MUTATED                                                  2
  MUC6 WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MUC6 MUTATED                                                          1
  MUC6 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MUC6 MUTATED                                                           1
  MUC6 WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MUC6 MUTATED                                          0
  MUC6 WILD-TYPE                                        3
D54V8, multiclass
                                                                   clus
vv                                                                  MUC6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  MUC6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       112
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V9, binary
                cls
clus               0   1
  MUC6 MUTATED     0  34
  MUC6 WILD-TYPE   5 250
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED      0   34
  MUC6 WILD-TYPE    5  250
     clus
vv    MUC6 MUTATED MUC6 WILD-TYPE
  NO             0              5
  YES           34            250
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MUC6 MUTATED    25   1   1   4
  MUC6 WILD-TYPE 202   9   9  20
D54V10, multiclass
    clus
vv   MUC6 MUTATED MUC6 WILD-TYPE
  R0           25            202
  R1            1              9
  R2            1              9
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MUC6 MUTATED       8                         0    22
  MUC6 WILD-TYPE    68                         4   146
D54V12, multiclass
                           clus
vv                          MUC6 MUTATED MUC6 WILD-TYPE
  ASIAN                                8             68
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               22            146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = GXYLT1 MUTATION ANALYSIS
D55V1, survival
                  sevent
clus2                0   1
  GXYLT1 MUTATED     9   3
  GXYLT1 WILD-TYPE 172  77
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
              12              249 
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
               3               77 
$`GXYLT1 MUTATED`
TCGA-B7-5816 TCGA-BR-6802 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8382 
       26.70        30.90        19.50         0.26        19.17        15.85 
TCGA-CD-8529 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-5733 TCGA-F1-6874 
        0.13         6.58         0.10        12.62        21.07        14.47 

$`GXYLT1 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        6.18        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
       14.04         3.32        11.80        14.79         0.26         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
        0.07         0.07         0.07         0.07         0.10         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 
       11.31        12.43        11.61        12.20        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       16.24        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
             0.1              0.0 
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
           30.90           105.07 
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
           15.16            12.56 
[1] "0.1 - 30.9 (15.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D55V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GXYLT1 MUTATED         0        0        3        0         1         1
  GXYLT1 WILD-TYPE       1        9       24       26        30        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GXYLT1 MUTATED           0          2          1          3        1
  GXYLT1 WILD-TYPE         3         47         35         21       23
D55V3, multiclass
            clus
vv           GXYLT1 MUTATED GXYLT1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                3               24
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              1               35
  STAGE IIIC              3               21
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GXYLT1 MUTATED     0   4   3   5
  GXYLT1 WILD-TYPE  11  68 119  70
D55V4, multiclass
    clus
vv   GXYLT1 MUTATED GXYLT1 WILD-TYPE
  T1              0               11
  T2              4               68
  T3              3              119
  T4              5               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  GXYLT1 MUTATED    6  1  3  2
  GXYLT1 WILD-TYPE 87 80 47 51
D55V5, multiclass
    clus
vv   GXYLT1 MUTATED GXYLT1 WILD-TYPE
  N0              6               87
  N1              1               80
  N2              3               47
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                  cls
clus                 0   1
  GXYLT1 MUTATED    11   1
  GXYLT1 WILD-TYPE 246  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GXYLT1 MUTATED     11    1
  GXYLT1 WILD-TYPE  246   17
   clus
vv  GXYLT1 MUTATED GXYLT1 WILD-TYPE
  0             11              246
  1              1               17
[1] 2 2
[1] FALSE
D55V7, binary
                  cls
clus                 0   1
  GXYLT1 MUTATED     5   7
  GXYLT1 WILD-TYPE 105 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GXYLT1 MUTATED      5    7
  GXYLT1 WILD-TYPE  105  172
        clus
vv       GXYLT1 MUTATED GXYLT1 WILD-TYPE
  FEMALE              5              105
  MALE                7              172
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GXYLT1 MUTATED                                       2
  GXYLT1 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GXYLT1 MUTATED                                                        7
  GXYLT1 WILD-TYPE                                                    128
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GXYLT1 MUTATED                                                                   2
  GXYLT1 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GXYLT1 MUTATED                                                  0
  GXYLT1 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GXYLT1 MUTATED                                                          1
  GXYLT1 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GXYLT1 MUTATED                                                           0
  GXYLT1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GXYLT1 MUTATED                                          0
  GXYLT1 WILD-TYPE                                        3
D55V8, multiclass
                                                                   clus
vv                                                                  GXYLT1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  GXYLT1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V9, binary
                  cls
clus                 0   1
  GXYLT1 MUTATED     0  12
  GXYLT1 WILD-TYPE   5 272
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GXYLT1 MUTATED      0   12
  GXYLT1 WILD-TYPE    5  272
     clus
vv    GXYLT1 MUTATED GXYLT1 WILD-TYPE
  NO               0                5
  YES             12              272
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GXYLT1 MUTATED     9   0   0   0
  GXYLT1 WILD-TYPE 218  10  10  24
D55V10, multiclass
    clus
vv   GXYLT1 MUTATED GXYLT1 WILD-TYPE
  R0              9              218
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GXYLT1 MUTATED       4                         0     7
  GXYLT1 WILD-TYPE    72                         4   161
D55V12, multiclass
                           clus
vv                          GXYLT1 MUTATED GXYLT1 WILD-TYPE
  ASIAN                                  4               72
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  7              161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = HLA-C MUTATION ANALYSIS
D56V1, survival
                 sevent
clus2               0   1
  HLA-C MUTATED     5   5
  HLA-C WILD-TYPE 176  75
  HLA-C MUTATED HLA-C WILD-TYPE 
             10             251 
  HLA-C MUTATED HLA-C WILD-TYPE 
              5              75 
$`HLA-C MUTATED`
TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8591 TCGA-BR-A4CS TCGA-CG-4306 
       12.26         0.26        19.17        13.45         1.48         1.02 
TCGA-CG-4465 TCGA-CG-5721 TCGA-HU-A4GQ TCGA-HU-A4GT 
        9.01         6.02         0.10         6.51 

$`HLA-C WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        19.50        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08        22.26        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
       29.98        47.05        19.07        12.03         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  HLA-C MUTATED HLA-C WILD-TYPE 
            0.1             0.0 
  HLA-C MUTATED HLA-C WILD-TYPE 
          19.17          105.07 
  HLA-C MUTATED HLA-C WILD-TYPE 
          6.265          12.790 
[1] "0.1 - 19.2 (6.3)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "3.8"
D56V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HLA-C MUTATED         0        0        2        0         1         1
  HLA-C WILD-TYPE       1        9       25       26        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HLA-C MUTATED           0          1          0          4        3
  HLA-C WILD-TYPE         3         48         36         20       21
D56V3, multiclass
            clus
vv           HLA-C MUTATED HLA-C WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             4              20
  STAGE IV               3              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HLA-C MUTATED     0   2   2   8
  HLA-C WILD-TYPE  11  70 120  67
D56V4, multiclass
    clus
vv   HLA-C MUTATED HLA-C WILD-TYPE
  T1             0              11
  T2             2              70
  T3             2             120
  T4             8              67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  HLA-C MUTATED    5  2  2  4
  HLA-C WILD-TYPE 88 79 48 49
D56V5, multiclass
    clus
vv   HLA-C MUTATED HLA-C WILD-TYPE
  N0             5              88
  N1             2              79
  N2             2              48
  N3             4              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                 cls
clus                0   1
  HLA-C MUTATED    11   2
  HLA-C WILD-TYPE 246  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-C MUTATED     11    2
  HLA-C WILD-TYPE  246   16
   clus
vv  HLA-C MUTATED HLA-C WILD-TYPE
  0            11             246
  1             2              16
[1] 2 2
[1] FALSE
D56V7, binary
                 cls
clus                0   1
  HLA-C MUTATED     6   7
  HLA-C WILD-TYPE 104 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-C MUTATED      6    7
  HLA-C WILD-TYPE  104  172
        clus
vv       HLA-C MUTATED HLA-C WILD-TYPE
  FEMALE             6             104
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  HLA-C MUTATED                                       1
  HLA-C WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HLA-C MUTATED                                                        8
  HLA-C WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HLA-C MUTATED                                                                   2
  HLA-C WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  HLA-C MUTATED                                                  2
  HLA-C WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  HLA-C MUTATED                                                          0
  HLA-C WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  HLA-C MUTATED                                                           0
  HLA-C WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  HLA-C MUTATED                                          0
  HLA-C WILD-TYPE                                        3
D56V8, multiclass
                                                                   clus
vv                                                                  HLA-C MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  HLA-C WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V9, binary
                 cls
clus                0   1
  HLA-C MUTATED     0  13
  HLA-C WILD-TYPE   5 271
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-C MUTATED      0   13
  HLA-C WILD-TYPE    5  271
     clus
vv    HLA-C MUTATED HLA-C WILD-TYPE
  NO              0               5
  YES            13             271
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HLA-C MUTATED     9   0   2   2
  HLA-C WILD-TYPE 218  10   8  22
D56V10, multiclass
    clus
vv   HLA-C MUTATED HLA-C WILD-TYPE
  R0             9             218
  R1             0              10
  R2             2               8
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HLA-C MUTATED       2                         0     7
  HLA-C WILD-TYPE    74                         4   161
D56V12, multiclass
                           clus
vv                          HLA-C MUTATED HLA-C WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 7             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = PRSS36 MUTATION ANALYSIS
D57V1, survival
                  sevent
clus2                0   1
  PRSS36 MUTATED     5   4
  PRSS36 WILD-TYPE 176  76
  PRSS36 MUTATED PRSS36 WILD-TYPE 
               9              252 
  PRSS36 MUTATED PRSS36 WILD-TYPE 
               4               76 
$`PRSS36 MUTATED`
TCGA-BR-4201 TCGA-BR-6566 TCGA-BR-8361 TCGA-BR-A4QL TCGA-CG-4305 TCGA-CG-4306 
       30.90        32.78        19.50        11.57        15.95         1.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-HU-A4GQ 
       28.96        65.10         0.10 

$`PRSS36 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       27.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  PRSS36 MUTATED PRSS36 WILD-TYPE 
             0.1              0.0 
  PRSS36 MUTATED PRSS36 WILD-TYPE 
           65.10           105.07 
  PRSS36 MUTATED PRSS36 WILD-TYPE 
          19.500           12.575 
[1] "0.1 - 65.1 (19.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D57V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRSS36 MUTATED         0        1        2        1         1         0
  PRSS36 WILD-TYPE       1        8       25       25        30        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRSS36 MUTATED           0          0          1          2        1
  PRSS36 WILD-TYPE         3         49         35         22       23
D57V3, multiclass
            clus
vv           PRSS36 MUTATED PRSS36 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                2               25
  STAGE II                1               25
  STAGE IIA               1               30
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              1               35
  STAGE IIIC              2               22
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PRSS36 MUTATED     1   4   3   2
  PRSS36 WILD-TYPE  10  68 119  73
D57V4, multiclass
    clus
vv   PRSS36 MUTATED PRSS36 WILD-TYPE
  T1              1               10
  T2              4               68
  T3              3              119
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  PRSS36 MUTATED    4  2  3  1
  PRSS36 WILD-TYPE 89 79 47 52
D57V5, multiclass
    clus
vv   PRSS36 MUTATED PRSS36 WILD-TYPE
  N0              4               89
  N1              2               79
  N2              3               47
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                  cls
clus                 0   1
  PRSS36 MUTATED    10   1
  PRSS36 WILD-TYPE 247  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS36 MUTATED     10    1
  PRSS36 WILD-TYPE  247   17
   clus
vv  PRSS36 MUTATED PRSS36 WILD-TYPE
  0             10              247
  1              1               17
[1] 2 2
[1] FALSE
D57V7, binary
                  cls
clus                 0   1
  PRSS36 MUTATED     5   6
  PRSS36 WILD-TYPE 105 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS36 MUTATED      5    6
  PRSS36 WILD-TYPE  105  173
        clus
vv       PRSS36 MUTATED PRSS36 WILD-TYPE
  FEMALE              5              105
  MALE                6              173
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PRSS36 MUTATED                                       0
  PRSS36 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PRSS36 MUTATED                                                        7
  PRSS36 WILD-TYPE                                                    128
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PRSS36 MUTATED                                                                   3
  PRSS36 WILD-TYPE                                                                37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PRSS36 MUTATED                                                  1
  PRSS36 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PRSS36 MUTATED                                                          0
  PRSS36 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PRSS36 MUTATED                                                           0
  PRSS36 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PRSS36 MUTATED                                          0
  PRSS36 WILD-TYPE                                        3
D57V8, multiclass
                                                                   clus
vv                                                                  PRSS36 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  PRSS36 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V9, binary
                  cls
clus                 0   1
  PRSS36 MUTATED     0  11
  PRSS36 WILD-TYPE   5 273
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS36 MUTATED      0   11
  PRSS36 WILD-TYPE    5  273
     clus
vv    PRSS36 MUTATED PRSS36 WILD-TYPE
  NO               0                5
  YES             11              273
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PRSS36 MUTATED     8   0   1   2
  PRSS36 WILD-TYPE 219  10   9  22
D57V10, multiclass
    clus
vv   PRSS36 MUTATED PRSS36 WILD-TYPE
  R0              8              219
  R1              0               10
  R2              1                9
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRSS36 MUTATED       1                         0     5
  PRSS36 WILD-TYPE    75                         4   163
D57V12, multiclass
                           clus
vv                          PRSS36 MUTATED PRSS36 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  5              163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = ZFHX4 MUTATION ANALYSIS
D58V1, survival
                 sevent
clus2               0   1
  ZFHX4 MUTATED    35  10
  ZFHX4 WILD-TYPE 146  70
  ZFHX4 MUTATED ZFHX4 WILD-TYPE 
             45             216 
  ZFHX4 MUTATED ZFHX4 WILD-TYPE 
             10              70 
$`ZFHX4 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6706 TCGA-BR-7707 
       26.70         6.97        30.90        34.68        18.05        23.93 
TCGA-BR-7851 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8368 
       12.43        14.43        12.26        20.55        19.50         4.31 
TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 
       15.85         5.39         1.12        15.81        13.45        15.81 
TCGA-BR-A4QL TCGA-CD-5800 TCGA-CD-A48C TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4305 
       11.57        13.15        11.61        12.62        20.02        15.95 
TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-5717 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 
       19.07         9.01         6.97         6.02       105.07        65.10 
TCGA-CG-5733 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-A4YY TCGA-FP-A4BE 
       21.07        10.26        12.79        10.55        13.78        11.08 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G8 TCGA-HU-A4GP TCGA-HU-A4GT 
       11.41        12.10        10.62        11.84         8.98         6.51 
TCGA-HU-A4GX TCGA-HU-A4H8 TCGA-HU-A4HD 
       10.19         8.88        27.42 

$`ZFHX4 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 
       11.70         6.61         4.64         7.43        18.35         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       12.82         9.21        24.76        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       17.49         0.69         9.60         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
       16.31         2.20        15.58         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8484 
       11.80        19.17        14.79         0.26         3.72        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        9.21        20.22        12.79         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4301 TCGA-CG-4304 
       12.43         6.58        12.20         0.10         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       29.98        47.05        12.03         0.00        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       22.98        30.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       12.03        28.96        79.07         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
       18.54        18.61        17.85        13.35        17.19        15.22 
TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       15.98        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       16.44         5.92        15.16        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GU 
       22.75        25.81        11.77        29.98         0.10         6.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        9.67        21.21         3.45        18.81         3.39         2.53 

  ZFHX4 MUTATED ZFHX4 WILD-TYPE 
           1.12            0.00 
  ZFHX4 MUTATED ZFHX4 WILD-TYPE 
         105.07           79.07 
  ZFHX4 MUTATED ZFHX4 WILD-TYPE 
         12.620          12.625 
[1] "1.1 - 105.1 (12.6)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.7"
D58V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZFHX4 MUTATED         1        0        7        6         6         7
  ZFHX4 WILD-TYPE       0        9       20       20        25        37
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFHX4 MUTATED           1          8          5          4        4
  ZFHX4 WILD-TYPE         2         41         31         20       20
D58V3, multiclass
            clus
vv           ZFHX4 MUTATED ZFHX4 WILD-TYPE
  STAGE I                1               0
  STAGE IA               0               9
  STAGE IB               7              20
  STAGE II               6              20
  STAGE IIA              6              25
  STAGE IIB              7              37
  STAGE III              1               2
  STAGE IIIA             8              41
  STAGE IIIB             5              31
  STAGE IIIC             4              20
  STAGE IV               4              20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZFHX4 MUTATED     2  16  16  17
  ZFHX4 WILD-TYPE   9  56 106  58
D58V4, multiclass
    clus
vv   ZFHX4 MUTATED ZFHX4 WILD-TYPE
  T1             2               9
  T2            16              56
  T3            16             106
  T4            17              58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ZFHX4 MUTATED   18 16  9  7
  ZFHX4 WILD-TYPE 75 65 41 46
D58V5, multiclass
    clus
vv   ZFHX4 MUTATED ZFHX4 WILD-TYPE
  N0            18              75
  N1            16              65
  N2             9              41
  N3             7              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                 cls
clus                0   1
  ZFHX4 MUTATED    48   2
  ZFHX4 WILD-TYPE 209  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX4 MUTATED     48    2
  ZFHX4 WILD-TYPE  209   16
   clus
vv  ZFHX4 MUTATED ZFHX4 WILD-TYPE
  0            48             209
  1             2              16
[1] 2 2
[1] FALSE
D58V7, binary
                 cls
clus                0   1
  ZFHX4 MUTATED    27  26
  ZFHX4 WILD-TYPE  83 153
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX4 MUTATED     27   26
  ZFHX4 WILD-TYPE   83  153
        clus
vv       ZFHX4 MUTATED ZFHX4 WILD-TYPE
  FEMALE            27              83
  MALE              26             153
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZFHX4 MUTATED                                       8
  ZFHX4 WILD-TYPE                                    42
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZFHX4 MUTATED                                                       29
  ZFHX4 WILD-TYPE                                                    106
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZFHX4 MUTATED                                                                   7
  ZFHX4 WILD-TYPE                                                                33
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZFHX4 MUTATED                                                  6
  ZFHX4 WILD-TYPE                                               32
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZFHX4 MUTATED                                                          1
  ZFHX4 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZFHX4 MUTATED                                                           2
  ZFHX4 WILD-TYPE                                                         4
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZFHX4 MUTATED                                          0
  ZFHX4 WILD-TYPE                                        3
D58V8, multiclass
                                                                   clus
vv                                                                  ZFHX4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       29
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ZFHX4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          42
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        106
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V9, binary
                 cls
clus                0   1
  ZFHX4 MUTATED     2  51
  ZFHX4 WILD-TYPE   3 233
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX4 MUTATED      2   51
  ZFHX4 WILD-TYPE    3  233
     clus
vv    ZFHX4 MUTATED ZFHX4 WILD-TYPE
  NO              2               3
  YES            51             233
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ZFHX4 MUTATED    42   0   1   7
  ZFHX4 WILD-TYPE 185  10   9  17
D58V10, multiclass
    clus
vv   ZFHX4 MUTATED ZFHX4 WILD-TYPE
  R0            42             185
  R1             0              10
  R2             1               9
  RX             7              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZFHX4 MUTATED      13                         2    28
  ZFHX4 WILD-TYPE    63                         2   140
D58V12, multiclass
                           clus
vv                          ZFHX4 MUTATED ZFHX4 WILD-TYPE
  ASIAN                                13              63
  BLACK OR AFRICAN AMERICAN             2               2
  WHITE                                28             140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = C6ORF89 MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  C6ORF89 MUTATED     7   1
  C6ORF89 WILD-TYPE 174  79
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
                8               253 
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
                1                79 
$`C6ORF89 MUTATED`
TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8591 TCGA-CD-A4MG TCGA-D7-A4YT TCGA-FP-A4BE 
       19.17        15.85        13.45         6.58        14.27        11.08 
TCGA-HU-A4G8 TCGA-HU-A4GT 
       11.84         6.51 

$`C6ORF89 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       11.80        14.79         0.26         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       17.19        18.21        14.66        21.14        20.91        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
             6.51              0.00 
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
            19.17            105.07 
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
           12.645            12.620 
[1] "6.5 - 19.2 (12.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.1"
D59V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C6ORF89 MUTATED         1        0        0        0         3         1
  C6ORF89 WILD-TYPE       0        9       27       26        28        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF89 MUTATED           0          1          0          3        0
  C6ORF89 WILD-TYPE         3         48         36         21       24
D59V3, multiclass
            clus
vv           C6ORF89 MUTATED C6ORF89 WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                 0                 9
  STAGE IB                 0                27
  STAGE II                 0                26
  STAGE IIA                3                28
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               0                36
  STAGE IIIC               3                21
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C6ORF89 MUTATED     1   1   4   3
  C6ORF89 WILD-TYPE  10  71 118  72
D59V4, multiclass
    clus
vv   C6ORF89 MUTATED C6ORF89 WILD-TYPE
  T1               1                10
  T2               1                71
  T3               4               118
  T4               3                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  C6ORF89 MUTATED    3  2  0  4
  C6ORF89 WILD-TYPE 90 79 50 49
D59V5, multiclass
    clus
vv   C6ORF89 MUTATED C6ORF89 WILD-TYPE
  N0               3                90
  N1               2                79
  N2               0                50
  N3               4                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                   cls
clus                  0   1
  C6ORF89 MUTATED     8   0
  C6ORF89 WILD-TYPE 249  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF89 MUTATED      8    0
  C6ORF89 WILD-TYPE  249   18
   clus
vv  C6ORF89 MUTATED C6ORF89 WILD-TYPE
  0               8               249
  1               0                18
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  C6ORF89 MUTATED     3   6
  C6ORF89 WILD-TYPE 107 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF89 MUTATED      3    6
  C6ORF89 WILD-TYPE  107  173
        clus
vv       C6ORF89 MUTATED C6ORF89 WILD-TYPE
  FEMALE               3               107
  MALE                 6               173
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C6ORF89 MUTATED                                       2
  C6ORF89 WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C6ORF89 MUTATED                                                        5
  C6ORF89 WILD-TYPE                                                    130
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C6ORF89 MUTATED                                                                   0
  C6ORF89 WILD-TYPE                                                                40
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C6ORF89 MUTATED                                                  2
  C6ORF89 WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C6ORF89 MUTATED                                                          0
  C6ORF89 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C6ORF89 MUTATED                                                           0
  C6ORF89 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C6ORF89 MUTATED                                          0
  C6ORF89 WILD-TYPE                                        3
D59V8, multiclass
                                                                   clus
vv                                                                  C6ORF89 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  C6ORF89 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V9, binary
                   cls
clus                  0   1
  C6ORF89 MUTATED     0   9
  C6ORF89 WILD-TYPE   5 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF89 MUTATED      0    9
  C6ORF89 WILD-TYPE    5  275
     clus
vv    C6ORF89 MUTATED C6ORF89 WILD-TYPE
  NO                0                 5
  YES               9               275
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C6ORF89 MUTATED     7   0   0   0
  C6ORF89 WILD-TYPE 220  10  10  24
D59V10, multiclass
    clus
vv   C6ORF89 MUTATED C6ORF89 WILD-TYPE
  R0               7               220
  R1               0                10
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C6ORF89 MUTATED       3                         2     4
  C6ORF89 WILD-TYPE    73                         2   164
D59V12, multiclass
                           clus
vv                          C6ORF89 MUTATED C6ORF89 WILD-TYPE
  ASIAN                                   3                73
  BLACK OR AFRICAN AMERICAN               2                 2
  WHITE                                   4               164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = SLC16A6 MUTATION ANALYSIS
D60V1, survival
                   sevent
clus2                 0   1
  SLC16A6 MUTATED     5   0
  SLC16A6 WILD-TYPE 176  80
  SLC16A6 MUTATED SLC16A6 WILD-TYPE 
                5               256 
  SLC16A6 MUTATED SLC16A6 WILD-TYPE 
                0                80 
$`SLC16A6 MUTATED`
TCGA-BR-7851 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8680 TCGA-HU-A4G8 
       12.43         0.95         4.31        15.81        11.84 

$`SLC16A6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  SLC16A6 MUTATED SLC16A6 WILD-TYPE 
             0.95              0.00 
  SLC16A6 MUTATED SLC16A6 WILD-TYPE 
            15.81            105.07 
  SLC16A6 MUTATED SLC16A6 WILD-TYPE 
            11.84             12.71 
[1] "0.9 - 15.8 (11.8)"  "0.0 - 105.1 (12.7)"
[1] "hr="     "9100000"
D60V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC16A6 MUTATED         0        0        1        1         1         2
  SLC16A6 WILD-TYPE       1        9       26       25        30        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC16A6 MUTATED           0          0          0          0        2
  SLC16A6 WILD-TYPE         3         49         36         24       22
D60V3, multiclass
            clus
vv           SLC16A6 MUTATED SLC16A6 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 1                25
  STAGE IIA                1                30
  STAGE IIB                2                42
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               0                36
  STAGE IIIC               0                24
  STAGE IV                 2                22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC16A6 MUTATED     0   2   2   3
  SLC16A6 WILD-TYPE  11  70 120  72
D60V4, multiclass
    clus
vv   SLC16A6 MUTATED SLC16A6 WILD-TYPE
  T1               0                11
  T2               2                70
  T3               2               120
  T4               3                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  SLC16A6 MUTATED    3  2  2  0
  SLC16A6 WILD-TYPE 90 79 48 53
D60V5, multiclass
    clus
vv   SLC16A6 MUTATED SLC16A6 WILD-TYPE
  N0               3                90
  N1               2                79
  N2               2                48
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                   cls
clus                  0   1
  SLC16A6 MUTATED     6   1
  SLC16A6 WILD-TYPE 251  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A6 MUTATED      6    1
  SLC16A6 WILD-TYPE  251   17
   clus
vv  SLC16A6 MUTATED SLC16A6 WILD-TYPE
  0               6               251
  1               1                17
[1] 2 2
[1] FALSE
D60V7, binary
                   cls
clus                  0   1
  SLC16A6 MUTATED     4   3
  SLC16A6 WILD-TYPE 106 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A6 MUTATED      4    3
  SLC16A6 WILD-TYPE  106  176
        clus
vv       SLC16A6 MUTATED SLC16A6 WILD-TYPE
  FEMALE               4               106
  MALE                 3               176
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SLC16A6 MUTATED                                       1
  SLC16A6 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC16A6 MUTATED                                                        3
  SLC16A6 WILD-TYPE                                                    132
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC16A6 MUTATED                                                                   1
  SLC16A6 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SLC16A6 MUTATED                                                  1
  SLC16A6 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SLC16A6 MUTATED                                                          1
  SLC16A6 WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SLC16A6 MUTATED                                                           0
  SLC16A6 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SLC16A6 MUTATED                                          0
  SLC16A6 WILD-TYPE                                        3
D60V8, multiclass
                                                                   clus
vv                                                                  SLC16A6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  SLC16A6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V9, binary
                   cls
clus                  0   1
  SLC16A6 MUTATED     1   6
  SLC16A6 WILD-TYPE   4 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A6 MUTATED      1    6
  SLC16A6 WILD-TYPE    4  278
     clus
vv    SLC16A6 MUTATED SLC16A6 WILD-TYPE
  NO                1                 4
  YES               6               278
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC16A6 MUTATED     5   0   0   1
  SLC16A6 WILD-TYPE 222  10  10  23
D60V10, multiclass
    clus
vv   SLC16A6 MUTATED SLC16A6 WILD-TYPE
  R0               5               222
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC16A6 MUTATED       2                         0     4
  SLC16A6 WILD-TYPE    74                         4   164
D60V12, multiclass
                           clus
vv                          SLC16A6 MUTATED SLC16A6 WILD-TYPE
  ASIAN                                   2                74
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   4               164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = PAFAH1B1 MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  PAFAH1B1 MUTATED     7   2
  PAFAH1B1 WILD-TYPE 174  78
  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE 
                 9                252 
  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE 
                 2                 78 
$`PAFAH1B1 MUTATED`
TCGA-BR-6452 TCGA-BR-8372 TCGA-BR-8680 TCGA-CG-4306 TCGA-CG-5721 TCGA-FP-A4BE 
       34.68        19.17        15.81         1.02         6.02        11.08 
TCGA-HU-8602 TCGA-HU-A4GN TCGA-HU-A4GQ 
       11.41        29.98         0.10 

$`PAFAH1B1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE 
               0.1                0.0 
  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE 
             34.68             105.07 
  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE 
             11.41              12.64 
[1] "0.1 - 34.7 (11.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.5"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PAFAH1B1 MUTATED         1        0        0        0         3         1
  PAFAH1B1 WILD-TYPE       0        9       27       26        28        43
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PAFAH1B1 MUTATED           0          0          0          2        3
  PAFAH1B1 WILD-TYPE         3         49         36         22       21
D61V3, multiclass
            clus
vv           PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                  0                  9
  STAGE IB                  0                 27
  STAGE II                  0                 26
  STAGE IIA                 3                 28
  STAGE IIB                 1                 43
  STAGE III                 0                  3
  STAGE IIIA                0                 49
  STAGE IIIB                0                 36
  STAGE IIIC                2                 22
  STAGE IV                  3                 21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  PAFAH1B1 MUTATED     2   1   3   5
  PAFAH1B1 WILD-TYPE   9  71 119  70
D61V4, multiclass
    clus
vv   PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  T1                2                  9
  T2                1                 71
  T3                3                119
  T4                5                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  PAFAH1B1 MUTATED    3  3  3  1
  PAFAH1B1 WILD-TYPE 90 78 47 52
D61V5, multiclass
    clus
vv   PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  N0                3                 90
  N1                3                 78
  N2                3                 47
  N3                1                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                    cls
clus                   0   1
  PAFAH1B1 MUTATED     9   2
  PAFAH1B1 WILD-TYPE 248  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PAFAH1B1 MUTATED      9    2
  PAFAH1B1 WILD-TYPE  248   16
   clus
vv  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  0                9                248
  1                2                 16
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  PAFAH1B1 MUTATED     4   8
  PAFAH1B1 WILD-TYPE 106 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PAFAH1B1 MUTATED      4    8
  PAFAH1B1 WILD-TYPE  106  171
        clus
vv       PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  FEMALE                4                106
  MALE                  8                171
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PAFAH1B1 MUTATED                                       1
  PAFAH1B1 WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PAFAH1B1 MUTATED                                                        7
  PAFAH1B1 WILD-TYPE                                                    128
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PAFAH1B1 MUTATED                                                                   1
  PAFAH1B1 WILD-TYPE                                                                39
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PAFAH1B1 MUTATED                                                  3
  PAFAH1B1 WILD-TYPE                                               35
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PAFAH1B1 MUTATED                                                          0
  PAFAH1B1 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PAFAH1B1 MUTATED                                                           0
  PAFAH1B1 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PAFAH1B1 MUTATED                                          0
  PAFAH1B1 WILD-TYPE                                        3
D61V8, multiclass
                                                                   clus
vv                                                                  PAFAH1B1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  PAFAH1B1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V9, binary
                    cls
clus                   0   1
  PAFAH1B1 MUTATED     0  12
  PAFAH1B1 WILD-TYPE   5 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PAFAH1B1 MUTATED      0   12
  PAFAH1B1 WILD-TYPE    5  272
     clus
vv    PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  NO                 0                  5
  YES               12                272
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  PAFAH1B1 MUTATED     9   0   1   2
  PAFAH1B1 WILD-TYPE 218  10   9  22
D61V10, multiclass
    clus
vv   PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  R0                9                218
  R1                0                 10
  R2                1                  9
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PAFAH1B1 MUTATED       4                         2     4
  PAFAH1B1 WILD-TYPE    72                         2   164
D61V12, multiclass
                           clus
vv                          PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  ASIAN                                    4                 72
  BLACK OR AFRICAN AMERICAN                2                  2
  WHITE                                    4                164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) Variable = WDR5 MUTATION ANALYSIS
D62V1, survival
                sevent
clus2              0   1
  WDR5 MUTATED     3   1
  WDR5 WILD-TYPE 178  79
  WDR5 MUTATED WDR5 WILD-TYPE 
             4            257 
  WDR5 MUTATED WDR5 WILD-TYPE 
             1             79 
$`WDR5 MUTATED`
TCGA-BR-7703 TCGA-BR-A4QL TCGA-CG-5718 TCGA-CG-5723 
       24.76        11.57        36.00       105.07 

$`WDR5 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  WDR5 MUTATED WDR5 WILD-TYPE 
         11.57           0.00 
  WDR5 MUTATED WDR5 WILD-TYPE 
        105.07          79.07 
  WDR5 MUTATED WDR5 WILD-TYPE 
         30.38          12.59 
[1] "11.6 - 105.1 (30.4)" "0.0 - 79.1 (12.6)"  
[1] "hr=" "3.7"
D62V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WDR5 MUTATED         0        1        0        2         0         0
  WDR5 WILD-TYPE       1        8       27       24        31        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WDR5 MUTATED           0          0          1          0        1
  WDR5 WILD-TYPE         3         49         35         24       23
D62V3, multiclass
            clus
vv           WDR5 MUTATED WDR5 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              0             27
  STAGE II              2             24
  STAGE IIA             0             31
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            1             35
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WDR5 MUTATED     1   2   2   1
  WDR5 WILD-TYPE  10  70 120  74
D62V4, multiclass
    clus
vv   WDR5 MUTATED WDR5 WILD-TYPE
  T1            1             10
  T2            2             70
  T3            2            120
  T4            1             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  WDR5 MUTATED    1  3  1  1
  WDR5 WILD-TYPE 92 78 49 52
D62V5, multiclass
    clus
vv   WDR5 MUTATED WDR5 WILD-TYPE
  N0            1             92
  N1            3             78
  N2            1             49
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                cls
clus               0   1
  WDR5 MUTATED     6   0
  WDR5 WILD-TYPE 251  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      6    0
  WDR5 WILD-TYPE  251   18
   clus
vv  WDR5 MUTATED WDR5 WILD-TYPE
  0            6            251
  1            0             18
[1] 2 2
[1] FALSE
D62V7, binary
                cls
clus               0   1
  WDR5 MUTATED     4   3
  WDR5 WILD-TYPE 106 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      4    3
  WDR5 WILD-TYPE  106  176
        clus
vv       WDR5 MUTATED WDR5 WILD-TYPE
  FEMALE            4            106
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  WDR5 MUTATED                                       0
  WDR5 WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WDR5 MUTATED                                                        5
  WDR5 WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WDR5 MUTATED                                                                   1
  WDR5 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  WDR5 MUTATED                                                  0
  WDR5 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  WDR5 MUTATED                                                          0
  WDR5 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  WDR5 MUTATED                                                           1
  WDR5 WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  WDR5 MUTATED                                          0
  WDR5 WILD-TYPE                                        3
D62V8, multiclass
                                                                   clus
vv                                                                  WDR5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  WDR5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V9, binary
                cls
clus               0   1
  WDR5 MUTATED     0   7
  WDR5 WILD-TYPE   5 277
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      0    7
  WDR5 WILD-TYPE    5  277
     clus
vv    WDR5 MUTATED WDR5 WILD-TYPE
  NO             0              5
  YES            7            277
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  WDR5 MUTATED     4   0   0   3
  WDR5 WILD-TYPE 223  10  10  21
D62V10, multiclass
    clus
vv   WDR5 MUTATED WDR5 WILD-TYPE
  R0            4            223
  R1            0             10
  R2            0             10
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WDR5 MUTATED       0                         0     5
  WDR5 WILD-TYPE    76                         4   163
D62V12, multiclass
                           clus
vv                          WDR5 MUTATED WDR5 WILD-TYPE
  ASIAN                                0             76
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                5            163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = DDX6 MUTATION ANALYSIS
D63V1, survival
                sevent
clus2              0   1
  DDX6 MUTATED     7   4
  DDX6 WILD-TYPE 174  76
  DDX6 MUTATED DDX6 WILD-TYPE 
            11            250 
  DDX6 MUTATED DDX6 WILD-TYPE 
             4             76 
$`DDX6 MUTATED`
TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8487 TCGA-CD-8529 TCGA-CG-4465 
        6.97        32.94        23.93         1.12         0.13         9.01 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 TCGA-HU-A4GQ 
        6.02       105.07        65.10        21.07         0.10 

$`DDX6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.10         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        1.02         0.99         0.99        12.03        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        11.77        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  DDX6 MUTATED DDX6 WILD-TYPE 
           0.1            0.0 
  DDX6 MUTATED DDX6 WILD-TYPE 
        105.07          79.07 
  DDX6 MUTATED DDX6 WILD-TYPE 
          9.01          12.64 
[1] "0.1 - 105.1 (9.0)" "0.0 - 79.1 (12.6)"
[1] "hr=" "1.3"
D63V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDX6 MUTATED         0        0        3        1         2         0
  DDX6 WILD-TYPE       1        9       24       25        29        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DDX6 MUTATED           0          2          0          1        3
  DDX6 WILD-TYPE         3         47         36         23       21
D63V3, multiclass
            clus
vv           DDX6 MUTATED DDX6 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              3             24
  STAGE II              1             25
  STAGE IIA             2             29
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            0             36
  STAGE IIIC            1             23
  STAGE IV              3             21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DDX6 MUTATED     1   5   3   4
  DDX6 WILD-TYPE  10  67 119  71
D63V4, multiclass
    clus
vv   DDX6 MUTATED DDX6 WILD-TYPE
  T1            1             10
  T2            5             67
  T3            3            119
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  DDX6 MUTATED    6  3  2  1
  DDX6 WILD-TYPE 87 78 48 52
D63V5, multiclass
    clus
vv   DDX6 MUTATED DDX6 WILD-TYPE
  N0            6             87
  N1            3             78
  N2            2             48
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                cls
clus               0   1
  DDX6 MUTATED    12   2
  DDX6 WILD-TYPE 245  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX6 MUTATED     12    2
  DDX6 WILD-TYPE  245   16
   clus
vv  DDX6 MUTATED DDX6 WILD-TYPE
  0           12            245
  1            2             16
[1] 2 2
[1] FALSE
D63V7, binary
                cls
clus               0   1
  DDX6 MUTATED     9   6
  DDX6 WILD-TYPE 101 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX6 MUTATED      9    6
  DDX6 WILD-TYPE  101  173
        clus
vv       DDX6 MUTATED DDX6 WILD-TYPE
  FEMALE            9            101
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DDX6 MUTATED                                       1
  DDX6 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DDX6 MUTATED                                                        8
  DDX6 WILD-TYPE                                                    127
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DDX6 MUTATED                                                                   4
  DDX6 WILD-TYPE                                                                36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DDX6 MUTATED                                                  1
  DDX6 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DDX6 MUTATED                                                          1
  DDX6 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DDX6 MUTATED                                                           0
  DDX6 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DDX6 MUTATED                                          0
  DDX6 WILD-TYPE                                        3
D63V8, multiclass
                                                                   clus
vv                                                                  DDX6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  DDX6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V9, binary
                cls
clus               0   1
  DDX6 MUTATED     0  15
  DDX6 WILD-TYPE   5 269
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX6 MUTATED      0   15
  DDX6 WILD-TYPE    5  269
     clus
vv    DDX6 MUTATED DDX6 WILD-TYPE
  NO             0              5
  YES           15            269
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DDX6 MUTATED    10   0   1   4
  DDX6 WILD-TYPE 217  10   9  20
D63V10, multiclass
    clus
vv   DDX6 MUTATED DDX6 WILD-TYPE
  R0           10            217
  R1            0             10
  R2            1              9
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDX6 MUTATED       2                         0     7
  DDX6 WILD-TYPE    74                         4   161
D63V12, multiclass
                           clus
vv                          DDX6 MUTATED DDX6 WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                7            161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = C9ORF131 MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  C9ORF131 MUTATED     8   2
  C9ORF131 WILD-TYPE 173  78
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                10                251 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                 2                 78 
$`C9ORF131 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8680 TCGA-CD-5802 
        6.97        30.90        34.68        12.26        15.81         0.30 
TCGA-CG-5728 TCGA-HU-A4G9 TCGA-HU-A4H3 TCGA-HU-A4H8 
       65.10        24.20        19.36         8.88 

$`C9ORF131 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5813 
        2.83         3.25        13.15        13.18         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       11.84         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
        2.10        12.95        23.84        12.30         9.67        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
               0.3                0.0 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
             65.10             105.07 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
            17.585             12.590 
[1] "0.3 - 65.1 (17.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.4"
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C9ORF131 MUTATED         1        1        2        1         1         1
  C9ORF131 WILD-TYPE       0        8       25       25        30        43
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF131 MUTATED           0          2          0          1        1
  C9ORF131 WILD-TYPE         3         47         36         23       23
D64V3, multiclass
            clus
vv           C9ORF131 MUTATED C9ORF131 WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                  1                  8
  STAGE IB                  2                 25
  STAGE II                  1                 25
  STAGE IIA                 1                 30
  STAGE IIB                 1                 43
  STAGE III                 0                  3
  STAGE IIIA                2                 47
  STAGE IIIB                0                 36
  STAGE IIIC                1                 23
  STAGE IV                  1                 23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C9ORF131 MUTATED     3   2   3   4
  C9ORF131 WILD-TYPE   8  70 119  71
D64V4, multiclass
    clus
vv   C9ORF131 MUTATED C9ORF131 WILD-TYPE
  T1                3                  8
  T2                2                 70
  T3                3                119
  T4                4                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  C9ORF131 MUTATED    6  4  1  1
  C9ORF131 WILD-TYPE 87 77 49 52
D64V5, multiclass
    clus
vv   C9ORF131 MUTATED C9ORF131 WILD-TYPE
  N0                6                 87
  N1                4                 77
  N2                1                 49
  N3                1                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                    cls
clus                   0   1
  C9ORF131 MUTATED    10   1
  C9ORF131 WILD-TYPE 247  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF131 MUTATED     10    1
  C9ORF131 WILD-TYPE  247   17
   clus
vv  C9ORF131 MUTATED C9ORF131 WILD-TYPE
  0               10                247
  1                1                 17
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  C9ORF131 MUTATED     7   6
  C9ORF131 WILD-TYPE 103 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF131 MUTATED      7    6
  C9ORF131 WILD-TYPE  103  173
        clus
vv       C9ORF131 MUTATED C9ORF131 WILD-TYPE
  FEMALE                7                103
  MALE                  6                173
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C9ORF131 MUTATED                                       1
  C9ORF131 WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C9ORF131 MUTATED                                                        8
  C9ORF131 WILD-TYPE                                                    127
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C9ORF131 MUTATED                                                                   1
  C9ORF131 WILD-TYPE                                                                39
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C9ORF131 MUTATED                                                  3
  C9ORF131 WILD-TYPE                                               35
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C9ORF131 MUTATED                                                          0
  C9ORF131 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C9ORF131 MUTATED                                                           0
  C9ORF131 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C9ORF131 MUTATED                                          0
  C9ORF131 WILD-TYPE                                        3
D64V8, multiclass
                                                                   clus
vv                                                                  C9ORF131 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  C9ORF131 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V9, binary
                    cls
clus                   0   1
  C9ORF131 MUTATED     0  13
  C9ORF131 WILD-TYPE   5 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF131 MUTATED      0   13
  C9ORF131 WILD-TYPE    5  271
     clus
vv    C9ORF131 MUTATED C9ORF131 WILD-TYPE
  NO                 0                  5
  YES               13                271
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C9ORF131 MUTATED     8   0   0   4
  C9ORF131 WILD-TYPE 219  10  10  20
D64V10, multiclass
    clus
vv   C9ORF131 MUTATED C9ORF131 WILD-TYPE
  R0                8                219
  R1                0                 10
  R2                0                 10
  RX                4                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C9ORF131 MUTATED       5                         1     6
  C9ORF131 WILD-TYPE    71                         3   162
D64V12, multiclass
                           clus
vv                          C9ORF131 MUTATED C9ORF131 WILD-TYPE
  ASIAN                                    5                 71
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                    6                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(65) Variable = PLOD3 MUTATION ANALYSIS
D65V1, survival
                 sevent
clus2               0   1
  PLOD3 MUTATED    11   2
  PLOD3 WILD-TYPE 170  78
  PLOD3 MUTATED PLOD3 WILD-TYPE 
             13             248 
  PLOD3 MUTATED PLOD3 WILD-TYPE 
              2              78 
$`PLOD3 MUTATED`
TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8487 TCGA-CD-A4MI 
       34.68         0.26         4.31        19.17         1.12         0.10 
TCGA-CG-4465 TCGA-CG-5723 TCGA-D7-A4Z0 TCGA-FP-A4BE TCGA-HU-A4GX TCGA-HU-A4H3 
        9.01       105.07        14.76        11.08        10.19        19.36 
TCGA-HU-A4H5 
       12.30 

$`PLOD3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        19.50        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
       26.33        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
       29.98        47.05        19.07        12.03         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         6.02         0.99        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
        5.03        13.58         0.56         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.51         6.25         0.26         2.10        12.95        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  PLOD3 MUTATED PLOD3 WILD-TYPE 
            0.1             0.0 
  PLOD3 MUTATED PLOD3 WILD-TYPE 
         105.07           79.07 
  PLOD3 MUTATED PLOD3 WILD-TYPE 
          11.08           12.71 
[1] "0.1 - 105.1 (11.1)" "0.0 - 79.1 (12.7)" 
[1] "hr=" "2.5"
D65V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLOD3 MUTATED         0        0        3        1         3         1
  PLOD3 WILD-TYPE       1        9       24       25        28        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLOD3 MUTATED           0          0          1          3        1
  PLOD3 WILD-TYPE         3         49         35         21       23
D65V3, multiclass
            clus
vv           PLOD3 MUTATED PLOD3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               3              24
  STAGE II               1              25
  STAGE IIA              3              28
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             3              21
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PLOD3 MUTATED     0   5   5   4
  PLOD3 WILD-TYPE  11  67 117  71
D65V4, multiclass
    clus
vv   PLOD3 MUTATED PLOD3 WILD-TYPE
  T1             0              11
  T2             5              67
  T3             5             117
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PLOD3 MUTATED    6  2  2  3
  PLOD3 WILD-TYPE 87 79 48 50
D65V5, multiclass
    clus
vv   PLOD3 MUTATED PLOD3 WILD-TYPE
  N0             6              87
  N1             2              79
  N2             2              48
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                 cls
clus                0   1
  PLOD3 MUTATED    12   1
  PLOD3 WILD-TYPE 245  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLOD3 MUTATED     12    1
  PLOD3 WILD-TYPE  245   17
   clus
vv  PLOD3 MUTATED PLOD3 WILD-TYPE
  0            12             245
  1             1              17
[1] 2 2
[1] FALSE
D65V7, binary
                 cls
clus                0   1
  PLOD3 MUTATED     8   6
  PLOD3 WILD-TYPE 102 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLOD3 MUTATED      8    6
  PLOD3 WILD-TYPE  102  173
        clus
vv       PLOD3 MUTATED PLOD3 WILD-TYPE
  FEMALE             8             102
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PLOD3 MUTATED                                       3
  PLOD3 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLOD3 MUTATED                                                        9
  PLOD3 WILD-TYPE                                                    126
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLOD3 MUTATED                                                                   0
  PLOD3 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PLOD3 MUTATED                                                  0
  PLOD3 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PLOD3 MUTATED                                                          1
  PLOD3 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PLOD3 MUTATED                                                           1
  PLOD3 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PLOD3 MUTATED                                          0
  PLOD3 WILD-TYPE                                        3
D65V8, multiclass
                                                                   clus
vv                                                                  PLOD3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  PLOD3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V9, binary
                 cls
clus                0   1
  PLOD3 MUTATED     0  14
  PLOD3 WILD-TYPE   5 270
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLOD3 MUTATED      0   14
  PLOD3 WILD-TYPE    5  270
     clus
vv    PLOD3 MUTATED PLOD3 WILD-TYPE
  NO              0               5
  YES            14             270
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PLOD3 MUTATED    11   0   1   1
  PLOD3 WILD-TYPE 216  10   9  23
D65V10, multiclass
    clus
vv   PLOD3 MUTATED PLOD3 WILD-TYPE
  R0            11             216
  R1             0              10
  R2             1               9
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLOD3 MUTATED       4                         1     7
  PLOD3 WILD-TYPE    72                         3   161
D65V12, multiclass
                           clus
vv                          PLOD3 MUTATED PLOD3 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 7             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = ZNF878 MUTATION ANALYSIS
D66V1, survival
                  sevent
clus2                0   1
  ZNF878 MUTATED     9   1
  ZNF878 WILD-TYPE 172  79
  ZNF878 MUTATED ZNF878 WILD-TYPE 
              10              251 
  ZNF878 MUTATED ZNF878 WILD-TYPE 
               1               79 
$`ZNF878 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8680 
        6.97        34.68         6.18        19.17         1.12        15.81 
TCGA-CG-5728 TCGA-D7-A4YY TCGA-HU-A4G8 TCGA-HU-A4GU 
       65.10        13.78        11.84         6.25 

$`ZNF878 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  ZNF878 MUTATED ZNF878 WILD-TYPE 
            1.12             0.00 
  ZNF878 MUTATED ZNF878 WILD-TYPE 
           65.10           105.07 
  ZNF878 MUTATED ZNF878 WILD-TYPE 
           12.81            12.62 
[1] "1.1 - 65.1 (12.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "3.7"
D66V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF878 MUTATED         0        0        2        0         3         2
  ZNF878 WILD-TYPE       1        9       25       26        28        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF878 MUTATED           0          1          1          1        1
  ZNF878 WILD-TYPE         3         48         35         23       23
D66V3, multiclass
            clus
vv           ZNF878 MUTATED ZNF878 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                2               25
  STAGE II                0               26
  STAGE IIA               3               28
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              1               23
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF878 MUTATED     0   2   7   2
  ZNF878 WILD-TYPE  11  70 115  73
D66V4, multiclass
    clus
vv   ZNF878 MUTATED ZNF878 WILD-TYPE
  T1              0               11
  T2              2               70
  T3              7              115
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZNF878 MUTATED    5  3  1  2
  ZNF878 WILD-TYPE 88 78 49 51
D66V5, multiclass
    clus
vv   ZNF878 MUTATED ZNF878 WILD-TYPE
  N0              5               88
  N1              3               78
  N2              1               49
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                  cls
clus                 0   1
  ZNF878 MUTATED    10   1
  ZNF878 WILD-TYPE 247  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF878 MUTATED     10    1
  ZNF878 WILD-TYPE  247   17
   clus
vv  ZNF878 MUTATED ZNF878 WILD-TYPE
  0             10              247
  1              1               17
[1] 2 2
[1] FALSE
D66V7, binary
                  cls
clus                 0   1
  ZNF878 MUTATED     5   7
  ZNF878 WILD-TYPE 105 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF878 MUTATED      5    7
  ZNF878 WILD-TYPE  105  172
        clus
vv       ZNF878 MUTATED ZNF878 WILD-TYPE
  FEMALE              5              105
  MALE                7              172
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZNF878 MUTATED                                       2
  ZNF878 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF878 MUTATED                                                        6
  ZNF878 WILD-TYPE                                                    129
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF878 MUTATED                                                                   3
  ZNF878 WILD-TYPE                                                                37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZNF878 MUTATED                                                  1
  ZNF878 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZNF878 MUTATED                                                          0
  ZNF878 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZNF878 MUTATED                                                           0
  ZNF878 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZNF878 MUTATED                                          0
  ZNF878 WILD-TYPE                                        3
D66V8, multiclass
                                                                   clus
vv                                                                  ZNF878 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ZNF878 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V9, binary
                  cls
clus                 0   1
  ZNF878 MUTATED     0  12
  ZNF878 WILD-TYPE   5 272
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF878 MUTATED      0   12
  ZNF878 WILD-TYPE    5  272
     clus
vv    ZNF878 MUTATED ZNF878 WILD-TYPE
  NO               0                5
  YES             12              272
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF878 MUTATED     9   0   0   2
  ZNF878 WILD-TYPE 218  10  10  22
D66V10, multiclass
    clus
vv   ZNF878 MUTATED ZNF878 WILD-TYPE
  R0              9              218
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF878 MUTATED       3                         0     7
  ZNF878 WILD-TYPE    73                         4   161
D66V12, multiclass
                           clus
vv                          ZNF878 MUTATED ZNF878 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  7              161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(67) Variable = SPG20 MUTATION ANALYSIS
D67V1, survival
                 sevent
clus2               0   1
  SPG20 MUTATED    14   3
  SPG20 WILD-TYPE 167  77
  SPG20 MUTATED SPG20 WILD-TYPE 
             17             244 
  SPG20 MUTATED SPG20 WILD-TYPE 
              3              77 
$`SPG20 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-8078 
        6.97        30.90        34.68        13.68        19.33        12.26 
TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CG-4305 
       20.55        19.50         1.12        13.45        11.57        15.95 
TCGA-CG-5723 TCGA-HU-8602 TCGA-HU-A4G2 TCGA-HU-A4GT TCGA-HU-A4H3 
      105.07        11.41        24.30         6.51        19.36 

$`SPG20 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       12.82         9.21        24.76        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 
       12.76        18.71        17.49        14.43         0.69         9.60 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
        9.21        20.22        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        13.64         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         6.02         0.99        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        5.52        26.47         5.92        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       10.62         0.76         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  SPG20 MUTATED SPG20 WILD-TYPE 
           1.12            0.00 
  SPG20 MUTATED SPG20 WILD-TYPE 
         105.07           79.07 
  SPG20 MUTATED SPG20 WILD-TYPE 
         15.950          12.495 
[1] "1.1 - 105.1 (15.9)" "0.0 - 79.1 (12.5)" 
[1] "hr=" "2.7"
D67V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPG20 MUTATED         0        0        0        2         4         5
  SPG20 WILD-TYPE       1        9       27       24        27        39
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPG20 MUTATED           0          1          1          3        0
  SPG20 WILD-TYPE         3         48         35         21       24
D67V3, multiclass
            clus
vv           SPG20 MUTATED SPG20 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               2              24
  STAGE IIA              4              27
  STAGE IIB              5              39
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             3              21
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SPG20 MUTATED     0   3   8   6
  SPG20 WILD-TYPE  11  69 114  69
D67V4, multiclass
    clus
vv   SPG20 MUTATED SPG20 WILD-TYPE
  T1             0              11
  T2             3              69
  T3             8             114
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  SPG20 MUTATED    7  7  1  3
  SPG20 WILD-TYPE 86 74 49 50
D67V5, multiclass
    clus
vv   SPG20 MUTATED SPG20 WILD-TYPE
  N0             7              86
  N1             7              74
  N2             1              49
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                 cls
clus                0   1
  SPG20 MUTATED    20   0
  SPG20 WILD-TYPE 237  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPG20 MUTATED     20    0
  SPG20 WILD-TYPE  237   18
   clus
vv  SPG20 MUTATED SPG20 WILD-TYPE
  0            20             237
  1             0              18
[1] 2 2
[1] FALSE
D67V7, binary
                 cls
clus                0   1
  SPG20 MUTATED    13   8
  SPG20 WILD-TYPE  97 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPG20 MUTATED     13    8
  SPG20 WILD-TYPE   97  171
        clus
vv       SPG20 MUTATED SPG20 WILD-TYPE
  FEMALE            13              97
  MALE               8             171
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SPG20 MUTATED                                       3
  SPG20 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SPG20 MUTATED                                                       17
  SPG20 WILD-TYPE                                                    118
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SPG20 MUTATED                                                                   0
  SPG20 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SPG20 MUTATED                                                  1
  SPG20 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SPG20 MUTATED                                                          0
  SPG20 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SPG20 MUTATED                                                           0
  SPG20 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SPG20 MUTATED                                          0
  SPG20 WILD-TYPE                                        3
D67V8, multiclass
                                                                   clus
vv                                                                  SPG20 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       17
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  SPG20 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        118
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V9, binary
                 cls
clus                0   1
  SPG20 MUTATED     0  21
  SPG20 WILD-TYPE   5 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPG20 MUTATED      0   21
  SPG20 WILD-TYPE    5  263
     clus
vv    SPG20 MUTATED SPG20 WILD-TYPE
  NO              0               5
  YES            21             263
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SPG20 MUTATED    15   0   0   6
  SPG20 WILD-TYPE 212  10  10  18
D67V10, multiclass
    clus
vv   SPG20 MUTATED SPG20 WILD-TYPE
  R0            15             212
  R1             0              10
  R2             0              10
  RX             6              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SPG20 MUTATED       4                         0    15
  SPG20 WILD-TYPE    72                         4   153
D67V12, multiclass
                           clus
vv                          SPG20 MUTATED SPG20 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                15             153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = C14ORF43 MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  C14ORF43 MUTATED    15   2
  C14ORF43 WILD-TYPE 166  78
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                17                244 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                 2                 78 
$`C14ORF43 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8372 TCGA-BR-8680 
        6.97        34.68        12.26         6.18        19.17        15.81 
TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-5721 TCGA-CG-5728 TCGA-HJ-7597 
       11.57         0.10         0.10         6.02        65.10        26.47 
TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU 
       11.41        11.84        29.98         6.51         6.25 

$`C14ORF43 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        2.66        16.31         2.20        15.58         7.40        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.13         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        28.96        79.07         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56        11.08         5.52         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       24.20         3.25        22.75        25.81        11.77         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
               0.1                0.0 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
             65.10             105.07 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
            11.570             12.775 
[1] "0.1 - 65.1 (11.6)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "3"  
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C14ORF43 MUTATED         0        0        2        1         4         4
  C14ORF43 WILD-TYPE       1        9       25       25        27        40
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF43 MUTATED           0          1          2          1        3
  C14ORF43 WILD-TYPE         3         48         34         23       21
D68V3, multiclass
            clus
vv           C14ORF43 MUTATED C14ORF43 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  2                 25
  STAGE II                  1                 25
  STAGE IIA                 4                 27
  STAGE IIB                 4                 40
  STAGE III                 0                  3
  STAGE IIIA                1                 48
  STAGE IIIB                2                 34
  STAGE IIIC                1                 23
  STAGE IV                  3                 21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C14ORF43 MUTATED     1   3  10   6
  C14ORF43 WILD-TYPE  10  69 112  69
D68V4, multiclass
    clus
vv   C14ORF43 MUTATED C14ORF43 WILD-TYPE
  T1                1                 10
  T2                3                 69
  T3               10                112
  T4                6                 69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  C14ORF43 MUTATED    8  6  2  2
  C14ORF43 WILD-TYPE 85 75 48 51
D68V5, multiclass
    clus
vv   C14ORF43 MUTATED C14ORF43 WILD-TYPE
  N0                8                 85
  N1                6                 75
  N2                2                 48
  N3                2                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                    cls
clus                   0   1
  C14ORF43 MUTATED    16   1
  C14ORF43 WILD-TYPE 241  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED     16    1
  C14ORF43 WILD-TYPE  241   17
   clus
vv  C14ORF43 MUTATED C14ORF43 WILD-TYPE
  0               16                241
  1                1                 17
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  C14ORF43 MUTATED    11   9
  C14ORF43 WILD-TYPE  99 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED     11    9
  C14ORF43 WILD-TYPE   99  170
        clus
vv       C14ORF43 MUTATED C14ORF43 WILD-TYPE
  FEMALE               11                 99
  MALE                  9                170
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C14ORF43 MUTATED                                       3
  C14ORF43 WILD-TYPE                                    47
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C14ORF43 MUTATED                                                       10
  C14ORF43 WILD-TYPE                                                    125
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C14ORF43 MUTATED                                                                   3
  C14ORF43 WILD-TYPE                                                                37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C14ORF43 MUTATED                                                  3
  C14ORF43 WILD-TYPE                                               35
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C14ORF43 MUTATED                                                          0
  C14ORF43 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C14ORF43 MUTATED                                                           0
  C14ORF43 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C14ORF43 MUTATED                                          1
  C14ORF43 WILD-TYPE                                        2
D68V8, multiclass
                                                                   clus
vv                                                                  C14ORF43 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  C14ORF43 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V9, binary
                    cls
clus                   0   1
  C14ORF43 MUTATED     0  20
  C14ORF43 WILD-TYPE   5 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED      0   20
  C14ORF43 WILD-TYPE    5  264
     clus
vv    C14ORF43 MUTATED C14ORF43 WILD-TYPE
  NO                 0                  5
  YES               20                264
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C14ORF43 MUTATED    14   0   0   4
  C14ORF43 WILD-TYPE 213  10  10  20
D68V10, multiclass
    clus
vv   C14ORF43 MUTATED C14ORF43 WILD-TYPE
  R0               14                213
  R1                0                 10
  R2                0                 10
  RX                4                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C14ORF43 MUTATED       8                         0    10
  C14ORF43 WILD-TYPE    68                         4   158
D68V12, multiclass
                           clus
vv                          C14ORF43 MUTATED C14ORF43 WILD-TYPE
  ASIAN                                    8                 68
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                   10                158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(69) Variable = FLNB MUTATION ANALYSIS
D69V1, survival
                sevent
clus2              0   1
  FLNB MUTATED    15   7
  FLNB WILD-TYPE 166  73
  FLNB MUTATED FLNB WILD-TYPE 
            22            239 
  FLNB MUTATED FLNB WILD-TYPE 
             7             73 
$`FLNB MUTATED`
TCGA-BR-4184 TCGA-BR-7851 TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8361 TCGA-BR-8368 
        6.97        12.43        14.43         9.60        19.50         4.31 
TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4CS TCGA-BR-A4QL TCGA-CD-8536 
        1.12        13.45        15.81         1.48        11.57         0.10 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-5721 TCGA-CG-5733 TCGA-HJ-7597 TCGA-HU-A4G8 
        6.58         0.10         6.02        21.07        26.47        11.84 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 
       29.98         6.51        10.19        19.36 

$`FLNB WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69        12.26        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
       16.31         2.20        15.58         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        9.34         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08        22.26        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        13.64         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 
        0.13         0.16         0.10         0.10         0.13         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ 
        9.34        11.31        12.43        11.61        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56        11.08         5.52         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
       11.77         8.98         0.10         6.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       12.95        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  FLNB MUTATED FLNB WILD-TYPE 
           0.1            0.0 
  FLNB MUTATED FLNB WILD-TYPE 
         29.98         105.07 
  FLNB MUTATED FLNB WILD-TYPE 
         10.88          12.79 
[1] "0.1 - 30.0 (10.9)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.3"
D69V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FLNB MUTATED         0        0        2        1         4         2
  FLNB WILD-TYPE       1        9       25       25        27        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FLNB MUTATED           1          3          2          6        2
  FLNB WILD-TYPE         2         46         34         18       22
D69V3, multiclass
            clus
vv           FLNB MUTATED FLNB WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              1             25
  STAGE IIA             4             27
  STAGE IIB             2             42
  STAGE III             1              2
  STAGE IIIA            3             46
  STAGE IIIB            2             34
  STAGE IIIC            6             18
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FLNB MUTATED     0   4   8  11
  FLNB WILD-TYPE  11  68 114  64
D69V4, multiclass
    clus
vv   FLNB MUTATED FLNB WILD-TYPE
  T1            0             11
  T2            4             68
  T3            8            114
  T4           11             64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  FLNB MUTATED    8  7  4  5
  FLNB WILD-TYPE 85 74 46 48
D69V5, multiclass
    clus
vv   FLNB MUTATED FLNB WILD-TYPE
  N0            8             85
  N1            7             74
  N2            4             46
  N3            5             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                cls
clus               0   1
  FLNB MUTATED    21   1
  FLNB WILD-TYPE 236  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLNB MUTATED     21    1
  FLNB WILD-TYPE  236   17
   clus
vv  FLNB MUTATED FLNB WILD-TYPE
  0           21            236
  1            1             17
[1] 2 2
[1] FALSE
D69V7, binary
                cls
clus               0   1
  FLNB MUTATED    13  11
  FLNB WILD-TYPE  97 168
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLNB MUTATED     13   11
  FLNB WILD-TYPE   97  168
        clus
vv       FLNB MUTATED FLNB WILD-TYPE
  FEMALE           13             97
  MALE             11            168
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FLNB MUTATED                                       4
  FLNB WILD-TYPE                                    46
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FLNB MUTATED                                                       11
  FLNB WILD-TYPE                                                    124
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FLNB MUTATED                                                                   4
  FLNB WILD-TYPE                                                                36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FLNB MUTATED                                                  3
  FLNB WILD-TYPE                                               35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FLNB MUTATED                                                          1
  FLNB WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FLNB MUTATED                                                           0
  FLNB WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FLNB MUTATED                                          1
  FLNB WILD-TYPE                                        2
D69V8, multiclass
                                                                   clus
vv                                                                  FLNB MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  FLNB WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V9, binary
                cls
clus               0   1
  FLNB MUTATED     0  24
  FLNB WILD-TYPE   5 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLNB MUTATED      0   24
  FLNB WILD-TYPE    5  260
     clus
vv    FLNB MUTATED FLNB WILD-TYPE
  NO             0              5
  YES           24            260
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FLNB MUTATED    18   0   0   3
  FLNB WILD-TYPE 209  10  10  21
D69V10, multiclass
    clus
vv   FLNB MUTATED FLNB WILD-TYPE
  R0           18            209
  R1            0             10
  R2            0             10
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FLNB MUTATED       9                         0    13
  FLNB WILD-TYPE    67                         4   155
D69V12, multiclass
                           clus
vv                          FLNB MUTATED FLNB WILD-TYPE
  ASIAN                                9             67
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               13            155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(70) Variable = GLI1 MUTATION ANALYSIS
D70V1, survival
                sevent
clus2              0   1
  GLI1 MUTATED     8   4
  GLI1 WILD-TYPE 173  76
  GLI1 MUTATED GLI1 WILD-TYPE 
            12            249 
  GLI1 MUTATED GLI1 WILD-TYPE 
             4             76 
$`GLI1 MUTATED`
TCGA-BR-6452 TCGA-BR-7851 TCGA-BR-8078 TCGA-CD-8536 TCGA-CG-4465 TCGA-CG-5723 
       34.68        12.43        12.26         0.10         9.01       105.07 
TCGA-CG-5726 TCGA-CG-5733 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4H3 
       28.96        21.07        11.41        11.84         0.10        19.36 

$`GLI1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10         4.01        69.04         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       26.47         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        11.77        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.25        10.19         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  GLI1 MUTATED GLI1 WILD-TYPE 
           0.1            0.0 
  GLI1 MUTATED GLI1 WILD-TYPE 
        105.07          79.07 
  GLI1 MUTATED GLI1 WILD-TYPE 
        12.345         12.660 
[1] "0.1 - 105.1 (12.3)" "0.0 - 79.1 (12.7)" 
[1] "hr=" "1.4"
D70V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GLI1 MUTATED         0        1        1        2         1         4
  GLI1 WILD-TYPE       1        8       26       24        30        40
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLI1 MUTATED           0          1          0          2        2
  GLI1 WILD-TYPE         3         48         36         22       22
D70V3, multiclass
            clus
vv           GLI1 MUTATED GLI1 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              1             26
  STAGE II              2             24
  STAGE IIA             1             30
  STAGE IIB             4             40
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            2             22
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GLI1 MUTATED     1   3   3   7
  GLI1 WILD-TYPE  10  69 119  68
D70V4, multiclass
    clus
vv   GLI1 MUTATED GLI1 WILD-TYPE
  T1            1             10
  T2            3             69
  T3            3            119
  T4            7             68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  GLI1 MUTATED    7  4  3  2
  GLI1 WILD-TYPE 86 77 47 51
D70V5, multiclass
    clus
vv   GLI1 MUTATED GLI1 WILD-TYPE
  N0            7             86
  N1            4             77
  N2            3             47
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                cls
clus               0   1
  GLI1 MUTATED    16   1
  GLI1 WILD-TYPE 241  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI1 MUTATED     16    1
  GLI1 WILD-TYPE  241   17
   clus
vv  GLI1 MUTATED GLI1 WILD-TYPE
  0           16            241
  1            1             17
[1] 2 2
[1] FALSE
D70V7, binary
                cls
clus               0   1
  GLI1 MUTATED    10   7
  GLI1 WILD-TYPE 100 172
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI1 MUTATED     10    7
  GLI1 WILD-TYPE  100  172
        clus
vv       GLI1 MUTATED GLI1 WILD-TYPE
  FEMALE           10            100
  MALE              7            172
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GLI1 MUTATED                                       4
  GLI1 WILD-TYPE                                    46
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GLI1 MUTATED                                                        8
  GLI1 WILD-TYPE                                                    127
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GLI1 MUTATED                                                                   4
  GLI1 WILD-TYPE                                                                36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GLI1 MUTATED                                                  1
  GLI1 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GLI1 MUTATED                                                          0
  GLI1 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GLI1 MUTATED                                                           0
  GLI1 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GLI1 MUTATED                                          0
  GLI1 WILD-TYPE                                        3
D70V8, multiclass
                                                                   clus
vv                                                                  GLI1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  GLI1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V9, binary
                cls
clus               0   1
  GLI1 MUTATED     0  17
  GLI1 WILD-TYPE   5 267
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI1 MUTATED      0   17
  GLI1 WILD-TYPE    5  267
     clus
vv    GLI1 MUTATED GLI1 WILD-TYPE
  NO             0              5
  YES           17            267
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GLI1 MUTATED    11   0   1   4
  GLI1 WILD-TYPE 216  10   9  20
D70V10, multiclass
    clus
vv   GLI1 MUTATED GLI1 WILD-TYPE
  R0           11            216
  R1            0             10
  R2            1              9
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GLI1 MUTATED       5                         0     7
  GLI1 WILD-TYPE    71                         4   161
D70V12, multiclass
                           clus
vv                          GLI1 MUTATED GLI1 WILD-TYPE
  ASIAN                                5             71
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                7            161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(71) Variable = PLAGL2 MUTATION ANALYSIS
D71V1, survival
                  sevent
clus2                0   1
  PLAGL2 MUTATED     5   2
  PLAGL2 WILD-TYPE 176  78
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               7              254 
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               2               78 
$`PLAGL2 MUTATED`
TCGA-BR-6566 TCGA-BR-7715 TCGA-BR-8059 TCGA-CG-5721 TCGA-FP-A4BE TCGA-HU-8602 
       32.78        15.42        14.43         6.02        11.08        11.41 
TCGA-HU-A4GQ 
        0.10 

$`PLAGL2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        23.93        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
             0.1              0.0 
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
           32.78           105.07 
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
           11.41            12.64 
[1] "0.1 - 32.8 (11.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1"  
D71V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLAGL2 MUTATED         0        0        0        0         3         1
  PLAGL2 WILD-TYPE       1        9       27       26        28        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLAGL2 MUTATED           1          0          0          1        1
  PLAGL2 WILD-TYPE         2         49         36         23       23
D71V3, multiclass
            clus
vv           PLAGL2 MUTATED PLAGL2 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               3               28
  STAGE IIB               1               43
  STAGE III               1                2
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PLAGL2 MUTATED     0   0   3   4
  PLAGL2 WILD-TYPE  11  72 119  71
D71V4, multiclass
    clus
vv   PLAGL2 MUTATED PLAGL2 WILD-TYPE
  T1              0               11
  T2              0               72
  T3              3              119
  T4              4               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  PLAGL2 MUTATED    4  2  1  0
  PLAGL2 WILD-TYPE 89 79 49 53
D71V5, multiclass
    clus
vv   PLAGL2 MUTATED PLAGL2 WILD-TYPE
  N0              4               89
  N1              2               79
  N2              1               49
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                  cls
clus                 0   1
  PLAGL2 MUTATED     7   0
  PLAGL2 WILD-TYPE 250  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLAGL2 MUTATED      7    0
  PLAGL2 WILD-TYPE  250   18
   clus
vv  PLAGL2 MUTATED PLAGL2 WILD-TYPE
  0              7              250
  1              0               18
[1] 2 2
[1] FALSE
D71V7, binary
                  cls
clus                 0   1
  PLAGL2 MUTATED     2   5
  PLAGL2 WILD-TYPE 108 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLAGL2 MUTATED      2    5
  PLAGL2 WILD-TYPE  108  174
        clus
vv       PLAGL2 MUTATED PLAGL2 WILD-TYPE
  FEMALE              2              108
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PLAGL2 MUTATED                                       1
  PLAGL2 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLAGL2 MUTATED                                                        3
  PLAGL2 WILD-TYPE                                                    132
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLAGL2 MUTATED                                                                   2
  PLAGL2 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PLAGL2 MUTATED                                                  1
  PLAGL2 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PLAGL2 MUTATED                                                          0
  PLAGL2 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PLAGL2 MUTATED                                                           0
  PLAGL2 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PLAGL2 MUTATED                                          0
  PLAGL2 WILD-TYPE                                        3
D71V8, multiclass
                                                                   clus
vv                                                                  PLAGL2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  PLAGL2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V9, binary
                  cls
clus                 0   1
  PLAGL2 MUTATED     0   7
  PLAGL2 WILD-TYPE   5 277
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLAGL2 MUTATED      0    7
  PLAGL2 WILD-TYPE    5  277
     clus
vv    PLAGL2 MUTATED PLAGL2 WILD-TYPE
  NO               0                5
  YES              7              277
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PLAGL2 MUTATED     7   0   0   0
  PLAGL2 WILD-TYPE 220  10  10  24
D71V10, multiclass
    clus
vv   PLAGL2 MUTATED PLAGL2 WILD-TYPE
  R0              7              220
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLAGL2 MUTATED       2                         1     3
  PLAGL2 WILD-TYPE    74                         3   165
D71V12, multiclass
                           clus
vv                          PLAGL2 MUTATED PLAGL2 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  3              165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(72) Variable = WNT16 MUTATION ANALYSIS
D72V1, survival
                 sevent
clus2               0   1
  WNT16 MUTATED     9   1
  WNT16 WILD-TYPE 172  79
  WNT16 MUTATED WNT16 WILD-TYPE 
             10             251 
  WNT16 MUTATED WNT16 WILD-TYPE 
              1              79 
$`WNT16 MUTATED`
TCGA-BR-8081 TCGA-BR-8372 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-5801 TCGA-CD-A4MJ 
       20.55        19.17        13.45        11.57        13.18        12.62 
TCGA-CG-5721 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GT 
        6.02        11.84        29.98         6.51 

$`WNT16 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.15         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       24.20         3.25        22.75        25.81        11.77         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  WNT16 MUTATED WNT16 WILD-TYPE 
           6.02            0.00 
  WNT16 MUTATED WNT16 WILD-TYPE 
          29.98          105.07 
  WNT16 MUTATED WNT16 WILD-TYPE 
          12.90           12.59 
[1] "6.0 - 30.0 (12.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "3.2"
D72V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WNT16 MUTATED         0        0        2        0         2         2
  WNT16 WILD-TYPE       1        9       25       26        29        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WNT16 MUTATED           0          1          1          2        1
  WNT16 WILD-TYPE         3         48         35         22       23
D72V3, multiclass
            clus
vv           WNT16 MUTATED WNT16 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             2              22
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WNT16 MUTATED     0   3   4   4
  WNT16 WILD-TYPE  11  69 118  71
D72V4, multiclass
    clus
vv   WNT16 MUTATED WNT16 WILD-TYPE
  T1             0              11
  T2             3              69
  T3             4             118
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  WNT16 MUTATED    4  5  0  3
  WNT16 WILD-TYPE 89 76 50 50
D72V5, multiclass
    clus
vv   WNT16 MUTATED WNT16 WILD-TYPE
  N0             4              89
  N1             5              76
  N2             0              50
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                 cls
clus                0   1
  WNT16 MUTATED    13   0
  WNT16 WILD-TYPE 244  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT16 MUTATED     13    0
  WNT16 WILD-TYPE  244   18
   clus
vv  WNT16 MUTATED WNT16 WILD-TYPE
  0            13             244
  1             0              18
[1] 2 2
[1] FALSE
D72V7, binary
                 cls
clus                0   1
  WNT16 MUTATED     6   7
  WNT16 WILD-TYPE 104 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT16 MUTATED      6    7
  WNT16 WILD-TYPE  104  172
        clus
vv       WNT16 MUTATED WNT16 WILD-TYPE
  FEMALE             6             104
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  WNT16 MUTATED                                       1
  WNT16 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WNT16 MUTATED                                                        8
  WNT16 WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WNT16 MUTATED                                                                   2
  WNT16 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  WNT16 MUTATED                                                  2
  WNT16 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  WNT16 MUTATED                                                          0
  WNT16 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  WNT16 MUTATED                                                           0
  WNT16 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  WNT16 MUTATED                                          0
  WNT16 WILD-TYPE                                        3
D72V8, multiclass
                                                                   clus
vv                                                                  WNT16 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  WNT16 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V9, binary
                 cls
clus                0   1
  WNT16 MUTATED     0  13
  WNT16 WILD-TYPE   5 271
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT16 MUTATED      0   13
  WNT16 WILD-TYPE    5  271
     clus
vv    WNT16 MUTATED WNT16 WILD-TYPE
  NO              0               5
  YES            13             271
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  WNT16 MUTATED     9   0   0   2
  WNT16 WILD-TYPE 218  10  10  22
D72V10, multiclass
    clus
vv   WNT16 MUTATED WNT16 WILD-TYPE
  R0             9             218
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WNT16 MUTATED       5                         0     6
  WNT16 WILD-TYPE    71                         4   162
D72V12, multiclass
                           clus
vv                          WNT16 MUTATED WNT16 WILD-TYPE
  ASIAN                                 5              71
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(73) Variable = IRF2 MUTATION ANALYSIS
D73V1, survival
                sevent
clus2              0   1
  IRF2 MUTATED     8   2
  IRF2 WILD-TYPE 173  78
  IRF2 MUTATED IRF2 WILD-TYPE 
            10            251 
  IRF2 MUTATED IRF2 WILD-TYPE 
             2             78 
$`IRF2 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7715 TCGA-BR-7851 TCGA-BR-8360 
       26.70         6.97        34.68        15.42        12.43         6.18 
TCGA-BR-8680 TCGA-CG-5726 TCGA-D7-6524 TCGA-HU-8245 
       15.81        28.96        17.85        12.59 

$`IRF2 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       28.01        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        20.55         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20        15.58         7.40        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 
        0.99         6.02         0.99       105.07        12.03        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  IRF2 MUTATED IRF2 WILD-TYPE 
          6.18           0.00 
  IRF2 MUTATED IRF2 WILD-TYPE 
         34.68         105.07 
  IRF2 MUTATED IRF2 WILD-TYPE 
        15.615         12.560 
[1] "6.2 - 34.7 (15.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.1"
D73V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IRF2 MUTATED         0        1        0        1         4         2
  IRF2 WILD-TYPE       1        8       27       25        27        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IRF2 MUTATED           0          1          0          0        2
  IRF2 WILD-TYPE         3         48         36         24       22
D73V3, multiclass
            clus
vv           IRF2 MUTATED IRF2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              0             27
  STAGE II              1             25
  STAGE IIA             4             27
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IRF2 MUTATED     1   1   5   4
  IRF2 WILD-TYPE  10  71 117  71
D73V4, multiclass
    clus
vv   IRF2 MUTATED IRF2 WILD-TYPE
  T1            1             10
  T2            1             71
  T3            5            117
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  IRF2 MUTATED    7  3  2  0
  IRF2 WILD-TYPE 86 78 48 53
D73V5, multiclass
    clus
vv   IRF2 MUTATED IRF2 WILD-TYPE
  N0            7             86
  N1            3             78
  N2            2             48
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                cls
clus               0   1
  IRF2 MUTATED    12   1
  IRF2 WILD-TYPE 245  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF2 MUTATED     12    1
  IRF2 WILD-TYPE  245   17
   clus
vv  IRF2 MUTATED IRF2 WILD-TYPE
  0           12            245
  1            1             17
[1] 2 2
[1] FALSE
D73V7, binary
                cls
clus               0   1
  IRF2 MUTATED     6   8
  IRF2 WILD-TYPE 104 171
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF2 MUTATED      6    8
  IRF2 WILD-TYPE  104  171
        clus
vv       IRF2 MUTATED IRF2 WILD-TYPE
  FEMALE            6            104
  MALE              8            171
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  IRF2 MUTATED                                       2
  IRF2 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IRF2 MUTATED                                                        7
  IRF2 WILD-TYPE                                                    128
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IRF2 MUTATED                                                                   3
  IRF2 WILD-TYPE                                                                37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  IRF2 MUTATED                                                  1
  IRF2 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  IRF2 MUTATED                                                          0
  IRF2 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  IRF2 MUTATED                                                           1
  IRF2 WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  IRF2 MUTATED                                          0
  IRF2 WILD-TYPE                                        3
D73V8, multiclass
                                                                   clus
vv                                                                  IRF2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  IRF2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V9, binary
                cls
clus               0   1
  IRF2 MUTATED     0  14
  IRF2 WILD-TYPE   5 270
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF2 MUTATED      0   14
  IRF2 WILD-TYPE    5  270
     clus
vv    IRF2 MUTATED IRF2 WILD-TYPE
  NO             0              5
  YES           14            270
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IRF2 MUTATED     8   1   0   5
  IRF2 WILD-TYPE 219   9  10  19
D73V10, multiclass
    clus
vv   IRF2 MUTATED IRF2 WILD-TYPE
  R0            8            219
  R1            1              9
  R2            0             10
  RX            5             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IRF2 MUTATED       2                         0    11
  IRF2 WILD-TYPE    74                         4   157
D73V12, multiclass
                           clus
vv                          IRF2 MUTATED IRF2 WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               11            157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(74) Variable = SPTY2D1 MUTATION ANALYSIS
D74V1, survival
                   sevent
clus2                 0   1
  SPTY2D1 MUTATED    10   3
  SPTY2D1 WILD-TYPE 171  77
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
               13               248 
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
                3                77 
$`SPTY2D1 MUTATED`
TCGA-BR-7851 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8372 TCGA-CD-5800 TCGA-CD-8525 
       12.43        19.50         4.31        19.17        13.15         0.07 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-HU-8243 
        6.58         6.02       105.07        28.96        65.10         5.92 
TCGA-HU-8602 
       11.41 

$`SPTY2D1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
       26.33        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.39         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
        0.99         0.99        12.03        79.07         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 
        0.56        11.08         5.52        26.47        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
             0.07              0.00 
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
           105.07             79.07 
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
            12.43             12.64 
[1] "0.1 - 105.1 (12.4)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "2"  
D74V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPTY2D1 MUTATED         0        1        2        2         1         2
  SPTY2D1 WILD-TYPE       1        8       25       24        30        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPTY2D1 MUTATED           0          1          0          3        1
  SPTY2D1 WILD-TYPE         3         48         36         21       23
D74V3, multiclass
            clus
vv           SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 1                 8
  STAGE IB                 2                25
  STAGE II                 2                24
  STAGE IIA                1                30
  STAGE IIB                2                42
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               0                36
  STAGE IIIC               3                21
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SPTY2D1 MUTATED     2   3   3   6
  SPTY2D1 WILD-TYPE   9  69 119  69
D74V4, multiclass
    clus
vv   SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  T1               2                 9
  T2               3                69
  T3               3               119
  T4               6                69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  SPTY2D1 MUTATED    7  4  1  2
  SPTY2D1 WILD-TYPE 86 77 49 51
D74V5, multiclass
    clus
vv   SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  N0               7                86
  N1               4                77
  N2               1                49
  N3               2                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
                   cls
clus                  0   1
  SPTY2D1 MUTATED    15   0
  SPTY2D1 WILD-TYPE 242  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPTY2D1 MUTATED     15    0
  SPTY2D1 WILD-TYPE  242   18
   clus
vv  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  0              15               242
  1               0                18
[1] 2 2
[1] FALSE
D74V7, binary
                   cls
clus                  0   1
  SPTY2D1 MUTATED     8   7
  SPTY2D1 WILD-TYPE 102 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPTY2D1 MUTATED      8    7
  SPTY2D1 WILD-TYPE  102  172
        clus
vv       SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  FEMALE               8               102
  MALE                 7               172
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SPTY2D1 MUTATED                                       2
  SPTY2D1 WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SPTY2D1 MUTATED                                                        6
  SPTY2D1 WILD-TYPE                                                    129
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SPTY2D1 MUTATED                                                                   4
  SPTY2D1 WILD-TYPE                                                                36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SPTY2D1 MUTATED                                                  1
  SPTY2D1 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SPTY2D1 MUTATED                                                          1
  SPTY2D1 WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SPTY2D1 MUTATED                                                           1
  SPTY2D1 WILD-TYPE                                                         5
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SPTY2D1 MUTATED                                          0
  SPTY2D1 WILD-TYPE                                        3
D74V8, multiclass
                                                                   clus
vv                                                                  SPTY2D1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  SPTY2D1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V9, binary
                   cls
clus                  0   1
  SPTY2D1 MUTATED     0  15
  SPTY2D1 WILD-TYPE   5 269
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPTY2D1 MUTATED      0   15
  SPTY2D1 WILD-TYPE    5  269
     clus
vv    SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  NO                0                 5
  YES              15               269
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SPTY2D1 MUTATED    12   0   0   2
  SPTY2D1 WILD-TYPE 215  10  10  22
D74V10, multiclass
    clus
vv   SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  R0              12               215
  R1               0                10
  R2               0                10
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SPTY2D1 MUTATED       5                         0     6
  SPTY2D1 WILD-TYPE    71                         4   162
D74V12, multiclass
                           clus
vv                          SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  ASIAN                                   5                71
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   6               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(75) Variable = GPSM3 MUTATION ANALYSIS
D75V1, survival
                 sevent
clus2               0   1
  GPSM3 MUTATED     7   4
  GPSM3 WILD-TYPE 174  76
  GPSM3 MUTATED GPSM3 WILD-TYPE 
             11             250 
  GPSM3 MUTATED GPSM3 WILD-TYPE 
              4              76 
$`GPSM3 MUTATED`
TCGA-BR-4201 TCGA-BR-7707 TCGA-BR-7851 TCGA-CD-A4MG TCGA-CG-4306 TCGA-HJ-7597 
       30.90        23.93        12.43         6.58         1.02        26.47 
TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H4 
       24.20        11.77         8.98         6.25        23.84 

$`GPSM3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56        11.08         5.52         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN 
       12.30        11.84         3.25        22.75        25.81        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       19.36        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  GPSM3 MUTATED GPSM3 WILD-TYPE 
           1.02            0.00 
  GPSM3 MUTATED GPSM3 WILD-TYPE 
          30.90          105.07 
  GPSM3 MUTATED GPSM3 WILD-TYPE 
          12.43           12.64 
[1] "1.0 - 30.9 (12.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1"  
D75V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPSM3 MUTATED         0        2        2        0         2         3
  GPSM3 WILD-TYPE       1        7       25       26        29        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPSM3 MUTATED           0          1          0          0        1
  GPSM3 WILD-TYPE         3         48         36         24       23
D75V3, multiclass
            clus
vv           GPSM3 MUTATED GPSM3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               2               7
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              3              41
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GPSM3 MUTATED     2   5   3   2
  GPSM3 WILD-TYPE   9  67 119  73
D75V4, multiclass
    clus
vv   GPSM3 MUTATED GPSM3 WILD-TYPE
  T1             2               9
  T2             5              67
  T3             3             119
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  GPSM3 MUTATED    7  2  2  0
  GPSM3 WILD-TYPE 86 79 48 53
D75V5, multiclass
    clus
vv   GPSM3 MUTATED GPSM3 WILD-TYPE
  N0             7              86
  N1             2              79
  N2             2              48
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V6, binary
                 cls
clus                0   1
  GPSM3 MUTATED    10   1
  GPSM3 WILD-TYPE 247  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM3 MUTATED     10    1
  GPSM3 WILD-TYPE  247   17
   clus
vv  GPSM3 MUTATED GPSM3 WILD-TYPE
  0            10             247
  1             1              17
[1] 2 2
[1] FALSE
D75V7, binary
                 cls
clus                0   1
  GPSM3 MUTATED     7   5
  GPSM3 WILD-TYPE 103 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM3 MUTATED      7    5
  GPSM3 WILD-TYPE  103  174
        clus
vv       GPSM3 MUTATED GPSM3 WILD-TYPE
  FEMALE             7             103
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GPSM3 MUTATED                                       3
  GPSM3 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPSM3 MUTATED                                                        4
  GPSM3 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPSM3 MUTATED                                                                   1
  GPSM3 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GPSM3 MUTATED                                                  3
  GPSM3 WILD-TYPE                                               35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GPSM3 MUTATED                                                          0
  GPSM3 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GPSM3 MUTATED                                                           0
  GPSM3 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GPSM3 MUTATED                                          1
  GPSM3 WILD-TYPE                                        2
D75V8, multiclass
                                                                   clus
vv                                                                  GPSM3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  GPSM3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V9, binary
                 cls
clus                0   1
  GPSM3 MUTATED     0  12
  GPSM3 WILD-TYPE   5 272
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM3 MUTATED      0   12
  GPSM3 WILD-TYPE    5  272
     clus
vv    GPSM3 MUTATED GPSM3 WILD-TYPE
  NO              0               5
  YES            12             272
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GPSM3 MUTATED     8   0   1   2
  GPSM3 WILD-TYPE 219  10   9  22
D75V10, multiclass
    clus
vv   GPSM3 MUTATED GPSM3 WILD-TYPE
  R0             8             219
  R1             0              10
  R2             1               9
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPSM3 MUTATED       6                         0     5
  GPSM3 WILD-TYPE    70                         4   163
D75V12, multiclass
                           clus
vv                          GPSM3 MUTATED GPSM3 WILD-TYPE
  ASIAN                                 6              70
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(76) Variable = STAT2 MUTATION ANALYSIS
D76V1, survival
                 sevent
clus2               0   1
  STAT2 MUTATED     5   3
  STAT2 WILD-TYPE 176  77
  STAT2 MUTATED STAT2 WILD-TYPE 
              8             253 
  STAT2 MUTATED STAT2 WILD-TYPE 
              3              77 
$`STAT2 MUTATED`
TCGA-BR-4184 TCGA-BR-7851 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-5721 TCGA-HU-A4G9 
        6.97        12.43        15.81         6.58         6.02        24.20 
TCGA-HU-A4GQ TCGA-HU-A4H4 
        0.10        23.84 

$`STAT2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        11.84         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  STAT2 MUTATED STAT2 WILD-TYPE 
            0.1             0.0 
  STAT2 MUTATED STAT2 WILD-TYPE 
          24.20          105.07 
  STAT2 MUTATED STAT2 WILD-TYPE 
           9.70           12.66 
[1] "0.1 - 24.2 (9.7)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.6"
D76V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  STAT2 MUTATED         0        1        0        0         1         2
  STAT2 WILD-TYPE       1        8       27       26        30        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STAT2 MUTATED           0          1          0          1        2
  STAT2 WILD-TYPE         3         48         36         23       22
D76V3, multiclass
            clus
vv           STAT2 MUTATED STAT2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STAT2 MUTATED     1   1   2   4
  STAT2 WILD-TYPE  10  71 120  71
D76V4, multiclass
    clus
vv   STAT2 MUTATED STAT2 WILD-TYPE
  T1             1              10
  T2             1              71
  T3             2             120
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  STAT2 MUTATED    3  3  3  0
  STAT2 WILD-TYPE 90 78 47 53
D76V5, multiclass
    clus
vv   STAT2 MUTATED STAT2 WILD-TYPE
  N0             3              90
  N1             3              78
  N2             3              47
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                 cls
clus                0   1
  STAT2 MUTATED     8   1
  STAT2 WILD-TYPE 249  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT2 MUTATED      8    1
  STAT2 WILD-TYPE  249   17
   clus
vv  STAT2 MUTATED STAT2 WILD-TYPE
  0             8             249
  1             1              17
[1] 2 2
[1] FALSE
D76V7, binary
                 cls
clus                0   1
  STAT2 MUTATED     4   6
  STAT2 WILD-TYPE 106 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT2 MUTATED      4    6
  STAT2 WILD-TYPE  106  173
        clus
vv       STAT2 MUTATED STAT2 WILD-TYPE
  FEMALE             4             106
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  STAT2 MUTATED                                       1
  STAT2 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  STAT2 MUTATED                                                        3
  STAT2 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  STAT2 MUTATED                                                                   2
  STAT2 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  STAT2 MUTATED                                                  4
  STAT2 WILD-TYPE                                               34
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  STAT2 MUTATED                                                          0
  STAT2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  STAT2 MUTATED                                                           0
  STAT2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  STAT2 MUTATED                                          0
  STAT2 WILD-TYPE                                        3
D76V8, multiclass
                                                                   clus
vv                                                                  STAT2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  STAT2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V9, binary
                 cls
clus                0   1
  STAT2 MUTATED     0  10
  STAT2 WILD-TYPE   5 274
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT2 MUTATED      0   10
  STAT2 WILD-TYPE    5  274
     clus
vv    STAT2 MUTATED STAT2 WILD-TYPE
  NO              0               5
  YES            10             274
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  STAT2 MUTATED     6   0   0   3
  STAT2 WILD-TYPE 221  10  10  21
D76V10, multiclass
    clus
vv   STAT2 MUTATED STAT2 WILD-TYPE
  R0             6             221
  R1             0              10
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STAT2 MUTATED       5                         0     4
  STAT2 WILD-TYPE    71                         4   164
D76V12, multiclass
                           clus
vv                          STAT2 MUTATED STAT2 WILD-TYPE
  ASIAN                                 5              71
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(77) Variable = PRRG3 MUTATION ANALYSIS
D77V1, survival
                 sevent
clus2               0   1
  PRRG3 MUTATED     5   2
  PRRG3 WILD-TYPE 176  78
  PRRG3 MUTATED PRRG3 WILD-TYPE 
              7             254 
  PRRG3 MUTATED PRRG3 WILD-TYPE 
              2              78 
$`PRRG3 MUTATED`
TCGA-BR-4280 TCGA-BR-8078 TCGA-BR-8360 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-5577 
        6.61        12.26         6.18         6.02       105.07        12.36 
TCGA-HJ-7597 
       26.47 

$`PRRG3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       11.08         5.52         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  PRRG3 MUTATED PRRG3 WILD-TYPE 
           6.02            0.00 
  PRRG3 MUTATED PRRG3 WILD-TYPE 
         105.07           79.07 
  PRRG3 MUTATED PRRG3 WILD-TYPE 
          12.26           12.71 
[1] "6.0 - 105.1 (12.3)" "0.0 - 79.1 (12.7)" 
[1] "hr=" "1.7"
D77V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRRG3 MUTATED         0        0        1        1         1         1
  PRRG3 WILD-TYPE       1        9       26       25        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRRG3 MUTATED           1          1          0          0        1
  PRRG3 WILD-TYPE         2         48         36         24       23
D77V3, multiclass
            clus
vv           PRRG3 MUTATED PRRG3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              1               2
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRRG3 MUTATED     1   4   1   2
  PRRG3 WILD-TYPE  10  68 121  73
D77V4, multiclass
    clus
vv   PRRG3 MUTATED PRRG3 WILD-TYPE
  T1             1              10
  T2             4              68
  T3             1             121
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PRRG3 MUTATED    3  3  0  1
  PRRG3 WILD-TYPE 90 78 50 52
D77V5, multiclass
    clus
vv   PRRG3 MUTATED PRRG3 WILD-TYPE
  N0             3              90
  N1             3              78
  N2             0              50
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V6, binary
                 cls
clus                0   1
  PRRG3 MUTATED     7   0
  PRRG3 WILD-TYPE 250  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG3 MUTATED      7    0
  PRRG3 WILD-TYPE  250   18
   clus
vv  PRRG3 MUTATED PRRG3 WILD-TYPE
  0             7             250
  1             0              18
[1] 2 2
[1] FALSE
D77V7, binary
                 cls
clus                0   1
  PRRG3 MUTATED     5   3
  PRRG3 WILD-TYPE 105 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG3 MUTATED      5    3
  PRRG3 WILD-TYPE  105  176
        clus
vv       PRRG3 MUTATED PRRG3 WILD-TYPE
  FEMALE             5             105
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PRRG3 MUTATED                                       0
  PRRG3 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PRRG3 MUTATED                                                        4
  PRRG3 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PRRG3 MUTATED                                                                   2
  PRRG3 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PRRG3 MUTATED                                                  1
  PRRG3 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PRRG3 MUTATED                                                          0
  PRRG3 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PRRG3 MUTATED                                                           0
  PRRG3 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PRRG3 MUTATED                                          1
  PRRG3 WILD-TYPE                                        2
D77V8, multiclass
                                                                   clus
vv                                                                  PRRG3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  PRRG3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V9, binary
                 cls
clus                0   1
  PRRG3 MUTATED     0   8
  PRRG3 WILD-TYPE   5 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG3 MUTATED      0    8
  PRRG3 WILD-TYPE    5  276
     clus
vv    PRRG3 MUTATED PRRG3 WILD-TYPE
  NO              0               5
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PRRG3 MUTATED     6   0   0   2
  PRRG3 WILD-TYPE 221  10  10  22
D77V10, multiclass
    clus
vv   PRRG3 MUTATED PRRG3 WILD-TYPE
  R0             6             221
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRRG3 MUTATED       0                         0     6
  PRRG3 WILD-TYPE    76                         4   162
D77V12, multiclass
                           clus
vv                          PRRG3 MUTATED PRRG3 WILD-TYPE
  ASIAN                                 0              76
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(78) Variable = TP53BP2 MUTATION ANALYSIS
D78V1, survival
                   sevent
clus2                 0   1
  TP53BP2 MUTATED    11   2
  TP53BP2 WILD-TYPE 170  78
  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
               13               248 
  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
                2                78 
$`TP53BP2 MUTATED`
TCGA-BR-6452 TCGA-BR-7715 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8680 
       34.68        15.42        12.26         4.31        15.85        15.81 
TCGA-CD-5801 TCGA-CG-4305 TCGA-CG-5733 TCGA-D7-A4YX TCGA-FP-A4BE TCGA-HU-A4GU 
       13.18        15.95        21.07        15.16        11.08         6.25 
TCGA-HU-A4GX 
       10.19 

$`TP53BP2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        23.93        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
        3.25        13.15         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       14.27        16.44         5.92        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
             4.31              0.00 
  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
            34.68            105.07 
  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
           15.160            12.575 
[1] "4.3 - 34.7 (15.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.1"
D78V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TP53BP2 MUTATED         0        0        1        1         3         3
  TP53BP2 WILD-TYPE       1        9       26       25        28        41
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TP53BP2 MUTATED           0          3          0          2        1
  TP53BP2 WILD-TYPE         3         46         36         22       23
D78V3, multiclass
            clus
vv           TP53BP2 MUTATED TP53BP2 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 1                25
  STAGE IIA                3                28
  STAGE IIB                3                41
  STAGE III                0                 3
  STAGE IIIA               3                46
  STAGE IIIB               0                36
  STAGE IIIC               2                22
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TP53BP2 MUTATED     0   3   6   5
  TP53BP2 WILD-TYPE  11  69 116  70
D78V4, multiclass
    clus
vv   TP53BP2 MUTATED TP53BP2 WILD-TYPE
  T1               0                11
  T2               3                69
  T3               6               116
  T4               5                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  TP53BP2 MUTATED    6  4  3  1
  TP53BP2 WILD-TYPE 87 77 47 52
D78V5, multiclass
    clus
vv   TP53BP2 MUTATED TP53BP2 WILD-TYPE
  N0               6                87
  N1               4                77
  N2               3                47
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V6, binary
                   cls
clus                  0   1
  TP53BP2 MUTATED    13   1
  TP53BP2 WILD-TYPE 244  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP2 MUTATED     13    1
  TP53BP2 WILD-TYPE  244   17
   clus
vv  TP53BP2 MUTATED TP53BP2 WILD-TYPE
  0              13               244
  1               1                17
[1] 2 2
[1] FALSE
D78V7, binary
                   cls
clus                  0   1
  TP53BP2 MUTATED     7   7
  TP53BP2 WILD-TYPE 103 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP2 MUTATED      7    7
  TP53BP2 WILD-TYPE  103  172
        clus
vv       TP53BP2 MUTATED TP53BP2 WILD-TYPE
  FEMALE               7               103
  MALE                 7               172
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TP53BP2 MUTATED                                       2
  TP53BP2 WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TP53BP2 MUTATED                                                       10
  TP53BP2 WILD-TYPE                                                    125
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TP53BP2 MUTATED                                                                   1
  TP53BP2 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TP53BP2 MUTATED                                                  1
  TP53BP2 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TP53BP2 MUTATED                                                          0
  TP53BP2 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TP53BP2 MUTATED                                                           0
  TP53BP2 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TP53BP2 MUTATED                                          0
  TP53BP2 WILD-TYPE                                        3
D78V8, multiclass
                                                                   clus
vv                                                                  TP53BP2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  TP53BP2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V9, binary
                   cls
clus                  0   1
  TP53BP2 MUTATED     0  14
  TP53BP2 WILD-TYPE   5 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP2 MUTATED      0   14
  TP53BP2 WILD-TYPE    5  270
     clus
vv    TP53BP2 MUTATED TP53BP2 WILD-TYPE
  NO                0                 5
  YES              14               270
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TP53BP2 MUTATED    13   0   0   1
  TP53BP2 WILD-TYPE 214  10  10  23
D78V10, multiclass
    clus
vv   TP53BP2 MUTATED TP53BP2 WILD-TYPE
  R0              13               214
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53BP2 MUTATED       4                         1     7
  TP53BP2 WILD-TYPE    72                         3   161
D78V12, multiclass
                           clus
vv                          TP53BP2 MUTATED TP53BP2 WILD-TYPE
  ASIAN                                   4                72
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   7               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(79) Variable = BCOR MUTATION ANALYSIS
D79V1, survival
                sevent
clus2              0   1
  BCOR MUTATED    11   7
  BCOR WILD-TYPE 170  73
  BCOR MUTATED BCOR WILD-TYPE 
            18            243 
  BCOR MUTATED BCOR WILD-TYPE 
             7             73 
$`BCOR MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6455 TCGA-BR-6707 TCGA-BR-7196 TCGA-BR-7707 
       26.70         6.97        13.87        19.89        12.82        23.93 
TCGA-BR-8366 TCGA-BR-8487 TCGA-CG-4306 TCGA-CG-4455 TCGA-CG-5721 TCGA-CG-5724 
        0.95         1.12         1.02        12.03         6.02        12.03 
TCGA-F1-A448 TCGA-HJ-7597 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4GQ TCGA-HU-A4GT 
       21.27        26.47        12.10        10.62         0.10         6.51 

$`BCOR WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6456 
        6.18         9.57         6.61        34.68        15.95        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       25.61        18.05         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       32.94         9.21        24.76        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        72.23         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8610 
        5.52         5.92        12.59        14.17        11.41         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU 
       22.75        25.81        11.77        29.98         8.98         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  BCOR MUTATED BCOR WILD-TYPE 
           0.1            0.0 
  BCOR MUTATED BCOR WILD-TYPE 
         26.70         105.07 
  BCOR MUTATED BCOR WILD-TYPE 
         12.03          12.76 
[1] "0.1 - 26.7 (12.0)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.5"
D79V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BCOR MUTATED         0        0        3        1         5         2
  BCOR WILD-TYPE       1        9       24       25        26        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BCOR MUTATED           0          2          2          1        4
  BCOR WILD-TYPE         3         47         34         23       20
D79V3, multiclass
            clus
vv           BCOR MUTATED BCOR WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              3             24
  STAGE II              1             25
  STAGE IIA             5             26
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            2             34
  STAGE IIIC            1             23
  STAGE IV              4             20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BCOR MUTATED     0   4  12   5
  BCOR WILD-TYPE  11  68 110  70
D79V4, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  T1            0             11
  T2            4             68
  T3           12            110
  T4            5             70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  BCOR MUTATED   10  4  3  3
  BCOR WILD-TYPE 83 77 47 50
D79V5, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  N0           10             83
  N1            4             77
  N2            3             47
  N3            3             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V6, binary
                cls
clus               0   1
  BCOR MUTATED    15   3
  BCOR WILD-TYPE 242  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED     15    3
  BCOR WILD-TYPE  242   15
   clus
vv  BCOR MUTATED BCOR WILD-TYPE
  0           15            242
  1            3             15
[1] 2 2
[1] FALSE
D79V7, binary
                cls
clus               0   1
  BCOR MUTATED     9  12
  BCOR WILD-TYPE 101 167
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED      9   12
  BCOR WILD-TYPE  101  167
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  FEMALE            9            101
  MALE             12            167
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  BCOR MUTATED                                       3
  BCOR WILD-TYPE                                    47
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BCOR MUTATED                                                       10
  BCOR WILD-TYPE                                                    125
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BCOR MUTATED                                                                   2
  BCOR WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  BCOR MUTATED                                                  3
  BCOR WILD-TYPE                                               35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  BCOR MUTATED                                                          2
  BCOR WILD-TYPE                                                       14
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  BCOR MUTATED                                                           0
  BCOR WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  BCOR MUTATED                                          1
  BCOR WILD-TYPE                                        2
D79V8, multiclass
                                                                   clus
vv                                                                  BCOR MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  BCOR WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V9, binary
                cls
clus               0   1
  BCOR MUTATED     0  21
  BCOR WILD-TYPE   5 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED      0   21
  BCOR WILD-TYPE    5  263
     clus
vv    BCOR MUTATED BCOR WILD-TYPE
  NO             0              5
  YES           21            263
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BCOR MUTATED    16   0   2   3
  BCOR WILD-TYPE 211  10   8  21
D79V10, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  R0           16            211
  R1            0             10
  R2            2              8
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCOR MUTATED       4                         0    12
  BCOR WILD-TYPE    72                         4   156
D79V12, multiclass
                           clus
vv                          BCOR MUTATED BCOR WILD-TYPE
  ASIAN                                4             72
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               12            156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(80) Variable = BCORL1 MUTATION ANALYSIS
D80V1, survival
                  sevent
clus2                0   1
  BCORL1 MUTATED    15   3
  BCORL1 WILD-TYPE 166  77
  BCORL1 MUTATED BCORL1 WILD-TYPE 
              18              243 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
               3               77 
$`BCORL1 MUTATED`
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-7851 TCGA-BR-8081 
        6.61        34.68        32.78        30.90        12.43        20.55 
TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-A4QL TCGA-CG-5723 TCGA-D7-5577 
        0.26        19.17         1.12        11.57       105.07        12.36 
TCGA-D7-6528 TCGA-F1-6874 TCGA-HJ-7597 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4H3 
       15.22        14.47        26.47        11.84        24.20        19.36 

$`BCORL1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
       18.35        30.90         6.18         9.57        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       25.61        18.05        19.89         8.98        21.11        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       28.01        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        9.60         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40         6.18        19.50        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
       13.78        14.76         0.62         7.99        16.24        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD 
        0.76        24.30         5.59        12.30         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.25        10.19         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  BCORL1 MUTATED BCORL1 WILD-TYPE 
            0.26             0.00 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
          105.07            79.07 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
          17.195           12.560 
[1] "0.3 - 105.1 (17.2)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "3.1"
D80V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BCORL1 MUTATED         0        1        4        1         3         3
  BCORL1 WILD-TYPE       1        8       23       25        28        41
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BCORL1 MUTATED           1          3          1          2        0
  BCORL1 WILD-TYPE         2         46         35         22       24
D80V3, multiclass
            clus
vv           BCORL1 MUTATED BCORL1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                4               23
  STAGE II                1               25
  STAGE IIA               3               28
  STAGE IIB               3               41
  STAGE III               1                2
  STAGE IIIA              3               46
  STAGE IIIB              1               35
  STAGE IIIC              2               22
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BCORL1 MUTATED     1   7   6   5
  BCORL1 WILD-TYPE  10  65 116  70
D80V4, multiclass
    clus
vv   BCORL1 MUTATED BCORL1 WILD-TYPE
  T1              1               10
  T2              7               65
  T3              6              116
  T4              5               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  BCORL1 MUTATED   11  4  1  4
  BCORL1 WILD-TYPE 82 77 49 49
D80V5, multiclass
    clus
vv   BCORL1 MUTATED BCORL1 WILD-TYPE
  N0             11               82
  N1              4               77
  N2              1               49
  N3              4               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                  cls
clus                 0   1
  BCORL1 MUTATED    19   0
  BCORL1 WILD-TYPE 238  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCORL1 MUTATED     19    0
  BCORL1 WILD-TYPE  238   18
   clus
vv  BCORL1 MUTATED BCORL1 WILD-TYPE
  0             19              238
  1              0               18
[1] 2 2
[1] FALSE
D80V7, binary
                  cls
clus                 0   1
  BCORL1 MUTATED    15   5
  BCORL1 WILD-TYPE  95 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCORL1 MUTATED     15    5
  BCORL1 WILD-TYPE   95  174
        clus
vv       BCORL1 MUTATED BCORL1 WILD-TYPE
  FEMALE             15               95
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  BCORL1 MUTATED                                       2
  BCORL1 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BCORL1 MUTATED                                                       12
  BCORL1 WILD-TYPE                                                    123
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BCORL1 MUTATED                                                                   2
  BCORL1 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  BCORL1 MUTATED                                                  3
  BCORL1 WILD-TYPE                                               35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  BCORL1 MUTATED                                                          0
  BCORL1 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  BCORL1 MUTATED                                                           0
  BCORL1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  BCORL1 MUTATED                                          1
  BCORL1 WILD-TYPE                                        2
D80V8, multiclass
                                                                   clus
vv                                                                  BCORL1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        12
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       1
                                                                   clus
vv                                                                  BCORL1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         123
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V9, binary
                  cls
clus                 0   1
  BCORL1 MUTATED     0  20
  BCORL1 WILD-TYPE   5 264
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCORL1 MUTATED      0   20
  BCORL1 WILD-TYPE    5  264
     clus
vv    BCORL1 MUTATED BCORL1 WILD-TYPE
  NO               0                5
  YES             20              264
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  BCORL1 MUTATED    16   0   0   3
  BCORL1 WILD-TYPE 211  10  10  21
D80V10, multiclass
    clus
vv   BCORL1 MUTATED BCORL1 WILD-TYPE
  R0             16              211
  R1              0               10
  R2              0               10
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCORL1 MUTATED       3                         0    16
  BCORL1 WILD-TYPE    73                         4   152
D80V12, multiclass
                           clus
vv                          BCORL1 MUTATED BCORL1 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                 16              152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(81) Variable = RALGAPB MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  RALGAPB MUTATED    12   3
  RALGAPB WILD-TYPE 169  77
  RALGAPB MUTATED RALGAPB WILD-TYPE 
               15               246 
  RALGAPB MUTATED RALGAPB WILD-TYPE 
                3                77 
$`RALGAPB MUTATED`
TCGA-BR-4184 TCGA-BR-8081 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-8690 TCGA-BR-A4J8 
        6.97        20.55         1.12        15.81        10.68        13.51 
TCGA-CG-5721 TCGA-CG-5733 TCGA-D7-A4YT TCGA-D7-A4YY TCGA-HU-A4G9 TCGA-HU-A4GQ 
        6.02        21.07        14.27        13.78        24.20         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 
        6.51        10.19        19.36 

$`RALGAPB WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       17.49        14.43         0.69        12.26         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       15.68         8.22        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4PD 
        0.72        14.17         0.53         0.66        19.36        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10         4.01        69.04         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 
       20.91        16.44         5.92        15.16        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        11.84         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY 
       25.81        11.77        29.98         8.98         6.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  RALGAPB MUTATED RALGAPB WILD-TYPE 
              0.1               0.0 
  RALGAPB MUTATED RALGAPB WILD-TYPE 
            24.20            105.07 
  RALGAPB MUTATED RALGAPB WILD-TYPE 
           13.510            12.605 
[1] "0.1 - 24.2 (13.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D81V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RALGAPB MUTATED         0        1        0        0         2         1
  RALGAPB WILD-TYPE       1        8       27       26        29        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RALGAPB MUTATED           0          3          3          3        2
  RALGAPB WILD-TYPE         3         46         33         21       22
D81V3, multiclass
            clus
vv           RALGAPB MUTATED RALGAPB WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 1                 8
  STAGE IB                 0                27
  STAGE II                 0                26
  STAGE IIA                2                29
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               3                46
  STAGE IIIB               3                33
  STAGE IIIC               3                21
  STAGE IV                 2                22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RALGAPB MUTATED     2   2   7   6
  RALGAPB WILD-TYPE   9  70 115  69
D81V4, multiclass
    clus
vv   RALGAPB MUTATED RALGAPB WILD-TYPE
  T1               2                 9
  T2               2                70
  T3               7               115
  T4               6                69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  RALGAPB MUTATED    4  3  4  5
  RALGAPB WILD-TYPE 89 78 46 48
D81V5, multiclass
    clus
vv   RALGAPB MUTATED RALGAPB WILD-TYPE
  N0               4                89
  N1               3                78
  N2               4                46
  N3               5                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V6, binary
                   cls
clus                  0   1
  RALGAPB MUTATED    15   1
  RALGAPB WILD-TYPE 242  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RALGAPB MUTATED     15    1
  RALGAPB WILD-TYPE  242   17
   clus
vv  RALGAPB MUTATED RALGAPB WILD-TYPE
  0              15               242
  1               1                17
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  RALGAPB MUTATED    10   8
  RALGAPB WILD-TYPE 100 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RALGAPB MUTATED     10    8
  RALGAPB WILD-TYPE  100  171
        clus
vv       RALGAPB MUTATED RALGAPB WILD-TYPE
  FEMALE              10               100
  MALE                 8               171
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RALGAPB MUTATED                                       2
  RALGAPB WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RALGAPB MUTATED                                                        9
  RALGAPB WILD-TYPE                                                    126
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RALGAPB MUTATED                                                                   2
  RALGAPB WILD-TYPE                                                                38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RALGAPB MUTATED                                                  5
  RALGAPB WILD-TYPE                                               33
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RALGAPB MUTATED                                                          0
  RALGAPB WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RALGAPB MUTATED                                                           0
  RALGAPB WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RALGAPB MUTATED                                          0
  RALGAPB WILD-TYPE                                        3
D81V8, multiclass
                                                                   clus
vv                                                                  RALGAPB MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  RALGAPB WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V9, binary
                   cls
clus                  0   1
  RALGAPB MUTATED     0  18
  RALGAPB WILD-TYPE   5 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RALGAPB MUTATED      0   18
  RALGAPB WILD-TYPE    5  266
     clus
vv    RALGAPB MUTATED RALGAPB WILD-TYPE
  NO                0                 5
  YES              18               266
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  RALGAPB MUTATED    14   0   0   4
  RALGAPB WILD-TYPE 213  10  10  20
D81V10, multiclass
    clus
vv   RALGAPB MUTATED RALGAPB WILD-TYPE
  R0              14               213
  R1               0                10
  R2               0                10
  RX               4                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RALGAPB MUTATED       6                         0    10
  RALGAPB WILD-TYPE    70                         4   158
D81V12, multiclass
                           clus
vv                          RALGAPB MUTATED RALGAPB WILD-TYPE
  ASIAN                                   6                70
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                  10               158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(82) Variable = BAX MUTATION ANALYSIS
D82V1, survival
               sevent
clus2             0   1
  BAX MUTATED     5   0
  BAX WILD-TYPE 176  80
  BAX MUTATED BAX WILD-TYPE 
            5           256 
  BAX MUTATED BAX WILD-TYPE 
            0            80 
$`BAX MUTATED`
TCGA-BR-7851 TCGA-BR-8361 TCGA-BR-8370 TCGA-CD-A4MJ TCGA-HU-A4H3 
       12.43        19.50         3.32        12.62        19.36 

$`BAX WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31        14.04        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  BAX MUTATED BAX WILD-TYPE 
         3.32          0.00 
  BAX MUTATED BAX WILD-TYPE 
        19.50        105.07 
  BAX MUTATED BAX WILD-TYPE 
       12.620        12.625 
[1] "3.3 - 19.5 (12.6)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "9200000"
D82V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BAX MUTATED         0        0        1        0         0         1
  BAX WILD-TYPE       1        9       26       26        31        43
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BAX MUTATED           0          0          1          2        0
  BAX WILD-TYPE         3         49         35         22       24
D82V3, multiclass
            clus
vv           BAX MUTATED BAX WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             9
  STAGE IB             1            26
  STAGE II             0            26
  STAGE IIA            0            31
  STAGE IIB            1            43
  STAGE III            0             3
  STAGE IIIA           0            49
  STAGE IIIB           1            35
  STAGE IIIC           2            22
  STAGE IV             0            24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  BAX MUTATED     1   1   1   3
  BAX WILD-TYPE  10  71 121  72
D82V4, multiclass
    clus
vv   BAX MUTATED BAX WILD-TYPE
  T1           1            10
  T2           1            71
  T3           1           121
  T4           3            72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  BAX MUTATED    2  0  1  2
  BAX WILD-TYPE 91 81 49 51
D82V5, multiclass
    clus
vv   BAX MUTATED BAX WILD-TYPE
  N0           2            91
  N1           0            81
  N2           1            49
  N3           2            51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V6, binary
               cls
clus              0   1
  BAX MUTATED     6   0
  BAX WILD-TYPE 251  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  BAX MUTATED      6    0
  BAX WILD-TYPE  251   18
   clus
vv  BAX MUTATED BAX WILD-TYPE
  0           6           251
  1           0            18
[1] 2 2
[1] FALSE
D82V7, binary
               cls
clus              0   1
  BAX MUTATED     3   3
  BAX WILD-TYPE 107 176
[1] "tbl2"
               cls
clus            [,1] [,2]
  BAX MUTATED      3    3
  BAX WILD-TYPE  107  176
        clus
vv       BAX MUTATED BAX WILD-TYPE
  FEMALE           3           107
  MALE             3           176
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  BAX MUTATED                                       2
  BAX WILD-TYPE                                    48
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BAX MUTATED                                                        3
  BAX WILD-TYPE                                                    132
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BAX MUTATED                                                                   1
  BAX WILD-TYPE                                                                39
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  BAX MUTATED                                                  0
  BAX WILD-TYPE                                               38
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  BAX MUTATED                                                          0
  BAX WILD-TYPE                                                       16
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  BAX MUTATED                                                           0
  BAX WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  BAX MUTATED                                          0
  BAX WILD-TYPE                                        3
D82V8, multiclass
                                                                   clus
vv                                                                  BAX MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  BAX WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V9, binary
               cls
clus              0   1
  BAX MUTATED     0   6
  BAX WILD-TYPE   5 278
[1] "tbl2"
               cls
clus            [,1] [,2]
  BAX MUTATED      0    6
  BAX WILD-TYPE    5  278
     clus
vv    BAX MUTATED BAX WILD-TYPE
  NO            0             5
  YES           6           278
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  BAX MUTATED     4   0   0   1
  BAX WILD-TYPE 223  10  10  23
D82V10, multiclass
    clus
vv   BAX MUTATED BAX WILD-TYPE
  R0           4           223
  R1           0            10
  R2           0            10
  RX           1            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BAX MUTATED       2                         0     4
  BAX WILD-TYPE    74                         4   164
D82V12, multiclass
                           clus
vv                          BAX MUTATED BAX WILD-TYPE
  ASIAN                               2            74
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                               4           164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(83) Variable = ATP2A1 MUTATION ANALYSIS
D83V1, survival
                  sevent
clus2                0   1
  ATP2A1 MUTATED    11   2
  ATP2A1 WILD-TYPE 170  78
  ATP2A1 MUTATED ATP2A1 WILD-TYPE 
              13              248 
  ATP2A1 MUTATED ATP2A1 WILD-TYPE 
               2               78 
$`ATP2A1 MUTATED`
TCGA-BR-7851 TCGA-BR-8360 TCGA-BR-8368 TCGA-BR-8487 TCGA-CD-8536 TCGA-CD-A4MG 
       12.43         6.18         4.31         1.12         0.10         6.58 
TCGA-CG-4306 TCGA-CG-5723 TCGA-D7-5578 TCGA-F1-A448 TCGA-FP-A4BE TCGA-HU-A4G9 
        1.02       105.07        12.66        21.27        11.08        24.20 
TCGA-HU-A4H8 
        8.88 

$`ATP2A1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         6.02         0.99        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        0.62         7.99        16.24        14.47        72.23         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        11.84         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       12.30         9.67        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  ATP2A1 MUTATED ATP2A1 WILD-TYPE 
             0.1              0.0 
  ATP2A1 MUTATED ATP2A1 WILD-TYPE 
          105.07            79.07 
  ATP2A1 MUTATED ATP2A1 WILD-TYPE 
            8.88            12.79 
[1] "0.1 - 105.1 (8.9)" "0.0 - 79.1 (12.8)"
[1] "hr=" "2.1"
D83V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATP2A1 MUTATED         1        1        2        2         4         1
  ATP2A1 WILD-TYPE       0        8       25       24        27        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP2A1 MUTATED           0          1          1          0        1
  ATP2A1 WILD-TYPE         3         48         35         24       23
D83V3, multiclass
            clus
vv           ATP2A1 MUTATED ATP2A1 WILD-TYPE
  STAGE I                 1                0
  STAGE IA                1                8
  STAGE IB                2               25
  STAGE II                2               24
  STAGE IIA               4               27
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              0               24
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATP2A1 MUTATED     3   2   8   1
  ATP2A1 WILD-TYPE   8  70 114  74
D83V4, multiclass
    clus
vv   ATP2A1 MUTATED ATP2A1 WILD-TYPE
  T1              3                8
  T2              2               70
  T3              8              114
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ATP2A1 MUTATED    8  3  2  1
  ATP2A1 WILD-TYPE 85 78 48 52
D83V5, multiclass
    clus
vv   ATP2A1 MUTATED ATP2A1 WILD-TYPE
  N0              8               85
  N1              3               78
  N2              2               48
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V6, binary
                  cls
clus                 0   1
  ATP2A1 MUTATED    13   1
  ATP2A1 WILD-TYPE 244  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2A1 MUTATED     13    1
  ATP2A1 WILD-TYPE  244   17
   clus
vv  ATP2A1 MUTATED ATP2A1 WILD-TYPE
  0             13              244
  1              1               17
[1] 2 2
[1] FALSE
D83V7, binary
                  cls
clus                 0   1
  ATP2A1 MUTATED     4  11
  ATP2A1 WILD-TYPE 106 168
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2A1 MUTATED      4   11
  ATP2A1 WILD-TYPE  106  168
        clus
vv       ATP2A1 MUTATED ATP2A1 WILD-TYPE
  FEMALE              4              106
  MALE               11              168
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ATP2A1 MUTATED                                       1
  ATP2A1 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ATP2A1 MUTATED                                                        8
  ATP2A1 WILD-TYPE                                                    127
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ATP2A1 MUTATED                                                                   2
  ATP2A1 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ATP2A1 MUTATED                                                  3
  ATP2A1 WILD-TYPE                                               35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ATP2A1 MUTATED                                                          1
  ATP2A1 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ATP2A1 MUTATED                                                           0
  ATP2A1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ATP2A1 MUTATED                                          0
  ATP2A1 WILD-TYPE                                        3
D83V8, multiclass
                                                                   clus
vv                                                                  ATP2A1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ATP2A1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V9, binary
                  cls
clus                 0   1
  ATP2A1 MUTATED     0  15
  ATP2A1 WILD-TYPE   5 269
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2A1 MUTATED      0   15
  ATP2A1 WILD-TYPE    5  269
     clus
vv    ATP2A1 MUTATED ATP2A1 WILD-TYPE
  NO               0                5
  YES             15              269
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ATP2A1 MUTATED    12   0   1   1
  ATP2A1 WILD-TYPE 215  10   9  23
D83V10, multiclass
    clus
vv   ATP2A1 MUTATED ATP2A1 WILD-TYPE
  R0             12              215
  R1              0               10
  R2              1                9
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATP2A1 MUTATED       4                         2     7
  ATP2A1 WILD-TYPE    72                         2   161
D83V12, multiclass
                           clus
vv                          ATP2A1 MUTATED ATP2A1 WILD-TYPE
  ASIAN                                  4               72
  BLACK OR AFRICAN AMERICAN              2                2
  WHITE                                  7              161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(84) Variable = CCDC88A MUTATION ANALYSIS
D84V1, survival
                   sevent
clus2                 0   1
  CCDC88A MUTATED    11   5
  CCDC88A WILD-TYPE 170  75
  CCDC88A MUTATED CCDC88A WILD-TYPE 
               16               245 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
                5                75 
$`CCDC88A MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6707 TCGA-BR-8363 TCGA-BR-8487 
       26.70        30.90        34.68        19.89         0.26         1.12 
TCGA-BR-8680 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-5721 TCGA-D7-6528 TCGA-F1-6874 
       15.81         1.02         8.05         6.02        15.22        14.47 
TCGA-FP-A4BE TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4H3 
       11.08        11.84         0.10        19.36 

$`CCDC88A WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       25.61        18.05         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       13.35        17.19        10.26        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       16.24        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       12.95        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  CCDC88A MUTATED CCDC88A WILD-TYPE 
              0.1               0.0 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
            34.68            105.07 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
           13.155            12.620 
[1] "0.1 - 34.7 (13.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1"  
D84V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC88A MUTATED         0        0        4        1         4         2
  CCDC88A WILD-TYPE       1        9       23       25        27        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC88A MUTATED           0          1          0          2        4
  CCDC88A WILD-TYPE         3         48         36         22       20
D84V3, multiclass
            clus
vv           CCDC88A MUTATED CCDC88A WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 4                23
  STAGE II                 1                25
  STAGE IIA                4                27
  STAGE IIB                2                42
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               0                36
  STAGE IIIC               2                22
  STAGE IV                 4                20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC88A MUTATED     0   6   6   7
  CCDC88A WILD-TYPE  11  66 116  68
D84V4, multiclass
    clus
vv   CCDC88A MUTATED CCDC88A WILD-TYPE
  T1               0                11
  T2               6                66
  T3               6               116
  T4               7                68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  CCDC88A MUTATED   10  3  4  1
  CCDC88A WILD-TYPE 83 78 46 52
D84V5, multiclass
    clus
vv   CCDC88A MUTATED CCDC88A WILD-TYPE
  N0              10                83
  N1               3                78
  N2               4                46
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V6, binary
                   cls
clus                  0   1
  CCDC88A MUTATED    18   2
  CCDC88A WILD-TYPE 239  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED     18    2
  CCDC88A WILD-TYPE  239   16
   clus
vv  CCDC88A MUTATED CCDC88A WILD-TYPE
  0              18               239
  1               2                16
[1] 2 2
[1] FALSE
D84V7, binary
                   cls
clus                  0   1
  CCDC88A MUTATED    11   9
  CCDC88A WILD-TYPE  99 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED     11    9
  CCDC88A WILD-TYPE   99  170
        clus
vv       CCDC88A MUTATED CCDC88A WILD-TYPE
  FEMALE              11                99
  MALE                 9               170
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CCDC88A MUTATED                                       3
  CCDC88A WILD-TYPE                                    47
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CCDC88A MUTATED                                                       10
  CCDC88A WILD-TYPE                                                    125
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CCDC88A MUTATED                                                                   4
  CCDC88A WILD-TYPE                                                                36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CCDC88A MUTATED                                                  3
  CCDC88A WILD-TYPE                                               35
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CCDC88A MUTATED                                                          0
  CCDC88A WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CCDC88A MUTATED                                                           0
  CCDC88A WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CCDC88A MUTATED                                          0
  CCDC88A WILD-TYPE                                        3
D84V8, multiclass
                                                                   clus
vv                                                                  CCDC88A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  CCDC88A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V9, binary
                   cls
clus                  0   1
  CCDC88A MUTATED     0  20
  CCDC88A WILD-TYPE   5 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED      0   20
  CCDC88A WILD-TYPE    5  264
     clus
vv    CCDC88A MUTATED CCDC88A WILD-TYPE
  NO                0                 5
  YES              20               264
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CCDC88A MUTATED    14   0   1   4
  CCDC88A WILD-TYPE 213  10   9  20
D84V10, multiclass
    clus
vv   CCDC88A MUTATED CCDC88A WILD-TYPE
  R0              14               213
  R1               0                10
  R2               1                 9
  RX               4                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC88A MUTATED       4                         1    11
  CCDC88A WILD-TYPE    72                         3   157
D84V12, multiclass
                           clus
vv                          CCDC88A MUTATED CCDC88A WILD-TYPE
  ASIAN                                   4                72
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                  11               157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(85) Variable = BTBD7 MUTATION ANALYSIS
D85V1, survival
                 sevent
clus2               0   1
  BTBD7 MUTATED    11   5
  BTBD7 WILD-TYPE 170  75
  BTBD7 MUTATED BTBD7 WILD-TYPE 
             16             245 
  BTBD7 MUTATED BTBD7 WILD-TYPE 
              5              75 
$`BTBD7 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8372 
        6.97        30.90        34.68        23.93        12.26        19.17 
TCGA-CD-A4MI TCGA-CG-4469 TCGA-CG-5726 TCGA-F1-6874 TCGA-HJ-7597 TCGA-HU-8602 
        0.10         7.07        28.96        14.47        26.47        11.41 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-HU-A4H8 
        6.25        10.19        23.84         8.88 

$`BTBD7 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 
       31.20        32.94        12.82         9.21        24.76        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        20.55         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        0.62         7.99        16.24        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56        11.08         5.52         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GY 
       11.77        29.98         8.98         0.10         6.51         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
        2.10        12.95        19.36        12.30         9.67        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  BTBD7 MUTATED BTBD7 WILD-TYPE 
            0.1             0.0 
  BTBD7 MUTATED BTBD7 WILD-TYPE 
          34.68          105.07 
  BTBD7 MUTATED BTBD7 WILD-TYPE 
         13.365          12.620 
[1] "0.1 - 34.7 (13.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D85V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BTBD7 MUTATED         0        1        4        1         1         4
  BTBD7 WILD-TYPE       1        8       23       25        30        40
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BTBD7 MUTATED           0          2          1          2        1
  BTBD7 WILD-TYPE         3         47         35         22       23
D85V3, multiclass
            clus
vv           BTBD7 MUTATED BTBD7 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               4              23
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              4              40
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             1              35
  STAGE IIIC             2              22
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BTBD7 MUTATED     2   6   5   5
  BTBD7 WILD-TYPE   9  66 117  70
D85V4, multiclass
    clus
vv   BTBD7 MUTATED BTBD7 WILD-TYPE
  T1             2               9
  T2             6              66
  T3             5             117
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  BTBD7 MUTATED    8  5  2  2
  BTBD7 WILD-TYPE 85 76 48 51
D85V5, multiclass
    clus
vv   BTBD7 MUTATED BTBD7 WILD-TYPE
  N0             8              85
  N1             5              76
  N2             2              48
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V6, binary
                 cls
clus                0   1
  BTBD7 MUTATED    16   0
  BTBD7 WILD-TYPE 241  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD7 MUTATED     16    0
  BTBD7 WILD-TYPE  241   18
   clus
vv  BTBD7 MUTATED BTBD7 WILD-TYPE
  0            16             241
  1             0              18
[1] 2 2
[1] FALSE
D85V7, binary
                 cls
clus                0   1
  BTBD7 MUTATED     9   9
  BTBD7 WILD-TYPE 101 170
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD7 MUTATED      9    9
  BTBD7 WILD-TYPE  101  170
        clus
vv       BTBD7 MUTATED BTBD7 WILD-TYPE
  FEMALE             9             101
  MALE               9             170
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  BTBD7 MUTATED                                       3
  BTBD7 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BTBD7 MUTATED                                                        8
  BTBD7 WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BTBD7 MUTATED                                                                   3
  BTBD7 WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  BTBD7 MUTATED                                                  2
  BTBD7 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  BTBD7 MUTATED                                                          1
  BTBD7 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  BTBD7 MUTATED                                                           0
  BTBD7 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  BTBD7 MUTATED                                          1
  BTBD7 WILD-TYPE                                        2
D85V8, multiclass
                                                                   clus
vv                                                                  BTBD7 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  BTBD7 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V9, binary
                 cls
clus                0   1
  BTBD7 MUTATED     1  17
  BTBD7 WILD-TYPE   4 267
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD7 MUTATED      1   17
  BTBD7 WILD-TYPE    4  267
     clus
vv    BTBD7 MUTATED BTBD7 WILD-TYPE
  NO              1               4
  YES            17             267
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BTBD7 MUTATED    13   1   0   3
  BTBD7 WILD-TYPE 214   9  10  21
D85V10, multiclass
    clus
vv   BTBD7 MUTATED BTBD7 WILD-TYPE
  R0            13             214
  R1             1               9
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BTBD7 MUTATED       6                         0     9
  BTBD7 WILD-TYPE    70                         4   159
D85V12, multiclass
                           clus
vv                          BTBD7 MUTATED BTBD7 WILD-TYPE
  ASIAN                                 6              70
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 9             159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(86) Variable = ZC3H18 MUTATION ANALYSIS
D86V1, survival
                  sevent
clus2                0   1
  ZC3H18 MUTATED    12   5
  ZC3H18 WILD-TYPE 169  75
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
              17              244 
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
               5               75 
$`ZC3H18 MUTATED`
TCGA-BR-4201 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8591 
       30.90        32.78        23.93        20.55         0.26        13.45 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4465 TCGA-CG-5728 TCGA-D7-6815 TCGA-FP-A4BE 
        6.58        12.20         9.01        65.10        15.98        11.08 
TCGA-HU-8243 TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GX 
        5.92        24.20        29.98         6.51        10.19 

$`ZC3H18 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69        12.26         9.60         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        15.81         9.34         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MI TCGA-CD-A4MJ 
        9.34        11.31        12.43        11.61         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       19.07        12.03         0.00        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        0.99       105.07        12.03        28.96        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       13.35        17.19        10.26        15.22        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        0.56         5.52        26.47        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       11.84         3.25        22.75        25.81        11.77         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10         6.25         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
            0.26             0.00 
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
           65.10           105.07 
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
          13.450           12.605 
[1] "0.3 - 65.1 (13.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D86V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZC3H18 MUTATED         0        1        3        0         6         2
  ZC3H18 WILD-TYPE       1        8       24       26        25        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZC3H18 MUTATED           0          0          0          3        1
  ZC3H18 WILD-TYPE         3         49         36         21       23
D86V3, multiclass
            clus
vv           ZC3H18 MUTATED ZC3H18 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                3               24
  STAGE II                0               26
  STAGE IIA               6               25
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              3               21
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZC3H18 MUTATED     1   6   6   5
  ZC3H18 WILD-TYPE  10  66 116  70
D86V4, multiclass
    clus
vv   ZC3H18 MUTATED ZC3H18 WILD-TYPE
  T1              1               10
  T2              6               66
  T3              6              116
  T4              5               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZC3H18 MUTATED   10  1  2  3
  ZC3H18 WILD-TYPE 83 80 48 50
D86V5, multiclass
    clus
vv   ZC3H18 MUTATED ZC3H18 WILD-TYPE
  N0             10               83
  N1              1               80
  N2              2               48
  N3              3               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V6, binary
                  cls
clus                 0   1
  ZC3H18 MUTATED    16   1
  ZC3H18 WILD-TYPE 241  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H18 MUTATED     16    1
  ZC3H18 WILD-TYPE  241   17
   clus
vv  ZC3H18 MUTATED ZC3H18 WILD-TYPE
  0             16              241
  1              1               17
[1] 2 2
[1] FALSE
D86V7, binary
                  cls
clus                 0   1
  ZC3H18 MUTATED    13   5
  ZC3H18 WILD-TYPE  97 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H18 MUTATED     13    5
  ZC3H18 WILD-TYPE   97  174
        clus
vv       ZC3H18 MUTATED ZC3H18 WILD-TYPE
  FEMALE             13               97
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZC3H18 MUTATED                                       3
  ZC3H18 WILD-TYPE                                    47
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZC3H18 MUTATED                                                        9
  ZC3H18 WILD-TYPE                                                    126
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZC3H18 MUTATED                                                                   1
  ZC3H18 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZC3H18 MUTATED                                                  5
  ZC3H18 WILD-TYPE                                               33
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZC3H18 MUTATED                                                          0
  ZC3H18 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZC3H18 MUTATED                                                           0
  ZC3H18 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZC3H18 MUTATED                                          0
  ZC3H18 WILD-TYPE                                        3
D86V8, multiclass
                                                                   clus
vv                                                                  ZC3H18 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ZC3H18 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V9, binary
                  cls
clus                 0   1
  ZC3H18 MUTATED     0  18
  ZC3H18 WILD-TYPE   5 266
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H18 MUTATED      0   18
  ZC3H18 WILD-TYPE    5  266
     clus
vv    ZC3H18 MUTATED ZC3H18 WILD-TYPE
  NO               0                5
  YES             18              266
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZC3H18 MUTATED    13   0   1   2
  ZC3H18 WILD-TYPE 214  10   9  22
D86V10, multiclass
    clus
vv   ZC3H18 MUTATED ZC3H18 WILD-TYPE
  R0             13              214
  R1              0               10
  R2              1                9
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZC3H18 MUTATED       7                         1     8
  ZC3H18 WILD-TYPE    69                         3   160
D86V12, multiclass
                           clus
vv                          ZC3H18 MUTATED ZC3H18 WILD-TYPE
  ASIAN                                  7               69
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  8              160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(87) Variable = SLC10A6 MUTATION ANALYSIS
D87V1, survival
                   sevent
clus2                 0   1
  SLC10A6 MUTATED     5   2
  SLC10A6 WILD-TYPE 176  78
  SLC10A6 MUTATED SLC10A6 WILD-TYPE 
                7               254 
  SLC10A6 MUTATED SLC10A6 WILD-TYPE 
                2                78 
$`SLC10A6 MUTATED`
TCGA-BR-4201 TCGA-BR-8368 TCGA-BR-8680 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-5721 
       30.90         4.31        15.81         0.10         6.58         6.02 
TCGA-FP-A4BE 
       11.08 

$`SLC10A6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  SLC10A6 MUTATED SLC10A6 WILD-TYPE 
              0.1               0.0 
  SLC10A6 MUTATED SLC10A6 WILD-TYPE 
            30.90            105.07 
  SLC10A6 MUTATED SLC10A6 WILD-TYPE 
             6.58             12.71 
[1] "0.1 - 30.9 (6.6)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.2"
D87V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC10A6 MUTATED         0        0        1        1         2         0
  SLC10A6 WILD-TYPE       1        9       26       25        29        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC10A6 MUTATED           0          0          0          0        2
  SLC10A6 WILD-TYPE         3         49         36         24       22
D87V3, multiclass
            clus
vv           SLC10A6 MUTATED SLC10A6 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 1                25
  STAGE IIA                2                29
  STAGE IIB                0                44
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               0                36
  STAGE IIIC               0                24
  STAGE IV                 2                22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC10A6 MUTATED     1   2   3   2
  SLC10A6 WILD-TYPE  10  70 119  73
D87V4, multiclass
    clus
vv   SLC10A6 MUTATED SLC10A6 WILD-TYPE
  T1               1                10
  T2               2                70
  T3               3               119
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  SLC10A6 MUTATED    4  1  1  0
  SLC10A6 WILD-TYPE 89 80 49 53
D87V5, multiclass
    clus
vv   SLC10A6 MUTATED SLC10A6 WILD-TYPE
  N0               4                89
  N1               1                80
  N2               1                49
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V6, binary
                   cls
clus                  0   1
  SLC10A6 MUTATED     7   1
  SLC10A6 WILD-TYPE 250  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC10A6 MUTATED      7    1
  SLC10A6 WILD-TYPE  250   17
   clus
vv  SLC10A6 MUTATED SLC10A6 WILD-TYPE
  0               7               250
  1               1                17
[1] 2 2
[1] FALSE
D87V7, binary
                   cls
clus                  0   1
  SLC10A6 MUTATED     3   5
  SLC10A6 WILD-TYPE 107 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC10A6 MUTATED      3    5
  SLC10A6 WILD-TYPE  107  174
        clus
vv       SLC10A6 MUTATED SLC10A6 WILD-TYPE
  FEMALE               3               107
  MALE                 5               174
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SLC10A6 MUTATED                                       1
  SLC10A6 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC10A6 MUTATED                                                        5
  SLC10A6 WILD-TYPE                                                    130
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC10A6 MUTATED                                                                   1
  SLC10A6 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SLC10A6 MUTATED                                                  1
  SLC10A6 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SLC10A6 MUTATED                                                          0
  SLC10A6 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SLC10A6 MUTATED                                                           0
  SLC10A6 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SLC10A6 MUTATED                                          0
  SLC10A6 WILD-TYPE                                        3
D87V8, multiclass
                                                                   clus
vv                                                                  SLC10A6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  SLC10A6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V9, binary
                   cls
clus                  0   1
  SLC10A6 MUTATED     0   8
  SLC10A6 WILD-TYPE   5 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC10A6 MUTATED      0    8
  SLC10A6 WILD-TYPE    5  276
     clus
vv    SLC10A6 MUTATED SLC10A6 WILD-TYPE
  NO                0                 5
  YES               8               276
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC10A6 MUTATED     5   0   0   2
  SLC10A6 WILD-TYPE 222  10  10  22
D87V10, multiclass
    clus
vv   SLC10A6 MUTATED SLC10A6 WILD-TYPE
  R0               5               222
  R1               0                10
  R2               0                10
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC10A6 MUTATED       3                         1     3
  SLC10A6 WILD-TYPE    73                         3   165
D87V12, multiclass
                           clus
vv                          SLC10A6 MUTATED SLC10A6 WILD-TYPE
  ASIAN                                   3                73
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   3               165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(88) Variable = CR2 MUTATION ANALYSIS
D88V1, survival
               sevent
clus2             0   1
  CR2 MUTATED    16   1
  CR2 WILD-TYPE 165  79
  CR2 MUTATED CR2 WILD-TYPE 
           17           244 
  CR2 MUTATED CR2 WILD-TYPE 
            1            79 
$`CR2 MUTATED`
TCGA-B7-5816 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8680 
       26.70        12.26        20.55         4.31        15.85        15.81 
TCGA-CG-5721 TCGA-CG-5723 TCGA-EQ-8122 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4G9 
        6.02       105.07         7.99        11.41        11.84        24.20 
TCGA-HU-A4GH TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 
       11.77         6.51         6.25        10.19         2.10 

$`CR2 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 
       17.49        14.43         0.69         9.60         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        1.02         0.99         0.99        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
       14.76         0.62        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.30         5.59        12.30         3.25        22.75        25.81 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 
       29.98         8.98         0.10         0.26        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  CR2 MUTATED CR2 WILD-TYPE 
          2.1           0.0 
  CR2 MUTATED CR2 WILD-TYPE 
       105.07         79.07 
  CR2 MUTATED CR2 WILD-TYPE 
       11.770        12.775 
[1] "2.1 - 105.1 (11.8)" "0.0 - 79.1 (12.8)" 
[1] "hr=" "6.3"
D88V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CR2 MUTATED         0        2        1        2         1         7
  CR2 WILD-TYPE       1        7       26       24        30        37
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CR2 MUTATED           0          0          0          3        2
  CR2 WILD-TYPE         3         49         36         21       22
D88V3, multiclass
            clus
vv           CR2 MUTATED CR2 WILD-TYPE
  STAGE I              0             1
  STAGE IA             2             7
  STAGE IB             1            26
  STAGE II             2            24
  STAGE IIA            1            30
  STAGE IIB            7            37
  STAGE III            0             3
  STAGE IIIA           0            49
  STAGE IIIB           0            36
  STAGE IIIC           3            21
  STAGE IV             2            22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CR2 MUTATED     2   3   4   9
  CR2 WILD-TYPE   9  69 118  66
D88V4, multiclass
    clus
vv   CR2 MUTATED CR2 WILD-TYPE
  T1           2             9
  T2           3            69
  T3           4           118
  T4           9            66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  CR2 MUTATED    8  6  2  2
  CR2 WILD-TYPE 85 75 48 51
D88V5, multiclass
    clus
vv   CR2 MUTATED CR2 WILD-TYPE
  N0           8            85
  N1           6            75
  N2           2            48
  N3           2            51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V6, binary
               cls
clus              0   1
  CR2 MUTATED    18   1
  CR2 WILD-TYPE 239  17
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR2 MUTATED     18    1
  CR2 WILD-TYPE  239   17
   clus
vv  CR2 MUTATED CR2 WILD-TYPE
  0          18           239
  1           1            17
[1] 2 2
[1] FALSE
D88V7, binary
               cls
clus              0   1
  CR2 MUTATED    12   8
  CR2 WILD-TYPE  98 171
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR2 MUTATED     12    8
  CR2 WILD-TYPE   98  171
        clus
vv       CR2 MUTATED CR2 WILD-TYPE
  FEMALE          12            98
  MALE             8           171
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CR2 MUTATED                                       6
  CR2 WILD-TYPE                                    44
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CR2 MUTATED                                                        7
  CR2 WILD-TYPE                                                    128
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CR2 MUTATED                                                                   2
  CR2 WILD-TYPE                                                                38
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CR2 MUTATED                                                  4
  CR2 WILD-TYPE                                               34
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CR2 MUTATED                                                          1
  CR2 WILD-TYPE                                                       15
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CR2 MUTATED                                                           0
  CR2 WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CR2 MUTATED                                          0
  CR2 WILD-TYPE                                        3
D88V8, multiclass
                                                                   clus
vv                                                                  CR2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  CR2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        44
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V9, binary
               cls
clus              0   1
  CR2 MUTATED     1  19
  CR2 WILD-TYPE   4 265
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR2 MUTATED      1   19
  CR2 WILD-TYPE    4  265
     clus
vv    CR2 MUTATED CR2 WILD-TYPE
  NO            1             4
  YES          19           265
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  CR2 MUTATED    16   0   0   2
  CR2 WILD-TYPE 211  10  10  22
D88V10, multiclass
    clus
vv   CR2 MUTATED CR2 WILD-TYPE
  R0          16           211
  R1           0            10
  R2           0            10
  RX           2            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CR2 MUTATED       9                         0     8
  CR2 WILD-TYPE    67                         4   160
D88V12, multiclass
                           clus
vv                          CR2 MUTATED CR2 WILD-TYPE
  ASIAN                               9            67
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                               8           160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(89) Variable = ARHGAP5 MUTATION ANALYSIS
D89V1, survival
                   sevent
clus2                 0   1
  ARHGAP5 MUTATED    10   4
  ARHGAP5 WILD-TYPE 171  76
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
               14               247 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
                4                76 
$`ARHGAP5 MUTATED`
TCGA-BR-6452 TCGA-BR-7851 TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8487 
       34.68        12.43        14.43        20.55         4.31         1.12 
TCGA-BR-8589 TCGA-CD-8529 TCGA-CD-A4MG TCGA-CG-4305 TCGA-HJ-7597 TCGA-HU-A4G8 
       15.81         0.13         6.58        15.95        26.47        11.84 
TCGA-HU-A4GN TCGA-HU-A4GQ 
       29.98         0.10 

$`ARHGAP5 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69        12.26         9.60         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.07         0.10         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56        11.08         5.52         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       11.77         8.98         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
              0.1               0.0 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
            34.68            105.07 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
            13.43             12.62 
[1] "0.1 - 34.7 (13.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D89V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARHGAP5 MUTATED         0        0        4        1         4         3
  ARHGAP5 WILD-TYPE       1        9       23       25        27        41
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP5 MUTATED           1          0          1          1        1
  ARHGAP5 WILD-TYPE         2         49         35         23       23
D89V3, multiclass
            clus
vv           ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 4                23
  STAGE II                 1                25
  STAGE IIA                4                27
  STAGE IIB                3                41
  STAGE III                1                 2
  STAGE IIIA               0                49
  STAGE IIIB               1                35
  STAGE IIIC               1                23
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ARHGAP5 MUTATED     0   6   4   6
  ARHGAP5 WILD-TYPE  11  66 118  69
D89V4, multiclass
    clus
vv   ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  T1               0                11
  T2               6                66
  T3               4               118
  T4               6                69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  ARHGAP5 MUTATED   10  6  1  0
  ARHGAP5 WILD-TYPE 83 75 49 53
D89V5, multiclass
    clus
vv   ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  N0              10                83
  N1               6                75
  N2               1                49
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V6, binary
                   cls
clus                  0   1
  ARHGAP5 MUTATED    15   1
  ARHGAP5 WILD-TYPE 242  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP5 MUTATED     15    1
  ARHGAP5 WILD-TYPE  242   17
   clus
vv  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  0              15               242
  1               1                17
[1] 2 2
[1] FALSE
D89V7, binary
                   cls
clus                  0   1
  ARHGAP5 MUTATED     7  10
  ARHGAP5 WILD-TYPE 103 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP5 MUTATED      7   10
  ARHGAP5 WILD-TYPE  103  169
        clus
vv       ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  FEMALE               7               103
  MALE                10               169
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ARHGAP5 MUTATED                                       2
  ARHGAP5 WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ARHGAP5 MUTATED                                                        8
  ARHGAP5 WILD-TYPE                                                    127
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ARHGAP5 MUTATED                                                                   3
  ARHGAP5 WILD-TYPE                                                                37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ARHGAP5 MUTATED                                                  2
  ARHGAP5 WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ARHGAP5 MUTATED                                                          1
  ARHGAP5 WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ARHGAP5 MUTATED                                                           0
  ARHGAP5 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ARHGAP5 MUTATED                                          1
  ARHGAP5 WILD-TYPE                                        2
D89V8, multiclass
                                                                   clus
vv                                                                  ARHGAP5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  ARHGAP5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V9, binary
                   cls
clus                  0   1
  ARHGAP5 MUTATED     0  17
  ARHGAP5 WILD-TYPE   5 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP5 MUTATED      0   17
  ARHGAP5 WILD-TYPE    5  267
     clus
vv    ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  NO                0                 5
  YES              17               267
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ARHGAP5 MUTATED    14   0   0   1
  ARHGAP5 WILD-TYPE 213  10  10  23
D89V10, multiclass
    clus
vv   ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  R0              14               213
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP5 MUTATED       5                         0    10
  ARHGAP5 WILD-TYPE    71                         4   158
D89V12, multiclass
                           clus
vv                          ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  ASIAN                                   5                71
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                  10               158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(90) Variable = RASA1 MUTATION ANALYSIS
D90V1, survival
                 sevent
clus2               0   1
  RASA1 MUTATED    10   4
  RASA1 WILD-TYPE 171  76
  RASA1 MUTATED RASA1 WILD-TYPE 
             14             247 
  RASA1 MUTATED RASA1 WILD-TYPE 
              4              76 
$`RASA1 MUTATED`
TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7958 TCGA-BR-8286 TCGA-BR-8680 TCGA-CG-4301 
       32.78        32.94        12.76        12.95        15.81         3.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5726 TCGA-D7-6527 TCGA-D7-6815 TCGA-FP-7829 
       15.95         1.02        28.96        10.26        15.98        19.53 
TCGA-HU-A4GQ TCGA-HU-A4GX 
        0.10        10.19 

$`RASA1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         3.45         9.07        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8289 
        0.69        12.26         9.60        20.55         8.05         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4436 
       12.20         0.10        12.62        20.02        27.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       17.85        13.35        17.19        15.22        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 
       16.24        14.47        72.23        21.27         3.48        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       11.77        29.98         8.98         6.51         6.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  RASA1 MUTATED RASA1 WILD-TYPE 
            0.1             0.0 
  RASA1 MUTATED RASA1 WILD-TYPE 
          32.94          105.07 
  RASA1 MUTATED RASA1 WILD-TYPE 
          14.38           12.56 
[1] "0.1 - 32.9 (14.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D90V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RASA1 MUTATED         0        1        1        3         2         2
  RASA1 WILD-TYPE       1        8       26       23        29        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RASA1 MUTATED           0          0          1          2        3
  RASA1 WILD-TYPE         3         49         35         22       21
D90V3, multiclass
            clus
vv           RASA1 MUTATED RASA1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               1              26
  STAGE II               3              23
  STAGE IIA              2              29
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             2              22
  STAGE IV               3              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RASA1 MUTATED     2   4   6   5
  RASA1 WILD-TYPE   9  68 116  70
D90V4, multiclass
    clus
vv   RASA1 MUTATED RASA1 WILD-TYPE
  T1             2               9
  T2             4              68
  T3             6             116
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  RASA1 MUTATED    6  4  5  0
  RASA1 WILD-TYPE 87 77 45 53
D90V5, multiclass
    clus
vv   RASA1 MUTATED RASA1 WILD-TYPE
  N0             6              87
  N1             4              77
  N2             5              45
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V6, binary
                 cls
clus                0   1
  RASA1 MUTATED    13   3
  RASA1 WILD-TYPE 244  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED     13    3
  RASA1 WILD-TYPE  244   15
   clus
vv  RASA1 MUTATED RASA1 WILD-TYPE
  0            13             244
  1             3              15
[1] 2 2
[1] FALSE
D90V7, binary
                 cls
clus                0   1
  RASA1 MUTATED     7  10
  RASA1 WILD-TYPE 103 169
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED      7   10
  RASA1 WILD-TYPE  103  169
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  FEMALE             7             103
  MALE              10             169
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RASA1 MUTATED                                       1
  RASA1 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RASA1 MUTATED                                                        9
  RASA1 WILD-TYPE                                                    126
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RASA1 MUTATED                                                                   2
  RASA1 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RASA1 MUTATED                                                  3
  RASA1 WILD-TYPE                                               35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RASA1 MUTATED                                                          1
  RASA1 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RASA1 MUTATED                                                           1
  RASA1 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RASA1 MUTATED                                          0
  RASA1 WILD-TYPE                                        3
D90V8, multiclass
                                                                   clus
vv                                                                  RASA1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  RASA1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V9, binary
                 cls
clus                0   1
  RASA1 MUTATED     0  17
  RASA1 WILD-TYPE   5 267
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED      0   17
  RASA1 WILD-TYPE    5  267
     clus
vv    RASA1 MUTATED RASA1 WILD-TYPE
  NO              0               5
  YES            17             267
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RASA1 MUTATED    13   0   2   2
  RASA1 WILD-TYPE 214  10   8  22
D90V10, multiclass
    clus
vv   RASA1 MUTATED RASA1 WILD-TYPE
  R0            13             214
  R1             0              10
  R2             2               8
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RASA1 MUTATED       3                         0     9
  RASA1 WILD-TYPE    73                         4   159
D90V12, multiclass
                           clus
vv                          RASA1 MUTATED RASA1 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 9             159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(91) Variable = ZNF48 MUTATION ANALYSIS
D91V1, survival
                 sevent
clus2               0   1
  ZNF48 MUTATED     6   2
  ZNF48 WILD-TYPE 175  78
  ZNF48 MUTATED ZNF48 WILD-TYPE 
              8             253 
  ZNF48 MUTATED ZNF48 WILD-TYPE 
              2              78 
$`ZNF48 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8368 TCGA-CD-A48A 
       34.68        32.94        20.55         0.26         4.31        12.43 
TCGA-HU-A4G8 TCGA-HU-A4GQ 
       11.84         0.10 

$`ZNF48 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69        12.26         9.60         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
       19.50        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        3.42         9.34        11.31        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  ZNF48 MUTATED ZNF48 WILD-TYPE 
            0.1             0.0 
  ZNF48 MUTATED ZNF48 WILD-TYPE 
          34.68          105.07 
  ZNF48 MUTATED ZNF48 WILD-TYPE 
         12.135          12.660 
[1] "0.1 - 34.7 (12.1)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.4"
D91V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF48 MUTATED         0        0        3        0         3         2
  ZNF48 WILD-TYPE       1        9       24       26        28        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF48 MUTATED           0          0          0          1        0
  ZNF48 WILD-TYPE         3         49         36         23       24
D91V3, multiclass
            clus
vv           ZNF48 MUTATED ZNF48 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               3              24
  STAGE II               0              26
  STAGE IIA              3              28
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZNF48 MUTATED     1   3   4   2
  ZNF48 WILD-TYPE  10  69 118  73
D91V4, multiclass
    clus
vv   ZNF48 MUTATED ZNF48 WILD-TYPE
  T1             1              10
  T2             3              69
  T3             4             118
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ZNF48 MUTATED    7  1  1  0
  ZNF48 WILD-TYPE 86 80 49 53
D91V5, multiclass
    clus
vv   ZNF48 MUTATED ZNF48 WILD-TYPE
  N0             7              86
  N1             1              80
  N2             1              49
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V6, binary
                 cls
clus                0   1
  ZNF48 MUTATED    10   0
  ZNF48 WILD-TYPE 247  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF48 MUTATED     10    0
  ZNF48 WILD-TYPE  247   18
   clus
vv  ZNF48 MUTATED ZNF48 WILD-TYPE
  0            10             247
  1             0              18
[1] 2 2
[1] FALSE
D91V7, binary
                 cls
clus                0   1
  ZNF48 MUTATED     7   3
  ZNF48 WILD-TYPE 103 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF48 MUTATED      7    3
  ZNF48 WILD-TYPE  103  176
        clus
vv       ZNF48 MUTATED ZNF48 WILD-TYPE
  FEMALE             7             103
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZNF48 MUTATED                                       1
  ZNF48 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF48 MUTATED                                                        7
  ZNF48 WILD-TYPE                                                    128
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF48 MUTATED                                                                   1
  ZNF48 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZNF48 MUTATED                                                  1
  ZNF48 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZNF48 MUTATED                                                          0
  ZNF48 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZNF48 MUTATED                                                           0
  ZNF48 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZNF48 MUTATED                                          0
  ZNF48 WILD-TYPE                                        3
D91V8, multiclass
                                                                   clus
vv                                                                  ZNF48 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ZNF48 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V9, binary
                 cls
clus                0   1
  ZNF48 MUTATED     0  10
  ZNF48 WILD-TYPE   5 274
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF48 MUTATED      0   10
  ZNF48 WILD-TYPE    5  274
     clus
vv    ZNF48 MUTATED ZNF48 WILD-TYPE
  NO              0               5
  YES            10             274
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ZNF48 MUTATED     7   0   0   1
  ZNF48 WILD-TYPE 220  10  10  23
D91V10, multiclass
    clus
vv   ZNF48 MUTATED ZNF48 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF48 MUTATED       3                         0     6
  ZNF48 WILD-TYPE    73                         4   162
D91V12, multiclass
                           clus
vv                          ZNF48 MUTATED ZNF48 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(92) Variable = ADAM30 MUTATION ANALYSIS
D92V1, survival
                  sevent
clus2                0   1
  ADAM30 MUTATED     7   5
  ADAM30 WILD-TYPE 174  75
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              12              249 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
               5               75 
$`ADAM30 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8059 TCGA-BR-8382 TCGA-CD-5801 TCGA-CD-8525 
        6.97        30.90        14.43        15.85        13.18         0.07 
TCGA-CD-A486 TCGA-CD-A4MJ TCGA-CG-4306 TCGA-F1-6874 TCGA-HU-A4GT TCGA-HU-A4GU 
        3.42        12.62         1.02        14.47         6.51         6.25 

$`ADAM30 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        0.26         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.15         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.39         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
        0.16         0.10         0.10         0.13         0.10         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        0.62         7.99        16.24        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  ADAM30 MUTATED ADAM30 WILD-TYPE 
            0.07             0.00 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
           30.90           105.07 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
           9.795           12.660 
[1] "0.1 - 30.9 (9.8)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.9"
D92V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ADAM30 MUTATED         0        0        2        0         2         1
  ADAM30 WILD-TYPE       1        9       25       26        29        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAM30 MUTATED           1          3          0          1        2
  ADAM30 WILD-TYPE         2         46         36         23       22
D92V3, multiclass
            clus
vv           ADAM30 MUTATED ADAM30 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                2               25
  STAGE II                0               26
  STAGE IIA               2               29
  STAGE IIB               1               43
  STAGE III               1                2
  STAGE IIIA              3               46
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ADAM30 MUTATED     1   3   7   3
  ADAM30 WILD-TYPE  10  69 115  72
D92V4, multiclass
    clus
vv   ADAM30 MUTATED ADAM30 WILD-TYPE
  T1              1               10
  T2              3               69
  T3              7              115
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ADAM30 MUTATED    4  5  2  1
  ADAM30 WILD-TYPE 89 76 48 52
D92V5, multiclass
    clus
vv   ADAM30 MUTATED ADAM30 WILD-TYPE
  N0              4               89
  N1              5               76
  N2              2               48
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V6, binary
                  cls
clus                 0   1
  ADAM30 MUTATED    12   1
  ADAM30 WILD-TYPE 245  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED     12    1
  ADAM30 WILD-TYPE  245   17
   clus
vv  ADAM30 MUTATED ADAM30 WILD-TYPE
  0             12              245
  1              1               17
[1] 2 2
[1] FALSE
D92V7, binary
                  cls
clus                 0   1
  ADAM30 MUTATED     6   8
  ADAM30 WILD-TYPE 104 171
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      6    8
  ADAM30 WILD-TYPE  104  171
        clus
vv       ADAM30 MUTATED ADAM30 WILD-TYPE
  FEMALE              6              104
  MALE                8              171
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ADAM30 MUTATED                                       1
  ADAM30 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ADAM30 MUTATED                                                        9
  ADAM30 WILD-TYPE                                                    126
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ADAM30 MUTATED                                                                   2
  ADAM30 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ADAM30 MUTATED                                                  1
  ADAM30 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ADAM30 MUTATED                                                          1
  ADAM30 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ADAM30 MUTATED                                                           0
  ADAM30 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ADAM30 MUTATED                                          0
  ADAM30 WILD-TYPE                                        3
D92V8, multiclass
                                                                   clus
vv                                                                  ADAM30 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ADAM30 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V9, binary
                  cls
clus                 0   1
  ADAM30 MUTATED     0  14
  ADAM30 WILD-TYPE   5 270
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      0   14
  ADAM30 WILD-TYPE    5  270
     clus
vv    ADAM30 MUTATED ADAM30 WILD-TYPE
  NO               0                5
  YES             14              270
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ADAM30 MUTATED     7   0   1   4
  ADAM30 WILD-TYPE 220  10   9  20
D92V10, multiclass
    clus
vv   ADAM30 MUTATED ADAM30 WILD-TYPE
  R0              7              220
  R1              0               10
  R2              1                9
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ADAM30 MUTATED       6                         0     7
  ADAM30 WILD-TYPE    70                         4   161
D92V12, multiclass
                           clus
vv                          ADAM30 MUTATED ADAM30 WILD-TYPE
  ASIAN                                  6               70
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  7              161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(93) Variable = SETDB2 MUTATION ANALYSIS
D93V1, survival
                  sevent
clus2                0   1
  SETDB2 MUTATED     7   2
  SETDB2 WILD-TYPE 174  78
  SETDB2 MUTATED SETDB2 WILD-TYPE 
               9              252 
  SETDB2 MUTATED SETDB2 WILD-TYPE 
               2               78 
$`SETDB2 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8368 
       26.70         6.97        30.90        34.68        19.50         4.31 
TCGA-BR-8591 TCGA-CG-4305 TCGA-CG-4443 
       13.45        15.95        29.98 

$`SETDB2 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 
       11.70         6.61         4.64         7.43        18.35         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
       16.31         2.20        15.58         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       15.81         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  SETDB2 MUTATED SETDB2 WILD-TYPE 
            4.31             0.00 
  SETDB2 MUTATED SETDB2 WILD-TYPE 
           34.68           105.07 
  SETDB2 MUTATED SETDB2 WILD-TYPE 
          19.500           12.495 
[1] "4.3 - 34.7 (19.5)"  "0.0 - 105.1 (12.5)"
[1] "hr=" "2.3"
D93V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SETDB2 MUTATED         0        1        2        1         1         1
  SETDB2 WILD-TYPE       1        8       25       25        30        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SETDB2 MUTATED           0          1          0          2        0
  SETDB2 WILD-TYPE         3         48         36         22       24
D93V3, multiclass
            clus
vv           SETDB2 MUTATED SETDB2 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                2               25
  STAGE II                1               25
  STAGE IIA               1               30
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              2               22
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SETDB2 MUTATED     1   4   2   3
  SETDB2 WILD-TYPE  10  68 120  72
D93V4, multiclass
    clus
vv   SETDB2 MUTATED SETDB2 WILD-TYPE
  T1              1               10
  T2              4               68
  T3              2              120
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  SETDB2 MUTATED    5  2  1  1
  SETDB2 WILD-TYPE 88 79 49 52
D93V5, multiclass
    clus
vv   SETDB2 MUTATED SETDB2 WILD-TYPE
  N0              5               88
  N1              2               79
  N2              1               49
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V6, binary
                  cls
clus                 0   1
  SETDB2 MUTATED     9   0
  SETDB2 WILD-TYPE 248  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETDB2 MUTATED      9    0
  SETDB2 WILD-TYPE  248   18
   clus
vv  SETDB2 MUTATED SETDB2 WILD-TYPE
  0              9              248
  1              0               18
[1] 2 2
[1] FALSE
D93V7, binary
                  cls
clus                 0   1
  SETDB2 MUTATED     5   5
  SETDB2 WILD-TYPE 105 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETDB2 MUTATED      5    5
  SETDB2 WILD-TYPE  105  174
        clus
vv       SETDB2 MUTATED SETDB2 WILD-TYPE
  FEMALE              5              105
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SETDB2 MUTATED                                       1
  SETDB2 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SETDB2 MUTATED                                                        7
  SETDB2 WILD-TYPE                                                    128
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SETDB2 MUTATED                                                                   2
  SETDB2 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SETDB2 MUTATED                                                  0
  SETDB2 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SETDB2 MUTATED                                                          0
  SETDB2 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SETDB2 MUTATED                                                           0
  SETDB2 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SETDB2 MUTATED                                          0
  SETDB2 WILD-TYPE                                        3
D93V8, multiclass
                                                                   clus
vv                                                                  SETDB2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  SETDB2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V9, binary
                  cls
clus                 0   1
  SETDB2 MUTATED     0  10
  SETDB2 WILD-TYPE   5 274
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETDB2 MUTATED      0   10
  SETDB2 WILD-TYPE    5  274
     clus
vv    SETDB2 MUTATED SETDB2 WILD-TYPE
  NO               0                5
  YES             10              274
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SETDB2 MUTATED     8   0   0   2
  SETDB2 WILD-TYPE 219  10  10  22
D93V10, multiclass
    clus
vv   SETDB2 MUTATED SETDB2 WILD-TYPE
  R0              8              219
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SETDB2 MUTATED       0                         0     7
  SETDB2 WILD-TYPE    76                         4   161
D93V12, multiclass
                           clus
vv                          SETDB2 MUTATED SETDB2 WILD-TYPE
  ASIAN                                  0               76
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  7              161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(94) Variable = INPPL1 MUTATION ANALYSIS
D94V1, survival
                  sevent
clus2                0   1
  INPPL1 MUTATED    12   5
  INPPL1 WILD-TYPE 169  75
  INPPL1 MUTATED INPPL1 WILD-TYPE 
              17              244 
  INPPL1 MUTATED INPPL1 WILD-TYPE 
               5               75 
$`INPPL1 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-7707 
       26.70         6.97        30.90         9.57        34.68        23.93 
TCGA-BR-7851 TCGA-BR-8078 TCGA-BR-8361 TCGA-CD-5801 TCGA-CD-8536 TCGA-CG-4305 
       12.43        12.26        19.50        13.18         0.10        15.95 
TCGA-CG-4306 TCGA-CG-5721 TCGA-F1-A448 TCGA-HU-A4GT TCGA-HU-A4GU 
        1.02         6.02        21.27         6.51         6.25 

$`INPPL1 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 
       11.70         6.61         4.64         7.43        18.35         6.18 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       12.82         9.21        24.76        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
       11.57         5.13         2.83         3.25        13.15         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  INPPL1 MUTATED INPPL1 WILD-TYPE 
             0.1              0.0 
  INPPL1 MUTATED INPPL1 WILD-TYPE 
           34.68           105.07 
  INPPL1 MUTATED INPPL1 WILD-TYPE 
           12.43            12.64 
[1] "0.1 - 34.7 (12.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D94V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  INPPL1 MUTATED         0        0        2        3         2         4
  INPPL1 WILD-TYPE       1        9       25       23        29        40
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  INPPL1 MUTATED           0          2          1          1        3
  INPPL1 WILD-TYPE         3         47         35         23       21
D94V3, multiclass
            clus
vv           INPPL1 MUTATED INPPL1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                2               25
  STAGE II                3               23
  STAGE IIA               2               29
  STAGE IIB               4               40
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              1               35
  STAGE IIIC              1               23
  STAGE IV                3               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  INPPL1 MUTATED     0   5   9   6
  INPPL1 WILD-TYPE  11  67 113  69
D94V4, multiclass
    clus
vv   INPPL1 MUTATED INPPL1 WILD-TYPE
  T1              0               11
  T2              5               67
  T3              9              113
  T4              6               69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  INPPL1 MUTATED    8  7  3  1
  INPPL1 WILD-TYPE 85 74 47 52
D94V5, multiclass
    clus
vv   INPPL1 MUTATED INPPL1 WILD-TYPE
  N0              8               85
  N1              7               74
  N2              3               47
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V6, binary
                  cls
clus                 0   1
  INPPL1 MUTATED    19   1
  INPPL1 WILD-TYPE 238  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPPL1 MUTATED     19    1
  INPPL1 WILD-TYPE  238   17
   clus
vv  INPPL1 MUTATED INPPL1 WILD-TYPE
  0             19              238
  1              1               17
[1] 2 2
[1] FALSE
D94V7, binary
                  cls
clus                 0   1
  INPPL1 MUTATED    11  11
  INPPL1 WILD-TYPE  99 168
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPPL1 MUTATED     11   11
  INPPL1 WILD-TYPE   99  168
        clus
vv       INPPL1 MUTATED INPPL1 WILD-TYPE
  FEMALE             11               99
  MALE               11              168
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  INPPL1 MUTATED                                       2
  INPPL1 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  INPPL1 MUTATED                                                       15
  INPPL1 WILD-TYPE                                                    120
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  INPPL1 MUTATED                                                                   3
  INPPL1 WILD-TYPE                                                                37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  INPPL1 MUTATED                                                  1
  INPPL1 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  INPPL1 MUTATED                                                          1
  INPPL1 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  INPPL1 MUTATED                                                           0
  INPPL1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  INPPL1 MUTATED                                          0
  INPPL1 WILD-TYPE                                        3
D94V8, multiclass
                                                                   clus
vv                                                                  INPPL1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        15
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  INPPL1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         120
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V9, binary
                  cls
clus                 0   1
  INPPL1 MUTATED     0  22
  INPPL1 WILD-TYPE   5 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPPL1 MUTATED      0   22
  INPPL1 WILD-TYPE    5  262
     clus
vv    INPPL1 MUTATED INPPL1 WILD-TYPE
  NO               0                5
  YES             22              262
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  INPPL1 MUTATED    14   0   1   7
  INPPL1 WILD-TYPE 213  10   9  17
D94V10, multiclass
    clus
vv   INPPL1 MUTATED INPPL1 WILD-TYPE
  R0             14              213
  R1              0               10
  R2              1                9
  RX              7               17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  INPPL1 MUTATED       4                         0    14
  INPPL1 WILD-TYPE    72                         4   154
D94V12, multiclass
                           clus
vv                          INPPL1 MUTATED INPPL1 WILD-TYPE
  ASIAN                                  4               72
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                 14              154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(95) Variable = CTNND1 MUTATION ANALYSIS
D95V1, survival
                  sevent
clus2                0   1
  CTNND1 MUTATED    14   5
  CTNND1 WILD-TYPE 167  75
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              19              242 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
               5               75 
$`CTNND1 MUTATED`
TCGA-BR-4184 TCGA-BR-6566 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7851 TCGA-BR-8284 
        6.97        32.78        12.82        24.76        12.43         8.05 
TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8680 TCGA-CD-8536 TCGA-CG-4305 
        0.26        19.17        15.85        15.81         0.10        15.95 
TCGA-CG-4437 TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5733 TCGA-D7-A4Z0 TCGA-HU-A4GN 
        8.05         9.01         6.02        21.07        14.76        29.98 
TCGA-HU-A4H3 
       19.36 

$`CTNND1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 
       30.90        31.20        32.94         9.21        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       28.01        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        9.60        20.55        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40         6.18        19.50        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       47.05        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-EQ-5647 TCGA-EQ-8122 
       16.44         5.92        15.16        13.78         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  CTNND1 MUTATED CTNND1 WILD-TYPE 
             0.1              0.0 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
           32.78           105.07 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
          14.760           12.575 
[1] "0.1 - 32.8 (14.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D95V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CTNND1 MUTATED         0        1        1        3         2         2
  CTNND1 WILD-TYPE       1        8       26       23        29        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTNND1 MUTATED           0          2          0          4        4
  CTNND1 WILD-TYPE         3         47         36         20       20
D95V3, multiclass
            clus
vv           CTNND1 MUTATED CTNND1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                1               26
  STAGE II                3               23
  STAGE IIA               2               29
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              0               36
  STAGE IIIC              4               20
  STAGE IV                4               20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CTNND1 MUTATED     1   6   4   8
  CTNND1 WILD-TYPE  10  66 118  67
D95V4, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  T1              1               10
  T2              6               66
  T3              4              118
  T4              8               67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CTNND1 MUTATED    5  5  3  6
  CTNND1 WILD-TYPE 88 76 47 47
D95V5, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  N0              5               88
  N1              5               76
  N2              3               47
  N3              6               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V6, binary
                  cls
clus                 0   1
  CTNND1 MUTATED    15   3
  CTNND1 WILD-TYPE 242  15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED     15    3
  CTNND1 WILD-TYPE  242   15
   clus
vv  CTNND1 MUTATED CTNND1 WILD-TYPE
  0             15              242
  1              3               15
[1] 2 2
[1] FALSE
D95V7, binary
                  cls
clus                 0   1
  CTNND1 MUTATED     8  11
  CTNND1 WILD-TYPE 102 168
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED      8   11
  CTNND1 WILD-TYPE  102  168
        clus
vv       CTNND1 MUTATED CTNND1 WILD-TYPE
  FEMALE              8              102
  MALE               11              168
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CTNND1 MUTATED                                       2
  CTNND1 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CTNND1 MUTATED                                                        8
  CTNND1 WILD-TYPE                                                    127
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CTNND1 MUTATED                                                                   5
  CTNND1 WILD-TYPE                                                                35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CTNND1 MUTATED                                                  2
  CTNND1 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CTNND1 MUTATED                                                          1
  CTNND1 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CTNND1 MUTATED                                                           1
  CTNND1 WILD-TYPE                                                         5
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CTNND1 MUTATED                                          0
  CTNND1 WILD-TYPE                                        3
D95V8, multiclass
                                                                   clus
vv                                                                  CTNND1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  CTNND1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V9, binary
                  cls
clus                 0   1
  CTNND1 MUTATED     0  19
  CTNND1 WILD-TYPE   5 265
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED      0   19
  CTNND1 WILD-TYPE    5  265
     clus
vv    CTNND1 MUTATED CTNND1 WILD-TYPE
  NO               0                5
  YES             19              265
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CTNND1 MUTATED    17   0   1   1
  CTNND1 WILD-TYPE 210  10   9  23
D95V10, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  R0             17              210
  R1              0               10
  R2              1                9
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CTNND1 MUTATED       4                         0    10
  CTNND1 WILD-TYPE    72                         4   158
D95V12, multiclass
                           clus
vv                          CTNND1 MUTATED CTNND1 WILD-TYPE
  ASIAN                                  4               72
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                 10              158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(96) Variable = TFE3 MUTATION ANALYSIS
D96V1, survival
                sevent
clus2              0   1
  TFE3 MUTATED     6   1
  TFE3 WILD-TYPE 175  79
  TFE3 MUTATED TFE3 WILD-TYPE 
             7            254 
  TFE3 MUTATED TFE3 WILD-TYPE 
             1             79 
$`TFE3 MUTATED`
TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-A4CS TCGA-BR-A4QL 
       32.78        32.94        12.26         1.12         1.48        11.57 
TCGA-HU-A4G8 
       11.84 

$`TFE3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08        22.26        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  TFE3 MUTATED TFE3 WILD-TYPE 
          1.12           0.00 
  TFE3 MUTATED TFE3 WILD-TYPE 
         32.94         105.07 
  TFE3 MUTATED TFE3 WILD-TYPE 
         11.84          12.71 
[1] "1.1 - 32.9 (11.8)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "2.5"
D96V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TFE3 MUTATED         0        0        0        0         3         2
  TFE3 WILD-TYPE       1        9       27       26        28        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TFE3 MUTATED           0          1          1          1        0
  TFE3 WILD-TYPE         3         48         35         23       24
D96V3, multiclass
            clus
vv           TFE3 MUTATED TFE3 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              0             26
  STAGE IIA             3             28
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            1             23
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TFE3 MUTATED     0   0   5   3
  TFE3 WILD-TYPE  11  72 117  72
D96V4, multiclass
    clus
vv   TFE3 MUTATED TFE3 WILD-TYPE
  T1            0             11
  T2            0             72
  T3            5            117
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  TFE3 MUTATED    5  1  0  2
  TFE3 WILD-TYPE 88 80 50 51
D96V5, multiclass
    clus
vv   TFE3 MUTATED TFE3 WILD-TYPE
  N0            5             88
  N1            1             80
  N2            0             50
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V6, binary
                cls
clus               0   1
  TFE3 MUTATED     8   0
  TFE3 WILD-TYPE 249  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFE3 MUTATED      8    0
  TFE3 WILD-TYPE  249   18
   clus
vv  TFE3 MUTATED TFE3 WILD-TYPE
  0            8            249
  1            0             18
[1] 2 2
[1] FALSE
D96V7, binary
                cls
clus               0   1
  TFE3 MUTATED     7   1
  TFE3 WILD-TYPE 103 178
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFE3 MUTATED      7    1
  TFE3 WILD-TYPE  103  178
        clus
vv       TFE3 MUTATED TFE3 WILD-TYPE
  FEMALE            7            103
  MALE              1            178
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TFE3 MUTATED                                       1
  TFE3 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TFE3 MUTATED                                                        7
  TFE3 WILD-TYPE                                                    128
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TFE3 MUTATED                                                                   0
  TFE3 WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TFE3 MUTATED                                                  0
  TFE3 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TFE3 MUTATED                                                          0
  TFE3 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TFE3 MUTATED                                                           0
  TFE3 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TFE3 MUTATED                                          0
  TFE3 WILD-TYPE                                        3
D96V8, multiclass
                                                                   clus
vv                                                                  TFE3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  TFE3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V9, binary
                cls
clus               0   1
  TFE3 MUTATED     0   8
  TFE3 WILD-TYPE   5 276
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFE3 MUTATED      0    8
  TFE3 WILD-TYPE    5  276
     clus
vv    TFE3 MUTATED TFE3 WILD-TYPE
  NO             0              5
  YES            8            276
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TFE3 MUTATED     6   0   0   1
  TFE3 WILD-TYPE 221  10  10  23
D96V10, multiclass
    clus
vv   TFE3 MUTATED TFE3 WILD-TYPE
  R0            6            221
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TFE3 MUTATED       1                         0     7
  TFE3 WILD-TYPE    75                         4   161
D96V12, multiclass
                           clus
vv                          TFE3 MUTATED TFE3 WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                7            161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(97) Variable = SERPINI1 MUTATION ANALYSIS
D97V1, survival
                    sevent
clus2                  0   1
  SERPINI1 MUTATED     5   1
  SERPINI1 WILD-TYPE 176  79
  SERPINI1 MUTATED SERPINI1 WILD-TYPE 
                 6                255 
  SERPINI1 MUTATED SERPINI1 WILD-TYPE 
                 1                 79 
$`SERPINI1 MUTATED`
TCGA-BR-8360 TCGA-BR-8372 TCGA-BR-8589 TCGA-CG-4306 TCGA-HU-8602 TCGA-HU-A4H4 
        6.18        19.17        15.81         1.02        11.41        23.84 

$`SERPINI1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22         1.12        12.79         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  SERPINI1 MUTATED SERPINI1 WILD-TYPE 
              1.02               0.00 
  SERPINI1 MUTATED SERPINI1 WILD-TYPE 
             23.84             105.07 
  SERPINI1 MUTATED SERPINI1 WILD-TYPE 
             13.61              12.62 
[1] "1.0 - 23.8 (13.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.6"
D97V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SERPINI1 MUTATED         0        0        0        0         1         2
  SERPINI1 WILD-TYPE       1        9       27       26        30        42
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINI1 MUTATED           0          0          1          1        1
  SERPINI1 WILD-TYPE         3         49         35         23       23
D97V3, multiclass
            clus
vv           SERPINI1 MUTATED SERPINI1 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  0                 27
  STAGE II                  0                 26
  STAGE IIA                 1                 30
  STAGE IIB                 2                 42
  STAGE III                 0                  3
  STAGE IIIA                0                 49
  STAGE IIIB                1                 35
  STAGE IIIC                1                 23
  STAGE IV                  1                 23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SERPINI1 MUTATED     1   1   3   3
  SERPINI1 WILD-TYPE  10  71 119  72
D97V4, multiclass
    clus
vv   SERPINI1 MUTATED SERPINI1 WILD-TYPE
  T1                1                 10
  T2                1                 71
  T3                3                119
  T4                3                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  SERPINI1 MUTATED    2  1  2  1
  SERPINI1 WILD-TYPE 91 80 48 52
D97V5, multiclass
    clus
vv   SERPINI1 MUTATED SERPINI1 WILD-TYPE
  N0                2                 91
  N1                1                 80
  N2                2                 48
  N3                1                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V6, binary
                    cls
clus                   0   1
  SERPINI1 MUTATED     6   1
  SERPINI1 WILD-TYPE 251  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINI1 MUTATED      6    1
  SERPINI1 WILD-TYPE  251   17
   clus
vv  SERPINI1 MUTATED SERPINI1 WILD-TYPE
  0                6                251
  1                1                 17
[1] 2 2
[1] FALSE
D97V7, binary
                    cls
clus                   0   1
  SERPINI1 MUTATED     4   4
  SERPINI1 WILD-TYPE 106 175
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINI1 MUTATED      4    4
  SERPINI1 WILD-TYPE  106  175
        clus
vv       SERPINI1 MUTATED SERPINI1 WILD-TYPE
  FEMALE                4                106
  MALE                  4                175
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SERPINI1 MUTATED                                       1
  SERPINI1 WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SERPINI1 MUTATED                                                        5
  SERPINI1 WILD-TYPE                                                    130
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SERPINI1 MUTATED                                                                   1
  SERPINI1 WILD-TYPE                                                                39
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SERPINI1 MUTATED                                                  1
  SERPINI1 WILD-TYPE                                               37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SERPINI1 MUTATED                                                          0
  SERPINI1 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SERPINI1 MUTATED                                                           0
  SERPINI1 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SERPINI1 MUTATED                                          0
  SERPINI1 WILD-TYPE                                        3
D97V8, multiclass
                                                                   clus
vv                                                                  SERPINI1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  SERPINI1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V9, binary
                    cls
clus                   0   1
  SERPINI1 MUTATED     0   8
  SERPINI1 WILD-TYPE   5 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINI1 MUTATED      0    8
  SERPINI1 WILD-TYPE    5  276
     clus
vv    SERPINI1 MUTATED SERPINI1 WILD-TYPE
  NO                 0                  5
  YES                8                276
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  SERPINI1 MUTATED     5   0   1   2
  SERPINI1 WILD-TYPE 222  10   9  22
D97V10, multiclass
    clus
vv   SERPINI1 MUTATED SERPINI1 WILD-TYPE
  R0                5                222
  R1                0                 10
  R2                1                  9
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SERPINI1 MUTATED       2                         0     5
  SERPINI1 WILD-TYPE    74                         4   163
D97V12, multiclass
                           clus
vv                          SERPINI1 MUTATED SERPINI1 WILD-TYPE
  ASIAN                                    2                 74
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    5                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(98) Variable = SOX7 MUTATION ANALYSIS
D98V1, survival
                sevent
clus2              0   1
  SOX7 MUTATED     9   4
  SOX7 WILD-TYPE 172  76
  SOX7 MUTATED SOX7 WILD-TYPE 
            13            248 
  SOX7 MUTATED SOX7 WILD-TYPE 
             4             76 
$`SOX7 MUTATED`
TCGA-BR-4201 TCGA-BR-6453 TCGA-BR-8382 TCGA-BR-A4QL TCGA-CG-4465 TCGA-CG-5721 
       30.90        15.95        15.85        11.57         9.01         6.02 
TCGA-CG-5724 TCGA-CG-5726 TCGA-F1-6874 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       12.03        28.96        14.47        11.84        24.20         3.25 
TCGA-HU-A4H4 
       23.84 

$`SOX7 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6455 
       18.35         6.18         9.57         6.61        34.68        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5727 
       36.00         1.02         0.99         0.99       105.07        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 
       14.76         0.62         7.99        16.24        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GF 
        0.76        24.30         5.59        12.30        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        19.36        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  SOX7 MUTATED SOX7 WILD-TYPE 
          3.25           0.00 
  SOX7 MUTATED SOX7 WILD-TYPE 
         30.90         105.07 
  SOX7 MUTATED SOX7 WILD-TYPE 
        14.470         12.605 
[1] "3.2 - 30.9 (14.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D98V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SOX7 MUTATED         0        2        1        0         1         2
  SOX7 WILD-TYPE       1        7       26       26        30        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SOX7 MUTATED           0          1          2          1        3
  SOX7 WILD-TYPE         3         48         34         23       21
D98V3, multiclass
            clus
vv           SOX7 MUTATED SOX7 WILD-TYPE
  STAGE I               0              1
  STAGE IA              2              7
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             1             30
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            2             34
  STAGE IIIC            1             23
  STAGE IV              3             21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SOX7 MUTATED     2   4   3   5
  SOX7 WILD-TYPE   9  68 119  70
D98V4, multiclass
    clus
vv   SOX7 MUTATED SOX7 WILD-TYPE
  T1            2              9
  T2            4             68
  T3            3            119
  T4            5             70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  SOX7 MUTATED    4  3  2  4
  SOX7 WILD-TYPE 89 78 48 49
D98V5, multiclass
    clus
vv   SOX7 MUTATED SOX7 WILD-TYPE
  N0            4             89
  N1            3             78
  N2            2             48
  N3            4             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V6, binary
                cls
clus               0   1
  SOX7 MUTATED    13   2
  SOX7 WILD-TYPE 244  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX7 MUTATED     13    2
  SOX7 WILD-TYPE  244   16
   clus
vv  SOX7 MUTATED SOX7 WILD-TYPE
  0           13            244
  1            2             16
[1] 2 2
[1] FALSE
D98V7, binary
                cls
clus               0   1
  SOX7 MUTATED     9   6
  SOX7 WILD-TYPE 101 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX7 MUTATED      9    6
  SOX7 WILD-TYPE  101  173
        clus
vv       SOX7 MUTATED SOX7 WILD-TYPE
  FEMALE            9            101
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SOX7 MUTATED                                       4
  SOX7 WILD-TYPE                                    46
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SOX7 MUTATED                                                        6
  SOX7 WILD-TYPE                                                    129
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SOX7 MUTATED                                                                   3
  SOX7 WILD-TYPE                                                                37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SOX7 MUTATED                                                  2
  SOX7 WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SOX7 MUTATED                                                          0
  SOX7 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SOX7 MUTATED                                                           0
  SOX7 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SOX7 MUTATED                                          0
  SOX7 WILD-TYPE                                        3
D98V8, multiclass
                                                                   clus
vv                                                                  SOX7 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  SOX7 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V9, binary
                cls
clus               0   1
  SOX7 MUTATED     0  15
  SOX7 WILD-TYPE   5 269
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX7 MUTATED      0   15
  SOX7 WILD-TYPE    5  269
     clus
vv    SOX7 MUTATED SOX7 WILD-TYPE
  NO             0              5
  YES           15            269
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SOX7 MUTATED     9   0   2   3
  SOX7 WILD-TYPE 218  10   8  21
D98V10, multiclass
    clus
vv   SOX7 MUTATED SOX7 WILD-TYPE
  R0            9            218
  R1            0             10
  R2            2              8
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SOX7 MUTATED       4                         0     7
  SOX7 WILD-TYPE    72                         4   161
D98V12, multiclass
                           clus
vv                          SOX7 MUTATED SOX7 WILD-TYPE
  ASIAN                                4             72
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                7            161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(99) Variable = LEMD1 MUTATION ANALYSIS
D99V1, survival
                 sevent
clus2               0   1
  LEMD1 MUTATED     3   1
  LEMD1 WILD-TYPE 178  79
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              4             257 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              1              79 
$`LEMD1 MUTATED`
TCGA-BR-6452 TCGA-BR-8360 TCGA-CD-A4MG TCGA-FP-A4BE 
       34.68         6.18         6.58        11.08 

$`LEMD1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
        5.03        13.58         0.56         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  LEMD1 MUTATED LEMD1 WILD-TYPE 
           6.18            0.00 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
          34.68          105.07 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
           8.83           12.66 
[1] "6.2 - 34.7 (8.8)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.3"
D99V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LEMD1 MUTATED         0        0        0        0         4         0
  LEMD1 WILD-TYPE       1        9       27       26        27        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LEMD1 MUTATED           0          0          0          0        0
  LEMD1 WILD-TYPE         3         49         36         24       24
D99V3, multiclass
            clus
vv           LEMD1 MUTATED LEMD1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              4              27
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LEMD1 MUTATED     0   0   4   0
  LEMD1 WILD-TYPE  11  72 118  75
D99V4, multiclass
    clus
vv   LEMD1 MUTATED LEMD1 WILD-TYPE
  T1             0              11
  T2             0              72
  T3             4             118
  T4             0              75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  LEMD1 MUTATED    4  0  0  0
  LEMD1 WILD-TYPE 89 81 50 53
D99V5, multiclass
    clus
vv   LEMD1 MUTATED LEMD1 WILD-TYPE
  N0             4              89
  N1             0              81
  N2             0              50
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V6, binary
                 cls
clus                0   1
  LEMD1 MUTATED     4   0
  LEMD1 WILD-TYPE 253  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LEMD1 MUTATED      4    0
  LEMD1 WILD-TYPE  253   18
   clus
vv  LEMD1 MUTATED LEMD1 WILD-TYPE
  0             4             253
  1             0              18
[1] 2 2
[1] FALSE
D99V7, binary
                 cls
clus                0   1
  LEMD1 MUTATED     1   3
  LEMD1 WILD-TYPE 109 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LEMD1 MUTATED      1    3
  LEMD1 WILD-TYPE  109  176
        clus
vv       LEMD1 MUTATED LEMD1 WILD-TYPE
  FEMALE             1             109
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  LEMD1 MUTATED                                       1
  LEMD1 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LEMD1 MUTATED                                                        2
  LEMD1 WILD-TYPE                                                    133
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LEMD1 MUTATED                                                                   1
  LEMD1 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  LEMD1 MUTATED                                                  0
  LEMD1 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  LEMD1 MUTATED                                                          0
  LEMD1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  LEMD1 MUTATED                                                           0
  LEMD1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  LEMD1 MUTATED                                          0
  LEMD1 WILD-TYPE                                        3
D99V8, multiclass
                                                                   clus
vv                                                                  LEMD1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  LEMD1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V9, binary
                 cls
clus                0   1
  LEMD1 MUTATED     0   4
  LEMD1 WILD-TYPE   5 280
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LEMD1 MUTATED      0    4
  LEMD1 WILD-TYPE    5  280
     clus
vv    LEMD1 MUTATED LEMD1 WILD-TYPE
  NO              0               5
  YES             4             280
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LEMD1 MUTATED     3   0   0   0
  LEMD1 WILD-TYPE 224  10  10  24
D99V10, multiclass
    clus
vv   LEMD1 MUTATED LEMD1 WILD-TYPE
  R0             3             224
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LEMD1 MUTATED       1                         1     2
  LEMD1 WILD-TYPE    75                         3   166
D99V12, multiclass
                           clus
vv                          LEMD1 MUTATED LEMD1 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 2             166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(100) Variable = ARID1B MUTATION ANALYSIS
D100V1, survival
                  sevent
clus2                0   1
  ARID1B MUTATED    14   6
  ARID1B WILD-TYPE 167  74
  ARID1B MUTATED ARID1B WILD-TYPE 
              20              241 
  ARID1B MUTATED ARID1B WILD-TYPE 
               6               74 
$`ARID1B MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8284 
        6.97        30.90         6.61        34.68        20.55         8.05 
TCGA-BR-8361 TCGA-BR-8591 TCGA-BR-A4J4 TCGA-BR-A4QL TCGA-CD-5801 TCGA-CG-4465 
       19.50        13.45         0.53        11.57        13.18         9.01 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-A4G8 
        6.02       105.07        65.10        11.08        11.41        11.84 
TCGA-HU-A4GX TCGA-HU-A4H3 
       10.19        19.36 

$`ARID1B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       12.26         9.60        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J6 
       13.51        12.89         8.98         0.72        14.17         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.15         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        1.02         0.99         0.99        12.03        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
        5.03        13.58         0.56         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  ARID1B MUTATED ARID1B WILD-TYPE 
            0.53             0.00 
  ARID1B MUTATED ARID1B WILD-TYPE 
          105.07            79.07 
  ARID1B MUTATED ARID1B WILD-TYPE 
          11.705           12.660 
[1] "0.5 - 105.1 (11.7)" "0.0 - 79.1 (12.7)" 
[1] "hr=" "1.4"
D100V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARID1B MUTATED         0        0        1        2         2         3
  ARID1B WILD-TYPE       1        9       26       24        29        41
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID1B MUTATED           1          2          2          5        3
  ARID1B WILD-TYPE         2         47         34         19       21
D100V3, multiclass
            clus
vv           ARID1B MUTATED ARID1B WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                2               24
  STAGE IIA               2               29
  STAGE IIB               3               41
  STAGE III               1                2
  STAGE IIIA              2               47
  STAGE IIIB              2               34
  STAGE IIIC              5               19
  STAGE IV                3               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARID1B MUTATED     0   5   7  11
  ARID1B WILD-TYPE  11  67 115  64
D100V4, multiclass
    clus
vv   ARID1B MUTATED ARID1B WILD-TYPE
  T1              0               11
  T2              5               67
  T3              7              115
  T4             11               64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ARID1B MUTATED    5  9  4  5
  ARID1B WILD-TYPE 88 72 46 48
D100V5, multiclass
    clus
vv   ARID1B MUTATED ARID1B WILD-TYPE
  N0              5               88
  N1              9               72
  N2              4               46
  N3              5               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V6, binary
                  cls
clus                 0   1
  ARID1B MUTATED    24   1
  ARID1B WILD-TYPE 233  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1B MUTATED     24    1
  ARID1B WILD-TYPE  233   17
   clus
vv  ARID1B MUTATED ARID1B WILD-TYPE
  0             24              233
  1              1               17
[1] 2 2
[1] FALSE
D100V7, binary
                  cls
clus                 0   1
  ARID1B MUTATED    17  10
  ARID1B WILD-TYPE  93 169
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1B MUTATED     17   10
  ARID1B WILD-TYPE   93  169
        clus
vv       ARID1B MUTATED ARID1B WILD-TYPE
  FEMALE             17               93
  MALE               10              169
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ARID1B MUTATED                                       5
  ARID1B WILD-TYPE                                    45
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ARID1B MUTATED                                                       18
  ARID1B WILD-TYPE                                                    117
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ARID1B MUTATED                                                                   3
  ARID1B WILD-TYPE                                                                37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ARID1B MUTATED                                                  0
  ARID1B WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ARID1B MUTATED                                                          1
  ARID1B WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ARID1B MUTATED                                                           0
  ARID1B WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ARID1B MUTATED                                          0
  ARID1B WILD-TYPE                                        3
D100V8, multiclass
                                                                   clus
vv                                                                  ARID1B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        18
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ARID1B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         117
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V9, binary
                  cls
clus                 0   1
  ARID1B MUTATED     1  26
  ARID1B WILD-TYPE   4 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1B MUTATED      1   26
  ARID1B WILD-TYPE    4  258
     clus
vv    ARID1B MUTATED ARID1B WILD-TYPE
  NO               1                4
  YES             26              258
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ARID1B MUTATED    16   0   1   9
  ARID1B WILD-TYPE 211  10   9  15
D100V10, multiclass
    clus
vv   ARID1B MUTATED ARID1B WILD-TYPE
  R0             16              211
  R1              0               10
  R2              1                9
  RX              9               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID1B MUTATED       6                         1    15
  ARID1B WILD-TYPE    70                         3   153
D100V12, multiclass
                           clus
vv                          ARID1B MUTATED ARID1B WILD-TYPE
  ASIAN                                  6               70
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                 15              153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(101) Variable = PGM5 MUTATION ANALYSIS
D101V1, survival
                sevent
clus2              0   1
  PGM5 MUTATED    18   4
  PGM5 WILD-TYPE 163  76
  PGM5 MUTATED PGM5 WILD-TYPE 
            22            239 
  PGM5 MUTATED PGM5 WILD-TYPE 
             4             76 
$`PGM5 MUTATED`
TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8368 
       34.68        23.93        12.26        20.55        19.50         4.31 
TCGA-BR-8382 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4305 
       15.85        15.81        11.57         0.10         6.58        15.95 
TCGA-CG-4462 TCGA-D7-6521 TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-A4G8 
        0.00        18.54         5.92        11.08        11.41        11.84 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-HU-A4H8 
        0.10         6.51        19.36         8.88 

$`PGM5 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       14.43         0.69         9.60         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
       16.31         2.20        15.58         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        19.17        14.79         0.26         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 
       29.98        47.05        19.07        12.03         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
        5.03        13.58         0.56         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       11.77        29.98         8.98         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
        2.10        12.95        23.84        12.30         9.67        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  PGM5 MUTATED PGM5 WILD-TYPE 
          0.00           0.07 
  PGM5 MUTATED PGM5 WILD-TYPE 
         34.68         105.07 
  PGM5 MUTATED PGM5 WILD-TYPE 
        11.705         12.760 
[1] "0.0 - 34.7 (11.7)"  "0.1 - 105.1 (12.8)"
[1] "hr=" "1.5"
D101V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PGM5 MUTATED         0        0        3        3         4         5
  PGM5 WILD-TYPE       1        9       24       23        27        39
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PGM5 MUTATED           0          1          1          4        2
  PGM5 WILD-TYPE         3         48         35         20       22
D101V3, multiclass
            clus
vv           PGM5 MUTATED PGM5 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              3             24
  STAGE II              3             23
  STAGE IIA             4             27
  STAGE IIB             5             39
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            4             20
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PGM5 MUTATED     2   5   9   8
  PGM5 WILD-TYPE   9  67 113  67
D101V4, multiclass
    clus
vv   PGM5 MUTATED PGM5 WILD-TYPE
  T1            2              9
  T2            5             67
  T3            9            113
  T4            8             67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  PGM5 MUTATED   10  6  4  4
  PGM5 WILD-TYPE 83 75 46 49
D101V5, multiclass
    clus
vv   PGM5 MUTATED PGM5 WILD-TYPE
  N0           10             83
  N1            6             75
  N2            4             46
  N3            4             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V6, binary
                cls
clus               0   1
  PGM5 MUTATED    23   2
  PGM5 WILD-TYPE 234  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM5 MUTATED     23    2
  PGM5 WILD-TYPE  234   16
   clus
vv  PGM5 MUTATED PGM5 WILD-TYPE
  0           23            234
  1            2             16
[1] 2 2
[1] FALSE
D101V7, binary
                cls
clus               0   1
  PGM5 MUTATED    16   9
  PGM5 WILD-TYPE  94 170
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM5 MUTATED     16    9
  PGM5 WILD-TYPE   94  170
        clus
vv       PGM5 MUTATED PGM5 WILD-TYPE
  FEMALE           16             94
  MALE              9            170
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PGM5 MUTATED                                       6
  PGM5 WILD-TYPE                                    44
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PGM5 MUTATED                                                       13
  PGM5 WILD-TYPE                                                    122
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PGM5 MUTATED                                                                   0
  PGM5 WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PGM5 MUTATED                                                  5
  PGM5 WILD-TYPE                                               33
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PGM5 MUTATED                                                          1
  PGM5 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PGM5 MUTATED                                                           0
  PGM5 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PGM5 MUTATED                                          0
  PGM5 WILD-TYPE                                        3
D101V8, multiclass
                                                                   clus
vv                                                                  PGM5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      13
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  PGM5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         44
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       122
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V9, binary
                cls
clus               0   1
  PGM5 MUTATED     1  24
  PGM5 WILD-TYPE   4 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM5 MUTATED      1   24
  PGM5 WILD-TYPE    4  260
     clus
vv    PGM5 MUTATED PGM5 WILD-TYPE
  NO             1              4
  YES           24            260
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PGM5 MUTATED    20   0   1   2
  PGM5 WILD-TYPE 207  10   9  22
D101V10, multiclass
    clus
vv   PGM5 MUTATED PGM5 WILD-TYPE
  R0           20            207
  R1            0             10
  R2            1              9
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PGM5 MUTATED       9                         1    12
  PGM5 WILD-TYPE    67                         3   156
D101V12, multiclass
                           clus
vv                          PGM5 MUTATED PGM5 WILD-TYPE
  ASIAN                                9             67
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                               12            156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(102) Variable = FHOD3 MUTATION ANALYSIS
D102V1, survival
                 sevent
clus2               0   1
  FHOD3 MUTATED    15   7
  FHOD3 WILD-TYPE 166  73
  FHOD3 MUTATED FHOD3 WILD-TYPE 
             22             239 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
              7              73 
$`FHOD3 MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7197 TCGA-BR-7851 TCGA-BR-7958 
        6.97         6.61        34.68         9.21        12.43        12.76 
TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8487 
       12.26         8.05         6.18         0.26         4.31         1.12 
TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4466 TCGA-CG-5733 
        6.58        15.95         1.02         8.05        18.97        21.07 
TCGA-FP-7829 TCGA-HU-A4G9 TCGA-HU-A4GU TCGA-HU-A4H8 
       19.53        24.20         6.25         8.88 

$`FHOD3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       30.90         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       31.20        32.94        12.82        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       28.01        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
       19.50        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4438 
       12.62        20.02         3.02        27.02         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       14.47        72.23        21.27         3.48        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       11.84         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
       12.95        19.36        23.84        12.30         9.67        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  FHOD3 MUTATED FHOD3 WILD-TYPE 
           0.26            0.00 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
          34.68          105.07 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
          8.465          12.820 
[1] "0.3 - 34.7 (8.5)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.4"
D102V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FHOD3 MUTATED         0        1        4        3         4         4
  FHOD3 WILD-TYPE       1        8       23       23        27        40
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FHOD3 MUTATED           1          3          1          1        2
  FHOD3 WILD-TYPE         2         46         35         23       22
D102V3, multiclass
            clus
vv           FHOD3 MUTATED FHOD3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               4              23
  STAGE II               3              23
  STAGE IIA              4              27
  STAGE IIB              4              40
  STAGE III              1               2
  STAGE IIIA             3              46
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FHOD3 MUTATED     3   7   9   6
  FHOD3 WILD-TYPE   8  65 113  69
D102V4, multiclass
    clus
vv   FHOD3 MUTATED FHOD3 WILD-TYPE
  T1             3               8
  T2             7              65
  T3             9             113
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  FHOD3 MUTATED   13  8  3  1
  FHOD3 WILD-TYPE 80 73 47 52
D102V5, multiclass
    clus
vv   FHOD3 MUTATED FHOD3 WILD-TYPE
  N0            13              80
  N1             8              73
  N2             3              47
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V6, binary
                 cls
clus                0   1
  FHOD3 MUTATED    24   1
  FHOD3 WILD-TYPE 233  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD3 MUTATED     24    1
  FHOD3 WILD-TYPE  233   17
   clus
vv  FHOD3 MUTATED FHOD3 WILD-TYPE
  0            24             233
  1             1              17
[1] 2 2
[1] FALSE
D102V7, binary
                 cls
clus                0   1
  FHOD3 MUTATED    13  13
  FHOD3 WILD-TYPE  97 166
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD3 MUTATED     13   13
  FHOD3 WILD-TYPE   97  166
        clus
vv       FHOD3 MUTATED FHOD3 WILD-TYPE
  FEMALE            13              97
  MALE              13             166
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FHOD3 MUTATED                                       2
  FHOD3 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FHOD3 MUTATED                                                       15
  FHOD3 WILD-TYPE                                                    120
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FHOD3 MUTATED                                                                   6
  FHOD3 WILD-TYPE                                                                34
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FHOD3 MUTATED                                                  2
  FHOD3 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FHOD3 MUTATED                                                          1
  FHOD3 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FHOD3 MUTATED                                                           0
  FHOD3 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FHOD3 MUTATED                                          0
  FHOD3 WILD-TYPE                                        3
D102V8, multiclass
                                                                   clus
vv                                                                  FHOD3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       15
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  FHOD3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        120
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V9, binary
                 cls
clus                0   1
  FHOD3 MUTATED     0  26
  FHOD3 WILD-TYPE   5 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD3 MUTATED      0   26
  FHOD3 WILD-TYPE    5  258
     clus
vv    FHOD3 MUTATED FHOD3 WILD-TYPE
  NO              0               5
  YES            26             258
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FHOD3 MUTATED    18   0   1   6
  FHOD3 WILD-TYPE 209  10   9  18
D102V10, multiclass
    clus
vv   FHOD3 MUTATED FHOD3 WILD-TYPE
  R0            18             209
  R1             0              10
  R2             1               9
  RX             6              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FHOD3 MUTATED       4                         0    17
  FHOD3 WILD-TYPE    72                         4   151
D102V12, multiclass
                           clus
vv                          FHOD3 MUTATED FHOD3 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                17             151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(103) Variable = CABP5 MUTATION ANALYSIS
D103V1, survival
                 sevent
clus2               0   1
  CABP5 MUTATED     3   1
  CABP5 WILD-TYPE 178  79
  CABP5 MUTATED CABP5 WILD-TYPE 
              4             257 
  CABP5 MUTATED CABP5 WILD-TYPE 
              1              79 
$`CABP5 MUTATED`
TCGA-BR-6452 TCGA-BR-8361 TCGA-FP-A4BE TCGA-HU-A4GQ 
       34.68        19.50        11.08         0.10 

$`CABP5 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 
       59.54         5.03        13.58         0.56         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  CABP5 MUTATED CABP5 WILD-TYPE 
            0.1             0.0 
  CABP5 MUTATED CABP5 WILD-TYPE 
          34.68          105.07 
  CABP5 MUTATED CABP5 WILD-TYPE 
          15.29           12.62 
[1] "0.1 - 34.7 (15.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.5"
D103V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CABP5 MUTATED         0        0        1        0         2         0
  CABP5 WILD-TYPE       1        9       26       26        29        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CABP5 MUTATED           0          0          0          2        0
  CABP5 WILD-TYPE         3         49         36         22       24
D103V3, multiclass
            clus
vv           CABP5 MUTATED CABP5 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             2              22
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CABP5 MUTATED     0   1   2   2
  CABP5 WILD-TYPE  11  71 120  73
D103V4, multiclass
    clus
vv   CABP5 MUTATED CABP5 WILD-TYPE
  T1             0              11
  T2             1              71
  T3             2             120
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CABP5 MUTATED    3  0  2  0
  CABP5 WILD-TYPE 90 81 48 53
D103V5, multiclass
    clus
vv   CABP5 MUTATED CABP5 WILD-TYPE
  N0             3              90
  N1             0              81
  N2             2              48
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V6, binary
                 cls
clus                0   1
  CABP5 MUTATED     5   0
  CABP5 WILD-TYPE 252  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CABP5 MUTATED      5    0
  CABP5 WILD-TYPE  252   18
   clus
vv  CABP5 MUTATED CABP5 WILD-TYPE
  0             5             252
  1             0              18
[1] 2 2
[1] FALSE
D103V7, binary
                 cls
clus                0   1
  CABP5 MUTATED     2   3
  CABP5 WILD-TYPE 108 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CABP5 MUTATED      2    3
  CABP5 WILD-TYPE  108  176
        clus
vv       CABP5 MUTATED CABP5 WILD-TYPE
  FEMALE             2             108
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CABP5 MUTATED                                       0
  CABP5 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CABP5 MUTATED                                                        3
  CABP5 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CABP5 MUTATED                                                                   1
  CABP5 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CABP5 MUTATED                                                  1
  CABP5 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CABP5 MUTATED                                                          0
  CABP5 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CABP5 MUTATED                                                           0
  CABP5 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CABP5 MUTATED                                          0
  CABP5 WILD-TYPE                                        3
D103V8, multiclass
                                                                   clus
vv                                                                  CABP5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  CABP5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V9, binary
                 cls
clus                0   1
  CABP5 MUTATED     0   5
  CABP5 WILD-TYPE   5 279
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CABP5 MUTATED      0    5
  CABP5 WILD-TYPE    5  279
     clus
vv    CABP5 MUTATED CABP5 WILD-TYPE
  NO              0               5
  YES             5             279
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CABP5 MUTATED     5   0   0   0
  CABP5 WILD-TYPE 222  10  10  24
D103V10, multiclass
    clus
vv   CABP5 MUTATED CABP5 WILD-TYPE
  R0             5             222
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CABP5 MUTATED       1                         1     2
  CABP5 WILD-TYPE    75                         3   166
D103V12, multiclass
                           clus
vv                          CABP5 MUTATED CABP5 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 2             166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(104) Variable = TTF1 MUTATION ANALYSIS
D104V1, survival
                sevent
clus2              0   1
  TTF1 MUTATED    10   2
  TTF1 WILD-TYPE 171  78
  TTF1 MUTATED TTF1 WILD-TYPE 
            12            249 
  TTF1 MUTATED TTF1 WILD-TYPE 
             2             78 
$`TTF1 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8368 TCGA-BR-8382 
        6.97        30.90        34.68         6.18         4.31        15.85 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8680 TCGA-CG-4305 TCGA-D7-6822 TCGA-HU-A4GH 
        1.12        15.81        15.81        15.95        12.33        11.77 

$`TTF1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        2.66        16.31         2.20        15.58         7.40        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
        3.32        11.80        19.17        14.79         0.26         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 
        5.39        25.18         9.21        20.22        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.55        11.31        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  TTF1 MUTATED TTF1 WILD-TYPE 
          1.12           0.00 
  TTF1 MUTATED TTF1 WILD-TYPE 
         34.68         105.07 
  TTF1 MUTATED TTF1 WILD-TYPE 
         14.07          12.62 
[1] "1.1 - 34.7 (14.1)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2"  
D104V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TTF1 MUTATED         0        1        2        1         3         0
  TTF1 WILD-TYPE       1        8       25       25        28        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TTF1 MUTATED           0          1          1          1        2
  TTF1 WILD-TYPE         3         48         35         23       22
D104V3, multiclass
            clus
vv           TTF1 MUTATED TTF1 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              2             25
  STAGE II              1             25
  STAGE IIA             3             28
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            1             23
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TTF1 MUTATED     1   4   5   4
  TTF1 WILD-TYPE  10  68 117  71
D104V4, multiclass
    clus
vv   TTF1 MUTATED TTF1 WILD-TYPE
  T1            1             10
  T2            4             68
  T3            5            117
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  TTF1 MUTATED    6  3  2  1
  TTF1 WILD-TYPE 87 78 48 52
D104V5, multiclass
    clus
vv   TTF1 MUTATED TTF1 WILD-TYPE
  N0            6             87
  N1            3             78
  N2            2             48
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V6, binary
                cls
clus               0   1
  TTF1 MUTATED    11   1
  TTF1 WILD-TYPE 246  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED     11    1
  TTF1 WILD-TYPE  246   17
   clus
vv  TTF1 MUTATED TTF1 WILD-TYPE
  0           11            246
  1            1             17
[1] 2 2
[1] FALSE
D104V7, binary
                cls
clus               0   1
  TTF1 MUTATED     6   8
  TTF1 WILD-TYPE 104 171
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED      6    8
  TTF1 WILD-TYPE  104  171
        clus
vv       TTF1 MUTATED TTF1 WILD-TYPE
  FEMALE            6            104
  MALE              8            171
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TTF1 MUTATED                                       0
  TTF1 WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TTF1 MUTATED                                                       10
  TTF1 WILD-TYPE                                                    125
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TTF1 MUTATED                                                                   1
  TTF1 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TTF1 MUTATED                                                  3
  TTF1 WILD-TYPE                                               35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TTF1 MUTATED                                                          0
  TTF1 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TTF1 MUTATED                                                           0
  TTF1 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TTF1 MUTATED                                          0
  TTF1 WILD-TYPE                                        3
D104V8, multiclass
                                                                   clus
vv                                                                  TTF1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  TTF1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V9, binary
                cls
clus               0   1
  TTF1 MUTATED     0  14
  TTF1 WILD-TYPE   5 270
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED      0   14
  TTF1 WILD-TYPE    5  270
     clus
vv    TTF1 MUTATED TTF1 WILD-TYPE
  NO             0              5
  YES           14            270
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TTF1 MUTATED    10   0   0   4
  TTF1 WILD-TYPE 217  10  10  20
D104V10, multiclass
    clus
vv   TTF1 MUTATED TTF1 WILD-TYPE
  R0           10            217
  R1            0             10
  R2            0             10
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TTF1 MUTATED       2                         0    11
  TTF1 WILD-TYPE    74                         4   157
D104V12, multiclass
                           clus
vv                          TTF1 MUTATED TTF1 WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               11            157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(105) Variable = PHACTR4 MUTATION ANALYSIS
D105V1, survival
                   sevent
clus2                 0   1
  PHACTR4 MUTATED     5   3
  PHACTR4 WILD-TYPE 176  77
  PHACTR4 MUTATED PHACTR4 WILD-TYPE 
                8               253 
  PHACTR4 MUTATED PHACTR4 WILD-TYPE 
                3                77 
$`PHACTR4 MUTATED`
TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8487 TCGA-CG-5733 TCGA-D7-6525 TCGA-FP-7829 
       34.68         6.18         1.12        21.07        13.35        19.53 
TCGA-HU-A4GN TCGA-HU-A4GQ 
       29.98         0.10 

$`PHACTR4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 
       16.24        14.47        72.23        21.27         3.48        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       11.77         8.98         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  PHACTR4 MUTATED PHACTR4 WILD-TYPE 
              0.1               0.0 
  PHACTR4 MUTATED PHACTR4 WILD-TYPE 
            34.68            105.07 
  PHACTR4 MUTATED PHACTR4 WILD-TYPE 
            16.44             12.59 
[1] "0.1 - 34.7 (16.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1"  
D105V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PHACTR4 MUTATED         0        0        0        0         4         1
  PHACTR4 WILD-TYPE       1        9       27       26        27        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PHACTR4 MUTATED           0          2          0          1        0
  PHACTR4 WILD-TYPE         3         47         36         23       24
D105V3, multiclass
            clus
vv           PHACTR4 MUTATED PHACTR4 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 0                27
  STAGE II                 0                26
  STAGE IIA                4                27
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               2                47
  STAGE IIIB               0                36
  STAGE IIIC               1                23
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PHACTR4 MUTATED     0   3   4   1
  PHACTR4 WILD-TYPE  11  69 118  74
D105V4, multiclass
    clus
vv   PHACTR4 MUTATED PHACTR4 WILD-TYPE
  T1               0                11
  T2               3                69
  T3               4               118
  T4               1                74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  PHACTR4 MUTATED    3  2  3  0
  PHACTR4 WILD-TYPE 90 79 47 53
D105V5, multiclass
    clus
vv   PHACTR4 MUTATED PHACTR4 WILD-TYPE
  N0               3                90
  N1               2                79
  N2               3                47
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V6, binary
                   cls
clus                  0   1
  PHACTR4 MUTATED     8   0
  PHACTR4 WILD-TYPE 249  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR4 MUTATED      8    0
  PHACTR4 WILD-TYPE  249   18
   clus
vv  PHACTR4 MUTATED PHACTR4 WILD-TYPE
  0               8               249
  1               0                18
[1] 2 2
[1] FALSE
D105V7, binary
                   cls
clus                  0   1
  PHACTR4 MUTATED     3   5
  PHACTR4 WILD-TYPE 107 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR4 MUTATED      3    5
  PHACTR4 WILD-TYPE  107  174
        clus
vv       PHACTR4 MUTATED PHACTR4 WILD-TYPE
  FEMALE               3               107
  MALE                 5               174
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PHACTR4 MUTATED                                       1
  PHACTR4 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PHACTR4 MUTATED                                                        2
  PHACTR4 WILD-TYPE                                                    133
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PHACTR4 MUTATED                                                                   2
  PHACTR4 WILD-TYPE                                                                38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PHACTR4 MUTATED                                                  2
  PHACTR4 WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PHACTR4 MUTATED                                                          1
  PHACTR4 WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PHACTR4 MUTATED                                                           0
  PHACTR4 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PHACTR4 MUTATED                                          0
  PHACTR4 WILD-TYPE                                        3
D105V8, multiclass
                                                                   clus
vv                                                                  PHACTR4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  PHACTR4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V9, binary
                   cls
clus                  0   1
  PHACTR4 MUTATED     0   8
  PHACTR4 WILD-TYPE   5 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR4 MUTATED      0    8
  PHACTR4 WILD-TYPE    5  276
     clus
vv    PHACTR4 MUTATED PHACTR4 WILD-TYPE
  NO                0                 5
  YES               8               276
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PHACTR4 MUTATED     8   0   0   0
  PHACTR4 WILD-TYPE 219  10  10  24
D105V10, multiclass
    clus
vv   PHACTR4 MUTATED PHACTR4 WILD-TYPE
  R0               8               219
  R1               0                10
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHACTR4 MUTATED       2                         0     5
  PHACTR4 WILD-TYPE    74                         4   163
D105V12, multiclass
                           clus
vv                          PHACTR4 MUTATED PHACTR4 WILD-TYPE
  ASIAN                                   2                74
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   5               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(106) Variable = RBM43 MUTATION ANALYSIS
D106V1, survival
                 sevent
clus2               0   1
  RBM43 MUTATED     6   2
  RBM43 WILD-TYPE 175  78
  RBM43 MUTATED RBM43 WILD-TYPE 
              8             253 
  RBM43 MUTATED RBM43 WILD-TYPE 
              2              78 
$`RBM43 MUTATED`
TCGA-BR-4184 TCGA-BR-7197 TCGA-BR-8363 TCGA-CD-8531 TCGA-CG-5721 TCGA-CG-5723 
        6.97         9.21         0.26         0.10         6.02       105.07 
TCGA-HU-A4GU TCGA-HU-A4H5 
        6.25        12.30 

$`RBM43 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       21.11        30.90        31.20        32.94        12.82        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        19.50        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8535 
        0.07         0.10         0.13         0.16         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
        6.97        36.00         1.02         0.99         0.99        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       11.77        29.98         8.98         0.10         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        23.84         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  RBM43 MUTATED RBM43 WILD-TYPE 
            0.1             0.0 
  RBM43 MUTATED RBM43 WILD-TYPE 
         105.07           79.07 
  RBM43 MUTATED RBM43 WILD-TYPE 
           6.61           12.79 
[1] "0.1 - 105.1 (6.6)" "0.0 - 79.1 (12.8)"
[1] "hr=" "1.3"
D106V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RBM43 MUTATED         0        0        2        2         0         1
  RBM43 WILD-TYPE       1        9       25       24        31        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RBM43 MUTATED           0          2          0          0        1
  RBM43 WILD-TYPE         3         47         36         24       23
D106V3, multiclass
            clus
vv           RBM43 MUTATED RBM43 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               2              24
  STAGE IIA              0              31
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RBM43 MUTATED     0   3   4   1
  RBM43 WILD-TYPE  11  69 118  74
D106V4, multiclass
    clus
vv   RBM43 MUTATED RBM43 WILD-TYPE
  T1             0              11
  T2             3              69
  T3             4             118
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  RBM43 MUTATED    3  5  0  0
  RBM43 WILD-TYPE 90 76 50 53
D106V5, multiclass
    clus
vv   RBM43 MUTATED RBM43 WILD-TYPE
  N0             3              90
  N1             5              76
  N2             0              50
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V6, binary
                 cls
clus                0   1
  RBM43 MUTATED     8   0
  RBM43 WILD-TYPE 249  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM43 MUTATED      8    0
  RBM43 WILD-TYPE  249   18
   clus
vv  RBM43 MUTATED RBM43 WILD-TYPE
  0             8             249
  1             0              18
[1] 2 2
[1] FALSE
D106V7, binary
                 cls
clus                0   1
  RBM43 MUTATED     3   6
  RBM43 WILD-TYPE 107 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM43 MUTATED      3    6
  RBM43 WILD-TYPE  107  173
        clus
vv       RBM43 MUTATED RBM43 WILD-TYPE
  FEMALE             3             107
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RBM43 MUTATED                                       2
  RBM43 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RBM43 MUTATED                                                        5
  RBM43 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RBM43 MUTATED                                                                   1
  RBM43 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RBM43 MUTATED                                                  0
  RBM43 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RBM43 MUTATED                                                          0
  RBM43 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RBM43 MUTATED                                                           1
  RBM43 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RBM43 MUTATED                                          0
  RBM43 WILD-TYPE                                        3
D106V8, multiclass
                                                                   clus
vv                                                                  RBM43 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  RBM43 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V9, binary
                 cls
clus                0   1
  RBM43 MUTATED     0   9
  RBM43 WILD-TYPE   5 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM43 MUTATED      0    9
  RBM43 WILD-TYPE    5  275
     clus
vv    RBM43 MUTATED RBM43 WILD-TYPE
  NO              0               5
  YES             9             275
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RBM43 MUTATED     7   0   0   2
  RBM43 WILD-TYPE 220  10  10  22
D106V10, multiclass
    clus
vv   RBM43 MUTATED RBM43 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM43 MUTATED       3                         0     4
  RBM43 WILD-TYPE    73                         4   164
D106V12, multiclass
                           clus
vv                          RBM43 MUTATED RBM43 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(107) Variable = CDC25C MUTATION ANALYSIS
D107V1, survival
                  sevent
clus2                0   1
  CDC25C MUTATED     8   4
  CDC25C WILD-TYPE 173  76
  CDC25C MUTATED CDC25C WILD-TYPE 
              12              249 
  CDC25C MUTATED CDC25C WILD-TYPE 
               4               76 
$`CDC25C MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7851 TCGA-BR-8081 TCGA-BR-8680 TCGA-BR-8687 
        6.97        34.68        12.43        20.55        15.81         8.22 
TCGA-CD-8536 TCGA-D7-A4YU TCGA-HJ-7597 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4H8 
        0.10        16.44        26.47        29.98         0.10         8.88 

$`CDC25C WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69        12.26         9.60         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
        0.16         0.10         0.10         0.13         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GT 
        3.25        22.75        25.81        11.77         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  CDC25C MUTATED CDC25C WILD-TYPE 
             0.1              0.0 
  CDC25C MUTATED CDC25C WILD-TYPE 
           34.68           105.07 
  CDC25C MUTATED CDC25C WILD-TYPE 
           14.12            12.62 
[1] "0.1 - 34.7 (14.1)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D107V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDC25C MUTATED         0        0        2        1         2         2
  CDC25C WILD-TYPE       1        9       25       25        29        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDC25C MUTATED           0          2          1          2        1
  CDC25C WILD-TYPE         3         47         35         22       23
D107V3, multiclass
            clus
vv           CDC25C MUTATED CDC25C WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                2               25
  STAGE II                1               25
  STAGE IIA               2               29
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              1               35
  STAGE IIIC              2               22
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CDC25C MUTATED     1   2   4   6
  CDC25C WILD-TYPE  10  70 118  69
D107V4, multiclass
    clus
vv   CDC25C MUTATED CDC25C WILD-TYPE
  T1              1               10
  T2              2               70
  T3              4              118
  T4              6               69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CDC25C MUTATED    6  3  3  1
  CDC25C WILD-TYPE 87 78 47 52
D107V5, multiclass
    clus
vv   CDC25C MUTATED CDC25C WILD-TYPE
  N0              6               87
  N1              3               78
  N2              3               47
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V6, binary
                  cls
clus                 0   1
  CDC25C MUTATED    10   1
  CDC25C WILD-TYPE 247  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC25C MUTATED     10    1
  CDC25C WILD-TYPE  247   17
   clus
vv  CDC25C MUTATED CDC25C WILD-TYPE
  0             10              247
  1              1               17
[1] 2 2
[1] FALSE
D107V7, binary
                  cls
clus                 0   1
  CDC25C MUTATED     5   8
  CDC25C WILD-TYPE 105 171
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC25C MUTATED      5    8
  CDC25C WILD-TYPE  105  171
        clus
vv       CDC25C MUTATED CDC25C WILD-TYPE
  FEMALE              5              105
  MALE                8              171
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CDC25C MUTATED                                       0
  CDC25C WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CDC25C MUTATED                                                        6
  CDC25C WILD-TYPE                                                    129
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CDC25C MUTATED                                                                   1
  CDC25C WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CDC25C MUTATED                                                  5
  CDC25C WILD-TYPE                                               33
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CDC25C MUTATED                                                          0
  CDC25C WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CDC25C MUTATED                                                           0
  CDC25C WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CDC25C MUTATED                                          1
  CDC25C WILD-TYPE                                        2
D107V8, multiclass
                                                                   clus
vv                                                                  CDC25C MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       1
                                                                   clus
vv                                                                  CDC25C WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V9, binary
                  cls
clus                 0   1
  CDC25C MUTATED     0  13
  CDC25C WILD-TYPE   5 271
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC25C MUTATED      0   13
  CDC25C WILD-TYPE    5  271
     clus
vv    CDC25C MUTATED CDC25C WILD-TYPE
  NO               0                5
  YES             13              271
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CDC25C MUTATED    10   1   0   2
  CDC25C WILD-TYPE 217   9  10  22
D107V10, multiclass
    clus
vv   CDC25C MUTATED CDC25C WILD-TYPE
  R0             10              217
  R1              1                9
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDC25C MUTATED       5                         0     8
  CDC25C WILD-TYPE    71                         4   160
D107V12, multiclass
                           clus
vv                          CDC25C MUTATED CDC25C WILD-TYPE
  ASIAN                                  5               71
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  8              160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(108) Variable = GPR161 MUTATION ANALYSIS
D108V1, survival
                  sevent
clus2                0   1
  GPR161 MUTATED     6   3
  GPR161 WILD-TYPE 175  77
  GPR161 MUTATED GPR161 WILD-TYPE 
               9              252 
  GPR161 MUTATED GPR161 WILD-TYPE 
               3               77 
$`GPR161 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8078 TCGA-CD-8536 TCGA-CG-5723 TCGA-CG-5726 
        6.97        30.90        12.26         0.10       105.07        28.96 
TCGA-CG-5728 TCGA-FP-8211 TCGA-HU-A4H8 
       65.10        13.58         8.88 

$`GPR161 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       12.03        79.07         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       17.06        59.54         5.03         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  GPR161 MUTATED GPR161 WILD-TYPE 
             0.1              0.0 
  GPR161 MUTATED GPR161 WILD-TYPE 
          105.07            79.07 
  GPR161 MUTATED GPR161 WILD-TYPE 
          13.580           12.605 
[1] "0.1 - 105.1 (13.6)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.9"
D108V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPR161 MUTATED         0        1        2        2         0         2
  GPR161 WILD-TYPE       1        8       25       24        31        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR161 MUTATED           0          2          0          0        0
  GPR161 WILD-TYPE         3         47         36         24       24
D108V3, multiclass
            clus
vv           GPR161 MUTATED GPR161 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                2               25
  STAGE II                2               24
  STAGE IIA               0               31
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR161 MUTATED     2   3   5   1
  GPR161 WILD-TYPE   9  69 117  74
D108V4, multiclass
    clus
vv   GPR161 MUTATED GPR161 WILD-TYPE
  T1              2                9
  T2              3               69
  T3              5              117
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  GPR161 MUTATED    4  5  0  0
  GPR161 WILD-TYPE 89 76 50 53
D108V5, multiclass
    clus
vv   GPR161 MUTATED GPR161 WILD-TYPE
  N0              4               89
  N1              5               76
  N2              0               50
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V6, binary
                  cls
clus                 0   1
  GPR161 MUTATED     9   0
  GPR161 WILD-TYPE 248  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR161 MUTATED      9    0
  GPR161 WILD-TYPE  248   18
   clus
vv  GPR161 MUTATED GPR161 WILD-TYPE
  0              9              248
  1              0               18
[1] 2 2
[1] FALSE
D108V7, binary
                  cls
clus                 0   1
  GPR161 MUTATED     5   7
  GPR161 WILD-TYPE 105 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR161 MUTATED      5    7
  GPR161 WILD-TYPE  105  172
        clus
vv       GPR161 MUTATED GPR161 WILD-TYPE
  FEMALE              5              105
  MALE                7              172
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GPR161 MUTATED                                       0
  GPR161 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPR161 MUTATED                                                        9
  GPR161 WILD-TYPE                                                    126
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPR161 MUTATED                                                                   2
  GPR161 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GPR161 MUTATED                                                  1
  GPR161 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GPR161 MUTATED                                                          0
  GPR161 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GPR161 MUTATED                                                           0
  GPR161 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GPR161 MUTATED                                          0
  GPR161 WILD-TYPE                                        3
D108V8, multiclass
                                                                   clus
vv                                                                  GPR161 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  GPR161 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V9, binary
                  cls
clus                 0   1
  GPR161 MUTATED     0  12
  GPR161 WILD-TYPE   5 272
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR161 MUTATED      0   12
  GPR161 WILD-TYPE    5  272
     clus
vv    GPR161 MUTATED GPR161 WILD-TYPE
  NO               0                5
  YES             12              272
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GPR161 MUTATED     7   1   0   4
  GPR161 WILD-TYPE 220   9  10  20
D108V10, multiclass
    clus
vv   GPR161 MUTATED GPR161 WILD-TYPE
  R0              7              220
  R1              1                9
  R2              0               10
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPR161 MUTATED       3                         0     6
  GPR161 WILD-TYPE    73                         4   162
D108V12, multiclass
                           clus
vv                          GPR161 MUTATED GPR161 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(109) Variable = SVIL MUTATION ANALYSIS
D109V1, survival
                sevent
clus2              0   1
  SVIL MUTATED    17   4
  SVIL WILD-TYPE 164  76
  SVIL MUTATED SVIL WILD-TYPE 
            21            240 
  SVIL MUTATED SVIL WILD-TYPE 
             4             76 
$`SVIL MUTATED`
TCGA-BR-6452 TCGA-BR-6803 TCGA-BR-7707 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8368 
       34.68        31.20        23.93        19.50         0.26         4.31 
TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4PE TCGA-CD-A4MI TCGA-CG-4465 
       19.17         1.12        15.81        20.42         0.10         9.01 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-A4YV TCGA-HU-8602 
        6.02       105.07        28.96        65.10         5.92        11.41 
TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GX 
       11.84        29.98        10.19 

$`SVIL WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       19.36        13.51        20.65         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5730 
        1.02         0.99         0.99        12.03        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       16.44        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  SVIL MUTATED SVIL WILD-TYPE 
           0.1            0.0 
  SVIL MUTATED SVIL WILD-TYPE 
        105.07          79.07 
  SVIL MUTATED SVIL WILD-TYPE 
        15.810         12.605 
[1] "0.1 - 105.1 (15.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "2.6"
D109V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SVIL MUTATED         1        1        5        1         4         3
  SVIL WILD-TYPE       0        8       22       25        27        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SVIL MUTATED           0          1          1          4        4
  SVIL WILD-TYPE         3         48         35         20       20
D109V3, multiclass
            clus
vv           SVIL MUTATED SVIL WILD-TYPE
  STAGE I               1              0
  STAGE IA              1              8
  STAGE IB              5             22
  STAGE II              1             25
  STAGE IIA             4             27
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            4             20
  STAGE IV              4             20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SVIL MUTATED     3   7   6  10
  SVIL WILD-TYPE   8  65 116  65
D109V4, multiclass
    clus
vv   SVIL MUTATED SVIL WILD-TYPE
  T1            3              8
  T2            7             65
  T3            6            116
  T4           10             65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  SVIL MUTATED   11  7  4  3
  SVIL WILD-TYPE 82 74 46 50
D109V5, multiclass
    clus
vv   SVIL MUTATED SVIL WILD-TYPE
  N0           11             82
  N1            7             74
  N2            4             46
  N3            3             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V6, binary
                cls
clus               0   1
  SVIL MUTATED    23   2
  SVIL WILD-TYPE 234  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  SVIL MUTATED     23    2
  SVIL WILD-TYPE  234   16
   clus
vv  SVIL MUTATED SVIL WILD-TYPE
  0           23            234
  1            2             16
[1] 2 2
[1] FALSE
D109V7, binary
                cls
clus               0   1
  SVIL MUTATED    17   9
  SVIL WILD-TYPE  93 170
[1] "tbl2"
                cls
clus             [,1] [,2]
  SVIL MUTATED     17    9
  SVIL WILD-TYPE   93  170
        clus
vv       SVIL MUTATED SVIL WILD-TYPE
  FEMALE           17             93
  MALE              9            170
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SVIL MUTATED                                       6
  SVIL WILD-TYPE                                    44
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SVIL MUTATED                                                       14
  SVIL WILD-TYPE                                                    121
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SVIL MUTATED                                                                   3
  SVIL WILD-TYPE                                                                37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SVIL MUTATED                                                  3
  SVIL WILD-TYPE                                               35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SVIL MUTATED                                                          0
  SVIL WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SVIL MUTATED                                                           0
  SVIL WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SVIL MUTATED                                          0
  SVIL WILD-TYPE                                        3
D109V8, multiclass
                                                                   clus
vv                                                                  SVIL MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      14
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  SVIL WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         44
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       121
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V9, binary
                cls
clus               0   1
  SVIL MUTATED     0  26
  SVIL WILD-TYPE   5 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  SVIL MUTATED      0   26
  SVIL WILD-TYPE    5  258
     clus
vv    SVIL MUTATED SVIL WILD-TYPE
  NO             0              5
  YES           26            258
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SVIL MUTATED    20   0   1   3
  SVIL WILD-TYPE 207  10   9  21
D109V10, multiclass
    clus
vv   SVIL MUTATED SVIL WILD-TYPE
  R0           20            207
  R1            0             10
  R2            1              9
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SVIL MUTATED       6                         1    13
  SVIL WILD-TYPE    70                         3   155
D109V12, multiclass
                           clus
vv                          SVIL MUTATED SVIL WILD-TYPE
  ASIAN                                6             70
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                               13            155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(110) Variable = PMEPA1 MUTATION ANALYSIS
D110V1, survival
                  sevent
clus2                0   1
  PMEPA1 MUTATED     3   1
  PMEPA1 WILD-TYPE 178  79
  PMEPA1 MUTATED PMEPA1 WILD-TYPE 
               4              257 
  PMEPA1 MUTATED PMEPA1 WILD-TYPE 
               1               79 
$`PMEPA1 MUTATED`
TCGA-BR-6802 TCGA-BR-8363 TCGA-CG-5721 TCGA-HU-A4GT 
       30.90         0.26         6.02         6.51 

$`PMEPA1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        19.50        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  PMEPA1 MUTATED PMEPA1 WILD-TYPE 
            0.26             0.00 
  PMEPA1 MUTATED PMEPA1 WILD-TYPE 
           30.90           105.07 
  PMEPA1 MUTATED PMEPA1 WILD-TYPE 
           6.265           12.660 
[1] "0.3 - 30.9 (6.3)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1"  
D110V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PMEPA1 MUTATED         0        0        1        0         1         0
  PMEPA1 WILD-TYPE       1        9       26       26        30        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PMEPA1 MUTATED           0          2          0          0        1
  PMEPA1 WILD-TYPE         3         47         36         24       23
D110V3, multiclass
            clus
vv           PMEPA1 MUTATED PMEPA1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PMEPA1 MUTATED     0   1   2   2
  PMEPA1 WILD-TYPE  11  71 120  73
D110V4, multiclass
    clus
vv   PMEPA1 MUTATED PMEPA1 WILD-TYPE
  T1              0               11
  T2              1               71
  T3              2              120
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  PMEPA1 MUTATED    3  1  1  0
  PMEPA1 WILD-TYPE 90 80 49 53
D110V5, multiclass
    clus
vv   PMEPA1 MUTATED PMEPA1 WILD-TYPE
  N0              3               90
  N1              1               80
  N2              1               49
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V6, binary
                  cls
clus                 0   1
  PMEPA1 MUTATED     6   0
  PMEPA1 WILD-TYPE 251  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PMEPA1 MUTATED      6    0
  PMEPA1 WILD-TYPE  251   18
   clus
vv  PMEPA1 MUTATED PMEPA1 WILD-TYPE
  0              6              251
  1              0               18
[1] 2 2
[1] FALSE
D110V7, binary
                  cls
clus                 0   1
  PMEPA1 MUTATED     4   2
  PMEPA1 WILD-TYPE 106 177
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PMEPA1 MUTATED      4    2
  PMEPA1 WILD-TYPE  106  177
        clus
vv       PMEPA1 MUTATED PMEPA1 WILD-TYPE
  FEMALE              4              106
  MALE                2              177
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PMEPA1 MUTATED                                       0
  PMEPA1 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PMEPA1 MUTATED                                                        4
  PMEPA1 WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PMEPA1 MUTATED                                                                   1
  PMEPA1 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PMEPA1 MUTATED                                                  1
  PMEPA1 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PMEPA1 MUTATED                                                          0
  PMEPA1 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PMEPA1 MUTATED                                                           0
  PMEPA1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PMEPA1 MUTATED                                          0
  PMEPA1 WILD-TYPE                                        3
D110V8, multiclass
                                                                   clus
vv                                                                  PMEPA1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  PMEPA1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V9, binary
                  cls
clus                 0   1
  PMEPA1 MUTATED     0   6
  PMEPA1 WILD-TYPE   5 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PMEPA1 MUTATED      0    6
  PMEPA1 WILD-TYPE    5  278
     clus
vv    PMEPA1 MUTATED PMEPA1 WILD-TYPE
  NO               0                5
  YES              6              278
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PMEPA1 MUTATED     4   0   0   2
  PMEPA1 WILD-TYPE 223  10  10  22
D110V10, multiclass
    clus
vv   PMEPA1 MUTATED PMEPA1 WILD-TYPE
  R0              4              223
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PMEPA1 MUTATED       1                         0     4
  PMEPA1 WILD-TYPE    75                         4   164
D110V12, multiclass
                           clus
vv                          PMEPA1 MUTATED PMEPA1 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(111) Variable = FILIP1L MUTATION ANALYSIS
D111V1, survival
                   sevent
clus2                 0   1
  FILIP1L MUTATED    10   4
  FILIP1L WILD-TYPE 171  76
  FILIP1L MUTATED FILIP1L WILD-TYPE 
               14               247 
  FILIP1L MUTATED FILIP1L WILD-TYPE 
                4                76 
$`FILIP1L MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8372 
       34.68        12.26         6.18        19.50         0.26        19.17 
TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4J1 TCGA-BR-A4QL TCGA-D7-6525 TCGA-D7-6820 
       13.45        15.81         0.72        11.57        13.35        11.31 
TCGA-HU-A4GQ TCGA-HU-A4GX 
        0.10        10.19 

$`FILIP1L WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       15.81         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       13.51        12.89         8.98        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       11.77        29.98         8.98         6.51         6.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  FILIP1L MUTATED FILIP1L WILD-TYPE 
              0.1               0.0 
  FILIP1L MUTATED FILIP1L WILD-TYPE 
            34.68            105.07 
  FILIP1L MUTATED FILIP1L WILD-TYPE 
           11.915            12.660 
[1] "0.1 - 34.7 (11.9)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.1"
D111V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FILIP1L MUTATED         0        0        2        0         2         2
  FILIP1L WILD-TYPE       1        9       25       26        29        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FILIP1L MUTATED           0          3          1          5        1
  FILIP1L WILD-TYPE         3         46         35         19       23
D111V3, multiclass
            clus
vv           FILIP1L MUTATED FILIP1L WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 2                25
  STAGE II                 0                26
  STAGE IIA                2                29
  STAGE IIB                2                42
  STAGE III                0                 3
  STAGE IIIA               3                46
  STAGE IIIB               1                35
  STAGE IIIC               5                19
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FILIP1L MUTATED     1   4   3   9
  FILIP1L WILD-TYPE  10  68 119  66
D111V4, multiclass
    clus
vv   FILIP1L MUTATED FILIP1L WILD-TYPE
  T1               1                10
  T2               4                68
  T3               3               119
  T4               9                66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  FILIP1L MUTATED    6  2  5  3
  FILIP1L WILD-TYPE 87 79 45 50
D111V5, multiclass
    clus
vv   FILIP1L MUTATED FILIP1L WILD-TYPE
  N0               6                87
  N1               2                79
  N2               5                45
  N3               3                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V6, binary
                   cls
clus                  0   1
  FILIP1L MUTATED    16   1
  FILIP1L WILD-TYPE 241  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FILIP1L MUTATED     16    1
  FILIP1L WILD-TYPE  241   17
   clus
vv  FILIP1L MUTATED FILIP1L WILD-TYPE
  0              16               241
  1               1                17
[1] 2 2
[1] FALSE
D111V7, binary
                   cls
clus                  0   1
  FILIP1L MUTATED     8   9
  FILIP1L WILD-TYPE 102 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FILIP1L MUTATED      8    9
  FILIP1L WILD-TYPE  102  170
        clus
vv       FILIP1L MUTATED FILIP1L WILD-TYPE
  FEMALE               8               102
  MALE                 9               170
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FILIP1L MUTATED                                       2
  FILIP1L WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FILIP1L MUTATED                                                       10
  FILIP1L WILD-TYPE                                                    125
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FILIP1L MUTATED                                                                   2
  FILIP1L WILD-TYPE                                                                38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FILIP1L MUTATED                                                  3
  FILIP1L WILD-TYPE                                               35
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FILIP1L MUTATED                                                          0
  FILIP1L WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FILIP1L MUTATED                                                           0
  FILIP1L WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FILIP1L MUTATED                                          0
  FILIP1L WILD-TYPE                                        3
D111V8, multiclass
                                                                   clus
vv                                                                  FILIP1L MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  FILIP1L WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V9, binary
                   cls
clus                  0   1
  FILIP1L MUTATED     0  17
  FILIP1L WILD-TYPE   5 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FILIP1L MUTATED      0   17
  FILIP1L WILD-TYPE    5  267
     clus
vv    FILIP1L MUTATED FILIP1L WILD-TYPE
  NO                0                 5
  YES              17               267
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FILIP1L MUTATED    15   0   0   2
  FILIP1L WILD-TYPE 212  10  10  22
D111V10, multiclass
    clus
vv   FILIP1L MUTATED FILIP1L WILD-TYPE
  R0              15               212
  R1               0                10
  R2               0                10
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FILIP1L MUTATED       4                         0    12
  FILIP1L WILD-TYPE    72                         4   156
D111V12, multiclass
                           clus
vv                          FILIP1L MUTATED FILIP1L WILD-TYPE
  ASIAN                                   4                72
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                  12               156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(112) Variable = CTSC MUTATION ANALYSIS
D112V1, survival
                sevent
clus2              0   1
  CTSC MUTATED     6   1
  CTSC WILD-TYPE 175  79
  CTSC MUTATED CTSC WILD-TYPE 
             7            254 
  CTSC MUTATED CTSC WILD-TYPE 
             1             79 
$`CTSC MUTATED`
TCGA-BR-4201 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8372 TCGA-BR-A4QL TCGA-CD-A4MI 
       30.90        23.93        12.26        19.17        11.57         0.10 
TCGA-HU-A4G8 
       11.84 

$`CTSC WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        13.64         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  CTSC MUTATED CTSC WILD-TYPE 
           0.1            0.0 
  CTSC MUTATED CTSC WILD-TYPE 
         30.90         105.07 
  CTSC MUTATED CTSC WILD-TYPE 
         12.26          12.64 
[1] "0.1 - 30.9 (12.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.5"
D112V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CTSC MUTATED         0        0        1        0         0         2
  CTSC WILD-TYPE       1        9       26       26        31        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTSC MUTATED           0          1          2          1        0
  CTSC WILD-TYPE         3         48         34         23       24
D112V3, multiclass
            clus
vv           CTSC MUTATED CTSC WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             0             31
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            2             34
  STAGE IIIC            1             23
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CTSC MUTATED     0   2   3   3
  CTSC WILD-TYPE  11  70 119  72
D112V4, multiclass
    clus
vv   CTSC MUTATED CTSC WILD-TYPE
  T1            0             11
  T2            2             70
  T3            3            119
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  CTSC MUTATED    3  4  0  2
  CTSC WILD-TYPE 90 77 50 51
D112V5, multiclass
    clus
vv   CTSC MUTATED CTSC WILD-TYPE
  N0            3             90
  N1            4             77
  N2            0             50
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V6, binary
                cls
clus               0   1
  CTSC MUTATED    10   0
  CTSC WILD-TYPE 247  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSC MUTATED     10    0
  CTSC WILD-TYPE  247   18
   clus
vv  CTSC MUTATED CTSC WILD-TYPE
  0           10            247
  1            0             18
[1] 2 2
[1] FALSE
D112V7, binary
                cls
clus               0   1
  CTSC MUTATED     7   3
  CTSC WILD-TYPE 103 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSC MUTATED      7    3
  CTSC WILD-TYPE  103  176
        clus
vv       CTSC MUTATED CTSC WILD-TYPE
  FEMALE            7            103
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CTSC MUTATED                                       1
  CTSC WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CTSC MUTATED                                                        9
  CTSC WILD-TYPE                                                    126
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CTSC MUTATED                                                                   0
  CTSC WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CTSC MUTATED                                                  0
  CTSC WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CTSC MUTATED                                                          0
  CTSC WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CTSC MUTATED                                                           0
  CTSC WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CTSC MUTATED                                          0
  CTSC WILD-TYPE                                        3
D112V8, multiclass
                                                                   clus
vv                                                                  CTSC MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  CTSC WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V9, binary
                cls
clus               0   1
  CTSC MUTATED     0  10
  CTSC WILD-TYPE   5 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSC MUTATED      0   10
  CTSC WILD-TYPE    5  274
     clus
vv    CTSC MUTATED CTSC WILD-TYPE
  NO             0              5
  YES           10            274
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CTSC MUTATED     4   0   0   4
  CTSC WILD-TYPE 223  10  10  20
D112V10, multiclass
    clus
vv   CTSC MUTATED CTSC WILD-TYPE
  R0            4            223
  R1            0             10
  R2            0             10
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CTSC MUTATED       2                         0     8
  CTSC WILD-TYPE    74                         4   160
D112V12, multiclass
                           clus
vv                          CTSC MUTATED CTSC WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                8            160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(113) Variable = PAMR1 MUTATION ANALYSIS
D113V1, survival
                 sevent
clus2               0   1
  PAMR1 MUTATED     8   5
  PAMR1 WILD-TYPE 173  75
  PAMR1 MUTATED PAMR1 WILD-TYPE 
             13             248 
  PAMR1 MUTATED PAMR1 WILD-TYPE 
              5              75 
$`PAMR1 MUTATED`
TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8372 TCGA-CD-5801 TCGA-CD-A4MI 
       30.90         6.61        34.68        19.17        13.18         0.10 
TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5726 TCGA-F1-6874 TCGA-HU-8608 TCGA-HU-A4GT 
        1.02         6.02        28.96        14.47        10.62         6.51 
TCGA-HU-A4GU 
        6.25 

$`PAMR1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       18.35         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.15         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 
        0.99         0.99       105.07        12.03        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        0.62         7.99        16.24        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        11.41        12.10         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX 
       25.81        11.77        29.98         8.98         0.10        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  PAMR1 MUTATED PAMR1 WILD-TYPE 
            0.1             0.0 
  PAMR1 MUTATED PAMR1 WILD-TYPE 
          34.68          105.07 
  PAMR1 MUTATED PAMR1 WILD-TYPE 
          10.62           12.64 
[1] "0.1 - 34.7 (10.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D113V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PAMR1 MUTATED         0        1        1        0         2         1
  PAMR1 WILD-TYPE       1        8       26       26        29        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PAMR1 MUTATED           1          1          2          1        2
  PAMR1 WILD-TYPE         2         48         34         23       22
D113V3, multiclass
            clus
vv           PAMR1 MUTATED PAMR1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              1              43
  STAGE III              1               2
  STAGE IIIA             1              48
  STAGE IIIB             2              34
  STAGE IIIC             1              23
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PAMR1 MUTATED     2   4   6   3
  PAMR1 WILD-TYPE   9  68 116  72
D113V4, multiclass
    clus
vv   PAMR1 MUTATED PAMR1 WILD-TYPE
  T1             2               9
  T2             4              68
  T3             6             116
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PAMR1 MUTATED    4  6  2  1
  PAMR1 WILD-TYPE 89 75 48 52
D113V5, multiclass
    clus
vv   PAMR1 MUTATED PAMR1 WILD-TYPE
  N0             4              89
  N1             6              75
  N2             2              48
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V6, binary
                 cls
clus                0   1
  PAMR1 MUTATED    16   1
  PAMR1 WILD-TYPE 241  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAMR1 MUTATED     16    1
  PAMR1 WILD-TYPE  241   17
   clus
vv  PAMR1 MUTATED PAMR1 WILD-TYPE
  0            16             241
  1             1              17
[1] 2 2
[1] FALSE
D113V7, binary
                 cls
clus                0   1
  PAMR1 MUTATED     7  10
  PAMR1 WILD-TYPE 103 169
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAMR1 MUTATED      7   10
  PAMR1 WILD-TYPE  103  169
        clus
vv       PAMR1 MUTATED PAMR1 WILD-TYPE
  FEMALE             7             103
  MALE              10             169
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PAMR1 MUTATED                                       2
  PAMR1 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PAMR1 MUTATED                                                       10
  PAMR1 WILD-TYPE                                                    125
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PAMR1 MUTATED                                                                   3
  PAMR1 WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PAMR1 MUTATED                                                  2
  PAMR1 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PAMR1 MUTATED                                                          0
  PAMR1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PAMR1 MUTATED                                                           0
  PAMR1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PAMR1 MUTATED                                          0
  PAMR1 WILD-TYPE                                        3
D113V8, multiclass
                                                                   clus
vv                                                                  PAMR1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  PAMR1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V9, binary
                 cls
clus                0   1
  PAMR1 MUTATED     0  17
  PAMR1 WILD-TYPE   5 267
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAMR1 MUTATED      0   17
  PAMR1 WILD-TYPE    5  267
     clus
vv    PAMR1 MUTATED PAMR1 WILD-TYPE
  NO              0               5
  YES            17             267
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PAMR1 MUTATED     9   0   1   6
  PAMR1 WILD-TYPE 218  10   9  18
D113V10, multiclass
    clus
vv   PAMR1 MUTATED PAMR1 WILD-TYPE
  R0             9             218
  R1             0              10
  R2             1               9
  RX             6              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PAMR1 MUTATED       5                         0     9
  PAMR1 WILD-TYPE    71                         4   159
D113V12, multiclass
                           clus
vv                          PAMR1 MUTATED PAMR1 WILD-TYPE
  ASIAN                                 5              71
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 9             159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(114) Variable = USP21 MUTATION ANALYSIS
D114V1, survival
                 sevent
clus2               0   1
  USP21 MUTATED     8   2
  USP21 WILD-TYPE 173  78
  USP21 MUTATED USP21 WILD-TYPE 
             10             251 
  USP21 MUTATED USP21 WILD-TYPE 
              2              78 
$`USP21 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-A4QL 
       26.70         6.97        32.94        19.17         1.12        11.57 
TCGA-CG-4466 TCGA-CG-5718 TCGA-F1-6874 TCGA-FP-A4BE 
       18.97        36.00        14.47        11.08 

$`USP21 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
        7.07        22.98        30.97         6.97         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 
       14.76         0.62         7.99        16.24        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
        5.03        13.58         0.56         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  USP21 MUTATED USP21 WILD-TYPE 
           1.12            0.00 
  USP21 MUTATED USP21 WILD-TYPE 
          36.00          105.07 
  USP21 MUTATED USP21 WILD-TYPE 
          16.72           12.59 
[1] "1.1 - 36.0 (16.7)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.2"
D114V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  USP21 MUTATED         0        0        2        1         3         1
  USP21 WILD-TYPE       1        9       25       25        28        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  USP21 MUTATED           0          1          1          1        0
  USP21 WILD-TYPE         3         48         35         23       24
D114V3, multiclass
            clus
vv           USP21 MUTATED USP21 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               1              25
  STAGE IIA              3              28
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP21 MUTATED     1   3   5   2
  USP21 WILD-TYPE  10  69 117  73
D114V4, multiclass
    clus
vv   USP21 MUTATED USP21 WILD-TYPE
  T1             1              10
  T2             3              69
  T3             5             117
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  USP21 MUTATED    6  3  0  2
  USP21 WILD-TYPE 87 78 50 51
D114V5, multiclass
    clus
vv   USP21 MUTATED USP21 WILD-TYPE
  N0             6              87
  N1             3              78
  N2             0              50
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V6, binary
                 cls
clus                0   1
  USP21 MUTATED    12   0
  USP21 WILD-TYPE 245  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP21 MUTATED     12    0
  USP21 WILD-TYPE  245   18
   clus
vv  USP21 MUTATED USP21 WILD-TYPE
  0            12             245
  1             0              18
[1] 2 2
[1] FALSE
D114V7, binary
                 cls
clus                0   1
  USP21 MUTATED     8   5
  USP21 WILD-TYPE 102 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP21 MUTATED      8    5
  USP21 WILD-TYPE  102  174
        clus
vv       USP21 MUTATED USP21 WILD-TYPE
  FEMALE             8             102
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  USP21 MUTATED                                       1
  USP21 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  USP21 MUTATED                                                        9
  USP21 WILD-TYPE                                                    126
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  USP21 MUTATED                                                                   3
  USP21 WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  USP21 MUTATED                                                  0
  USP21 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  USP21 MUTATED                                                          0
  USP21 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  USP21 MUTATED                                                           0
  USP21 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  USP21 MUTATED                                          0
  USP21 WILD-TYPE                                        3
D114V8, multiclass
                                                                   clus
vv                                                                  USP21 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  USP21 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V9, binary
                 cls
clus                0   1
  USP21 MUTATED     0  13
  USP21 WILD-TYPE   5 271
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP21 MUTATED      0   13
  USP21 WILD-TYPE    5  271
     clus
vv    USP21 MUTATED USP21 WILD-TYPE
  NO              0               5
  YES            13             271
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USP21 MUTATED     9   0   0   4
  USP21 WILD-TYPE 218  10  10  20
D114V10, multiclass
    clus
vv   USP21 MUTATED USP21 WILD-TYPE
  R0             9             218
  R1             0              10
  R2             0              10
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  USP21 MUTATED       0                         1    10
  USP21 WILD-TYPE    76                         3   158
D114V12, multiclass
                           clus
vv                          USP21 MUTATED USP21 WILD-TYPE
  ASIAN                                 0              76
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                10             158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(115) Variable = PAX2 MUTATION ANALYSIS
D115V1, survival
                sevent
clus2              0   1
  PAX2 MUTATED     6   1
  PAX2 WILD-TYPE 175  79
  PAX2 MUTATED PAX2 WILD-TYPE 
             7            254 
  PAX2 MUTATED PAX2 WILD-TYPE 
             1             79 
$`PAX2 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8372 TCGA-CG-5721 TCGA-HU-A4GQ 
       26.70        34.68        32.94        19.17         6.02         0.10 
TCGA-HU-A4GU 
        6.25 

$`PAX2 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GX 
       25.81        11.77        29.98         8.98         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  PAX2 MUTATED PAX2 WILD-TYPE 
           0.1            0.0 
  PAX2 MUTATED PAX2 WILD-TYPE 
         34.68         105.07 
  PAX2 MUTATED PAX2 WILD-TYPE 
        19.170         12.605 
[1] "0.1 - 34.7 (19.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "3.1"
D115V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PAX2 MUTATED         0        0        0        0         2         2
  PAX2 WILD-TYPE       1        9       27       26        29        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PAX2 MUTATED           0          1          0          2        1
  PAX2 WILD-TYPE         3         48         36         22       23
D115V3, multiclass
            clus
vv           PAX2 MUTATED PAX2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              0             26
  STAGE IIA             2             29
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            2             22
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PAX2 MUTATED     0   0   3   5
  PAX2 WILD-TYPE  11  72 119  70
D115V4, multiclass
    clus
vv   PAX2 MUTATED PAX2 WILD-TYPE
  T1            0             11
  T2            0             72
  T3            3            119
  T4            5             70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  PAX2 MUTATED    4  2  1  1
  PAX2 WILD-TYPE 89 79 49 52
D115V5, multiclass
    clus
vv   PAX2 MUTATED PAX2 WILD-TYPE
  N0            4             89
  N1            2             79
  N2            1             49
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V6, binary
                cls
clus               0   1
  PAX2 MUTATED     8   0
  PAX2 WILD-TYPE 249  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX2 MUTATED      8    0
  PAX2 WILD-TYPE  249   18
   clus
vv  PAX2 MUTATED PAX2 WILD-TYPE
  0            8            249
  1            0             18
[1] 2 2
[1] FALSE
D115V7, binary
                cls
clus               0   1
  PAX2 MUTATED     4   4
  PAX2 WILD-TYPE 106 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX2 MUTATED      4    4
  PAX2 WILD-TYPE  106  175
        clus
vv       PAX2 MUTATED PAX2 WILD-TYPE
  FEMALE            4            106
  MALE              4            175
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PAX2 MUTATED                                       2
  PAX2 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PAX2 MUTATED                                                        4
  PAX2 WILD-TYPE                                                    131
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PAX2 MUTATED                                                                   1
  PAX2 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PAX2 MUTATED                                                  1
  PAX2 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PAX2 MUTATED                                                          0
  PAX2 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PAX2 MUTATED                                                           0
  PAX2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PAX2 MUTATED                                          0
  PAX2 WILD-TYPE                                        3
D115V8, multiclass
                                                                   clus
vv                                                                  PAX2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  PAX2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V9, binary
                cls
clus               0   1
  PAX2 MUTATED     0   8
  PAX2 WILD-TYPE   5 276
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX2 MUTATED      0    8
  PAX2 WILD-TYPE    5  276
     clus
vv    PAX2 MUTATED PAX2 WILD-TYPE
  NO             0              5
  YES            8            276
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PAX2 MUTATED     7   0   0   1
  PAX2 WILD-TYPE 220  10  10  23
D115V10, multiclass
    clus
vv   PAX2 MUTATED PAX2 WILD-TYPE
  R0            7            220
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PAX2 MUTATED       2                         0     5
  PAX2 WILD-TYPE    74                         4   163
D115V12, multiclass
                           clus
vv                          PAX2 MUTATED PAX2 WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                5            163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(116) Variable = ZFHX3 MUTATION ANALYSIS
D116V1, survival
                 sevent
clus2               0   1
  ZFHX3 MUTATED    23  10
  ZFHX3 WILD-TYPE 158  70
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             33             228 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             10              70 
$`ZFHX3 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7703 
       26.70         6.97        30.90        34.68        32.78        24.76 
TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8382 
       23.93        12.43        14.43        12.26        19.50        15.85 
TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
        1.12        15.81        11.57        11.61         6.58         0.10 
TCGA-CG-4306 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 
        1.02         0.99         6.02       105.07        65.10        21.07 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-FP-7829 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-A4GQ 
        7.99        14.47        19.53        14.17        11.41         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H4 
        6.51        10.19        23.84 

$`ZFHX3 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 
       11.70         6.61         4.64         7.43        18.35         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10         9.17        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       12.82         9.21        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
       16.31         2.20        15.58         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
        3.32        11.80        19.17        14.79         0.26         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
        0.99        12.03        28.96        79.07         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6875 
       15.16        13.78        14.76         0.62        16.24        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       21.27         3.48        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
        5.92        12.59        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY 
       25.81        11.77        29.98         8.98         6.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        19.36        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
            0.1             0.0 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
         105.07           79.07 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
         14.170          12.605 
[1] "0.1 - 105.1 (14.2)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.3"
D116V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZFHX3 MUTATED         0        1        4        2         5         8
  ZFHX3 WILD-TYPE       1        8       23       24        26        36
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFHX3 MUTATED           1          4          2          4        4
  ZFHX3 WILD-TYPE         2         45         34         20       20
D116V3, multiclass
            clus
vv           ZFHX3 MUTATED ZFHX3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               4              23
  STAGE II               2              24
  STAGE IIA              5              26
  STAGE IIB              8              36
  STAGE III              1               2
  STAGE IIIA             4              45
  STAGE IIIB             2              34
  STAGE IIIC             4              20
  STAGE IV               4              20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZFHX3 MUTATED     2   9  13  13
  ZFHX3 WILD-TYPE   9  63 109  62
D116V4, multiclass
    clus
vv   ZFHX3 MUTATED ZFHX3 WILD-TYPE
  T1             2               9
  T2             9              63
  T3            13             109
  T4            13              62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ZFHX3 MUTATED   15  9  9  2
  ZFHX3 WILD-TYPE 78 72 41 51
D116V5, multiclass
    clus
vv   ZFHX3 MUTATED ZFHX3 WILD-TYPE
  N0            15              78
  N1             9              72
  N2             9              41
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V6, binary
                 cls
clus                0   1
  ZFHX3 MUTATED    34   2
  ZFHX3 WILD-TYPE 223  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED     34    2
  ZFHX3 WILD-TYPE  223   16
   clus
vv  ZFHX3 MUTATED ZFHX3 WILD-TYPE
  0            34             223
  1             2              16
[1] 2 2
[1] FALSE
D116V7, binary
                 cls
clus                0   1
  ZFHX3 MUTATED    22  16
  ZFHX3 WILD-TYPE  88 163
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED     22   16
  ZFHX3 WILD-TYPE   88  163
        clus
vv       ZFHX3 MUTATED ZFHX3 WILD-TYPE
  FEMALE            22              88
  MALE              16             163
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZFHX3 MUTATED                                       4
  ZFHX3 WILD-TYPE                                    46
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZFHX3 MUTATED                                                       19
  ZFHX3 WILD-TYPE                                                    116
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZFHX3 MUTATED                                                                   7
  ZFHX3 WILD-TYPE                                                                33
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZFHX3 MUTATED                                                  5
  ZFHX3 WILD-TYPE                                               33
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZFHX3 MUTATED                                                          2
  ZFHX3 WILD-TYPE                                                       14
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZFHX3 MUTATED                                                           1
  ZFHX3 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZFHX3 MUTATED                                          0
  ZFHX3 WILD-TYPE                                        3
D116V8, multiclass
                                                                   clus
vv                                                                  ZFHX3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       19
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ZFHX3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        116
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V9, binary
                 cls
clus                0   1
  ZFHX3 MUTATED     1  37
  ZFHX3 WILD-TYPE   4 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED      1   37
  ZFHX3 WILD-TYPE    4  247
     clus
vv    ZFHX3 MUTATED ZFHX3 WILD-TYPE
  NO              1               4
  YES            37             247
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ZFHX3 MUTATED    27   0   1   6
  ZFHX3 WILD-TYPE 200  10   9  18
D116V10, multiclass
    clus
vv   ZFHX3 MUTATED ZFHX3 WILD-TYPE
  R0            27             200
  R1             0              10
  R2             1               9
  RX             6              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZFHX3 MUTATED      10                         0    21
  ZFHX3 WILD-TYPE    66                         4   147
D116V12, multiclass
                           clus
vv                          ZFHX3 MUTATED ZFHX3 WILD-TYPE
  ASIAN                                10              66
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                21             147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(117) Variable = EPHA2 MUTATION ANALYSIS
D117V1, survival
                 sevent
clus2               0   1
  EPHA2 MUTATED    15   5
  EPHA2 WILD-TYPE 166  75
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             20             241 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
              5              75 
$`EPHA2 MUTATED`
TCGA-BR-4201 TCGA-BR-6453 TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-A4MG 
       30.90        15.95        12.26         1.12        13.45         6.58 
TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-8576 TCGA-F1-A448 TCGA-FP-A4BE TCGA-HU-A4G9 
        6.02        28.96        14.66        21.27        11.08        24.20 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4H4 TCGA-HU-A4H8 
       23.84         8.88 

$`EPHA2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6455 
       18.35         6.18         9.57         6.61        34.68        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79        15.81         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 
        1.02         0.99         0.99       105.07        12.03        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        18.21        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        0.62         7.99        16.24        14.47        72.23         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        11.84         3.25        22.75        25.81 
TCGA-HU-A4GP TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
        8.98         0.26         2.10        12.95        19.36        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        9.67        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  EPHA2 MUTATED EPHA2 WILD-TYPE 
            0.1             0.0 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
          30.90          105.07 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
         12.015          12.660 
[1] "0.1 - 30.9 (12.0)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.3"
D117V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPHA2 MUTATED         1        3        1        0         6         3
  EPHA2 WILD-TYPE       0        6       26       26        25        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EPHA2 MUTATED           0          1          2          3        1
  EPHA2 WILD-TYPE         3         48         34         21       23
D117V3, multiclass
            clus
vv           EPHA2 MUTATED EPHA2 WILD-TYPE
  STAGE I                1               0
  STAGE IA               3               6
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              6              25
  STAGE IIB              3              41
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             2              34
  STAGE IIIC             3              21
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EPHA2 MUTATED     5   4   7   6
  EPHA2 WILD-TYPE   6  68 115  69
D117V4, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  T1             5               6
  T2             4              68
  T3             7             115
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  EPHA2 MUTATED    9  7  3  3
  EPHA2 WILD-TYPE 84 74 47 50
D117V5, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  N0             9              84
  N1             7              74
  N2             3              47
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V6, binary
                 cls
clus                0   1
  EPHA2 MUTATED    22   0
  EPHA2 WILD-TYPE 235  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED     22    0
  EPHA2 WILD-TYPE  235   18
   clus
vv  EPHA2 MUTATED EPHA2 WILD-TYPE
  0            22             235
  1             0              18
[1] 2 2
[1] FALSE
D117V7, binary
                 cls
clus                0   1
  EPHA2 MUTATED    10  13
  EPHA2 WILD-TYPE 100 166
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED     10   13
  EPHA2 WILD-TYPE  100  166
        clus
vv       EPHA2 MUTATED EPHA2 WILD-TYPE
  FEMALE            10             100
  MALE              13             166
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  EPHA2 MUTATED                                       3
  EPHA2 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EPHA2 MUTATED                                                        9
  EPHA2 WILD-TYPE                                                    126
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EPHA2 MUTATED                                                                   2
  EPHA2 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  EPHA2 MUTATED                                                  8
  EPHA2 WILD-TYPE                                               30
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  EPHA2 MUTATED                                                          1
  EPHA2 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  EPHA2 MUTATED                                                           0
  EPHA2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  EPHA2 MUTATED                                          0
  EPHA2 WILD-TYPE                                        3
D117V8, multiclass
                                                                   clus
vv                                                                  EPHA2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  EPHA2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               30
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V9, binary
                 cls
clus                0   1
  EPHA2 MUTATED     0  23
  EPHA2 WILD-TYPE   5 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      0   23
  EPHA2 WILD-TYPE    5  261
     clus
vv    EPHA2 MUTATED EPHA2 WILD-TYPE
  NO              0               5
  YES            23             261
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EPHA2 MUTATED    19   0   0   3
  EPHA2 WILD-TYPE 208  10  10  21
D117V10, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  R0            19             208
  R1             0              10
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EPHA2 MUTATED      10                         2     9
  EPHA2 WILD-TYPE    66                         2   159
D117V12, multiclass
                           clus
vv                          EPHA2 MUTATED EPHA2 WILD-TYPE
  ASIAN                                10              66
  BLACK OR AFRICAN AMERICAN             2               2
  WHITE                                 9             159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(118) Variable = PREPL MUTATION ANALYSIS
D118V1, survival
                 sevent
clus2               0   1
  PREPL MUTATED    16   2
  PREPL WILD-TYPE 165  78
  PREPL MUTATED PREPL WILD-TYPE 
             18             243 
  PREPL MUTATED PREPL WILD-TYPE 
              2              78 
$`PREPL MUTATED`
TCGA-BR-6452 TCGA-BR-6705 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8372 
       34.68        25.61        32.94        12.26         4.31        19.17 
TCGA-BR-8487 TCGA-BR-8589 TCGA-CD-5801 TCGA-CG-4305 TCGA-CG-5728 TCGA-D7-A4YU 
        1.12        15.81        13.18        15.95        65.10        16.44 
TCGA-F1-6874 TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4H8 
       14.47        25.81         6.51         6.25        23.84         8.88 

$`PREPL WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        32.78        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 
        5.39        25.18         9.21        20.22        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        28.96        79.07         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       18.21        14.66        21.14        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GN 
       11.84        24.20         3.25        22.75        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       19.36        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  PREPL MUTATED PREPL WILD-TYPE 
           1.12            0.00 
  PREPL MUTATED PREPL WILD-TYPE 
          65.10          105.07 
  PREPL MUTATED PREPL WILD-TYPE 
          15.88           12.43 
[1] "1.1 - 65.1 (15.9)"  "0.0 - 105.1 (12.4)"
[1] "hr=" "3.9"
D118V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PREPL MUTATED         1        0        4        1         5         3
  PREPL WILD-TYPE       0        9       23       25        26        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PREPL MUTATED           0          2          3          1        0
  PREPL WILD-TYPE         3         47         33         23       24
D118V3, multiclass
            clus
vv           PREPL MUTATED PREPL WILD-TYPE
  STAGE I                1               0
  STAGE IA               0               9
  STAGE IB               4              23
  STAGE II               1              25
  STAGE IIA              5              26
  STAGE IIB              3              41
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             3              33
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PREPL MUTATED     2   5   9   4
  PREPL WILD-TYPE   9  67 113  71
D118V4, multiclass
    clus
vv   PREPL MUTATED PREPL WILD-TYPE
  T1             2               9
  T2             5              67
  T3             9             113
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PREPL MUTATED   10  7  1  3
  PREPL WILD-TYPE 83 74 49 50
D118V5, multiclass
    clus
vv   PREPL MUTATED PREPL WILD-TYPE
  N0            10              83
  N1             7              74
  N2             1              49
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V6, binary
                 cls
clus                0   1
  PREPL MUTATED    21   0
  PREPL WILD-TYPE 236  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PREPL MUTATED     21    0
  PREPL WILD-TYPE  236   18
   clus
vv  PREPL MUTATED PREPL WILD-TYPE
  0            21             236
  1             0              18
[1] 2 2
[1] FALSE
D118V7, binary
                 cls
clus                0   1
  PREPL MUTATED    12  10
  PREPL WILD-TYPE  98 169
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PREPL MUTATED     12   10
  PREPL WILD-TYPE   98  169
        clus
vv       PREPL MUTATED PREPL WILD-TYPE
  FEMALE            12              98
  MALE              10             169
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PREPL MUTATED                                       1
  PREPL WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PREPL MUTATED                                                       14
  PREPL WILD-TYPE                                                    121
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PREPL MUTATED                                                                   2
  PREPL WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PREPL MUTATED                                                  5
  PREPL WILD-TYPE                                               33
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PREPL MUTATED                                                          0
  PREPL WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PREPL MUTATED                                                           0
  PREPL WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PREPL MUTATED                                          0
  PREPL WILD-TYPE                                        3
D118V8, multiclass
                                                                   clus
vv                                                                  PREPL MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       14
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  PREPL WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        121
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V9, binary
                 cls
clus                0   1
  PREPL MUTATED     0  22
  PREPL WILD-TYPE   5 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PREPL MUTATED      0   22
  PREPL WILD-TYPE    5  262
     clus
vv    PREPL MUTATED PREPL WILD-TYPE
  NO              0               5
  YES            22             262
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PREPL MUTATED    19   0   0   3
  PREPL WILD-TYPE 208  10  10  21
D118V10, multiclass
    clus
vv   PREPL MUTATED PREPL WILD-TYPE
  R0            19             208
  R1             0              10
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PREPL MUTATED       6                         1    13
  PREPL WILD-TYPE    70                         3   155
D118V12, multiclass
                           clus
vv                          PREPL MUTATED PREPL WILD-TYPE
  ASIAN                                 6              70
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                13             155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(119) Variable = RGL2 MUTATION ANALYSIS
D119V1, survival
                sevent
clus2              0   1
  RGL2 MUTATED     9   2
  RGL2 WILD-TYPE 172  78
  RGL2 MUTATED RGL2 WILD-TYPE 
            11            250 
  RGL2 MUTATED RGL2 WILD-TYPE 
             2             78 
$`RGL2 MUTATED`
TCGA-BR-8360 TCGA-BR-8591 TCGA-BR-8678 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CD-A4MJ 
        6.18        13.45        11.54        15.81         6.58        12.62 
TCGA-CG-4305 TCGA-CG-5721 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4H8 
       15.95         6.02        11.84         0.10         8.88 

$`RGL2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 
        9.34         6.28         7.53         0.49        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       12.20         0.10        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
       19.36        23.84        12.30         9.67        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  RGL2 MUTATED RGL2 WILD-TYPE 
           0.1            0.0 
  RGL2 MUTATED RGL2 WILD-TYPE 
         15.95         105.07 
  RGL2 MUTATED RGL2 WILD-TYPE 
        11.540         12.775 
[1] "0.1 - 15.9 (11.5)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.1"
D119V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RGL2 MUTATED         0        0        3        1         2         1
  RGL2 WILD-TYPE       1        9       24       25        29        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RGL2 MUTATED           0          0          0          2        2
  RGL2 WILD-TYPE         3         49         36         22       22
D119V3, multiclass
            clus
vv           RGL2 MUTATED RGL2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              3             24
  STAGE II              1             25
  STAGE IIA             2             29
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            2             22
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RGL2 MUTATED     1   3   3   4
  RGL2 WILD-TYPE  10  69 119  71
D119V4, multiclass
    clus
vv   RGL2 MUTATED RGL2 WILD-TYPE
  T1            1             10
  T2            3             69
  T3            3            119
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  RGL2 MUTATED    4  5  2  1
  RGL2 WILD-TYPE 89 76 48 52
D119V5, multiclass
    clus
vv   RGL2 MUTATED RGL2 WILD-TYPE
  N0            4             89
  N1            5             76
  N2            2             48
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V6, binary
                cls
clus               0   1
  RGL2 MUTATED    11   1
  RGL2 WILD-TYPE 246  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGL2 MUTATED     11    1
  RGL2 WILD-TYPE  246   17
   clus
vv  RGL2 MUTATED RGL2 WILD-TYPE
  0           11            246
  1            1             17
[1] 2 2
[1] FALSE
D119V7, binary
                cls
clus               0   1
  RGL2 MUTATED     2  10
  RGL2 WILD-TYPE 108 169
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGL2 MUTATED      2   10
  RGL2 WILD-TYPE  108  169
        clus
vv       RGL2 MUTATED RGL2 WILD-TYPE
  FEMALE            2            108
  MALE             10            169
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RGL2 MUTATED                                       2
  RGL2 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RGL2 MUTATED                                                        5
  RGL2 WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RGL2 MUTATED                                                                   2
  RGL2 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RGL2 MUTATED                                                  3
  RGL2 WILD-TYPE                                               35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RGL2 MUTATED                                                          0
  RGL2 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RGL2 MUTATED                                                           0
  RGL2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RGL2 MUTATED                                          0
  RGL2 WILD-TYPE                                        3
D119V8, multiclass
                                                                   clus
vv                                                                  RGL2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  RGL2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V9, binary
                cls
clus               0   1
  RGL2 MUTATED     0  12
  RGL2 WILD-TYPE   5 272
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGL2 MUTATED      0   12
  RGL2 WILD-TYPE    5  272
     clus
vv    RGL2 MUTATED RGL2 WILD-TYPE
  NO             0              5
  YES           12            272
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RGL2 MUTATED     8   0   0   1
  RGL2 WILD-TYPE 219  10  10  23
D119V10, multiclass
    clus
vv   RGL2 MUTATED RGL2 WILD-TYPE
  R0            8            219
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RGL2 MUTATED       6                         0     4
  RGL2 WILD-TYPE    70                         4   164
D119V12, multiclass
                           clus
vv                          RGL2 MUTATED RGL2 WILD-TYPE
  ASIAN                                6             70
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                4            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(120) Variable = ATP6V1C2 MUTATION ANALYSIS
D120V1, survival
                    sevent
clus2                  0   1
  ATP6V1C2 MUTATED     6   4
  ATP6V1C2 WILD-TYPE 175  76
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
                10                251 
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
                 4                 76 
$`ATP6V1C2 MUTATED`
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-8363 TCGA-CG-5723 TCGA-CG-5733 TCGA-HU-A4G3 
       34.68        15.95         0.26       105.07        21.07         5.59 
TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-IN-8663 
       24.20        29.98         0.10         3.39 

$`ATP6V1C2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6455 
       18.35        30.90         6.18         9.57         6.61        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        19.50        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        11.84         3.25        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         2.53 

  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
               0.1                0.0 
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
            105.07              79.07 
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
             18.51              12.59 
[1] "0.1 - 105.1 (18.5)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.2"
D120V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATP6V1C2 MUTATED         1        1        1        1         3         2
  ATP6V1C2 WILD-TYPE       0        8       26       25        28        42
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP6V1C2 MUTATED           0          1          0          1        0
  ATP6V1C2 WILD-TYPE         3         48         36         23       24
D120V3, multiclass
            clus
vv           ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                  1                  8
  STAGE IB                  1                 26
  STAGE II                  1                 25
  STAGE IIA                 3                 28
  STAGE IIB                 2                 42
  STAGE III                 0                  3
  STAGE IIIA                1                 48
  STAGE IIIB                0                 36
  STAGE IIIC                1                 23
  STAGE IV                  0                 24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ATP6V1C2 MUTATED     2   7   1   1
  ATP6V1C2 WILD-TYPE   9  65 121  74
D120V4, multiclass
    clus
vv   ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  T1                2                  9
  T2                7                 65
  T3                1                121
  T4                1                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  ATP6V1C2 MUTATED    3  5  4  0
  ATP6V1C2 WILD-TYPE 90 76 46 53
D120V5, multiclass
    clus
vv   ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  N0                3                 90
  N1                5                 76
  N2                4                 46
  N3                0                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V6, binary
                    cls
clus                   0   1
  ATP6V1C2 MUTATED    11   0
  ATP6V1C2 WILD-TYPE 246  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1C2 MUTATED     11    0
  ATP6V1C2 WILD-TYPE  246   18
   clus
vv  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  0               11                246
  1                0                 18
[1] 2 2
[1] FALSE
D120V7, binary
                    cls
clus                   0   1
  ATP6V1C2 MUTATED     5   7
  ATP6V1C2 WILD-TYPE 105 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1C2 MUTATED      5    7
  ATP6V1C2 WILD-TYPE  105  172
        clus
vv       ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  FEMALE                5                105
  MALE                  7                172
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ATP6V1C2 MUTATED                                       0
  ATP6V1C2 WILD-TYPE                                    50
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ATP6V1C2 MUTATED                                                        7
  ATP6V1C2 WILD-TYPE                                                    128
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ATP6V1C2 MUTATED                                                                   1
  ATP6V1C2 WILD-TYPE                                                                39
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ATP6V1C2 MUTATED                                                  4
  ATP6V1C2 WILD-TYPE                                               34
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ATP6V1C2 MUTATED                                                          0
  ATP6V1C2 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ATP6V1C2 MUTATED                                                           0
  ATP6V1C2 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ATP6V1C2 MUTATED                                          0
  ATP6V1C2 WILD-TYPE                                        3
D120V8, multiclass
                                                                   clus
vv                                                                  ATP6V1C2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  ATP6V1C2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V9, binary
                    cls
clus                   0   1
  ATP6V1C2 MUTATED     0  12
  ATP6V1C2 WILD-TYPE   5 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1C2 MUTATED      0   12
  ATP6V1C2 WILD-TYPE    5  272
     clus
vv    ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  NO                 0                  5
  YES               12                272
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  ATP6V1C2 MUTATED    11   0   0   1
  ATP6V1C2 WILD-TYPE 216  10  10  23
D120V10, multiclass
    clus
vv   ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  R0               11                216
  R1                0                 10
  R2                0                 10
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATP6V1C2 MUTATED       4                         1     5
  ATP6V1C2 WILD-TYPE    72                         3   163
D120V12, multiclass
                           clus
vv                          ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  ASIAN                                    4                 72
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                    5                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(121) Variable = CDC14A MUTATION ANALYSIS
D121V1, survival
                  sevent
clus2                0   1
  CDC14A MUTATED     9   2
  CDC14A WILD-TYPE 172  78
  CDC14A MUTATED CDC14A WILD-TYPE 
              11              250 
  CDC14A MUTATED CDC14A WILD-TYPE 
               2               78 
$`CDC14A MUTATED`
TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-A4QL 
       34.68        23.93        12.26         4.31         1.12        11.57 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-5721 TCGA-D7-5577 TCGA-HU-A4GU 
        9.01         7.07         6.02        12.36         6.25 

$`CDC14A WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
       29.98        47.05        19.07        12.03         0.00        18.97 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04        21.07         7.99        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  CDC14A MUTATED CDC14A WILD-TYPE 
            1.12             0.00 
  CDC14A MUTATED CDC14A WILD-TYPE 
           34.68           105.07 
  CDC14A MUTATED CDC14A WILD-TYPE 
            9.01            12.79 
[1] "1.1 - 34.7 (9.0)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.3"
D121V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDC14A MUTATED         1        0        2        1         2         2
  CDC14A WILD-TYPE       0        9       25       25        29        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDC14A MUTATED           0          2          1          0        3
  CDC14A WILD-TYPE         3         47         35         24       21
D121V3, multiclass
            clus
vv           CDC14A MUTATED CDC14A WILD-TYPE
  STAGE I                 1                0
  STAGE IA                0                9
  STAGE IB                2               25
  STAGE II                1               25
  STAGE IIA               2               29
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              1               35
  STAGE IIIC              0               24
  STAGE IV                3               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CDC14A MUTATED     1   4   5   4
  CDC14A WILD-TYPE  10  68 117  71
D121V4, multiclass
    clus
vv   CDC14A MUTATED CDC14A WILD-TYPE
  T1              1               10
  T2              4               68
  T3              5              117
  T4              4               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CDC14A MUTATED    6  4  0  4
  CDC14A WILD-TYPE 87 77 50 49
D121V5, multiclass
    clus
vv   CDC14A MUTATED CDC14A WILD-TYPE
  N0              6               87
  N1              4               77
  N2              0               50
  N3              4               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V6, binary
                  cls
clus                 0   1
  CDC14A MUTATED    13   1
  CDC14A WILD-TYPE 244  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC14A MUTATED     13    1
  CDC14A WILD-TYPE  244   17
   clus
vv  CDC14A MUTATED CDC14A WILD-TYPE
  0             13              244
  1              1               17
[1] 2 2
[1] FALSE
D121V7, binary
                  cls
clus                 0   1
  CDC14A MUTATED    10   5
  CDC14A WILD-TYPE 100 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC14A MUTATED     10    5
  CDC14A WILD-TYPE  100  174
        clus
vv       CDC14A MUTATED CDC14A WILD-TYPE
  FEMALE             10              100
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CDC14A MUTATED                                       2
  CDC14A WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CDC14A MUTATED                                                        9
  CDC14A WILD-TYPE                                                    126
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CDC14A MUTATED                                                                   2
  CDC14A WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CDC14A MUTATED                                                  1
  CDC14A WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CDC14A MUTATED                                                          1
  CDC14A WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CDC14A MUTATED                                                           0
  CDC14A WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CDC14A MUTATED                                          0
  CDC14A WILD-TYPE                                        3
D121V8, multiclass
                                                                   clus
vv                                                                  CDC14A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  CDC14A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V9, binary
                  cls
clus                 0   1
  CDC14A MUTATED     1  14
  CDC14A WILD-TYPE   4 270
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC14A MUTATED      1   14
  CDC14A WILD-TYPE    4  270
     clus
vv    CDC14A MUTATED CDC14A WILD-TYPE
  NO               1                4
  YES             14              270
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CDC14A MUTATED    11   1   1   2
  CDC14A WILD-TYPE 216   9   9  22
D121V10, multiclass
    clus
vv   CDC14A MUTATED CDC14A WILD-TYPE
  R0             11              216
  R1              1                9
  R2              1                9
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDC14A MUTATED       1                         1     9
  CDC14A WILD-TYPE    75                         3   159
D121V12, multiclass
                           clus
vv                          CDC14A MUTATED CDC14A WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  9              159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(122) Variable = DDX17 MUTATION ANALYSIS
D122V1, survival
                 sevent
clus2               0   1
  DDX17 MUTATED     9   3
  DDX17 WILD-TYPE 172  77
  DDX17 MUTATED DDX17 WILD-TYPE 
             12             249 
  DDX17 MUTATED DDX17 WILD-TYPE 
              3              77 
$`DDX17 MUTATED`
TCGA-BR-4184 TCGA-BR-6566 TCGA-BR-7851 TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8368 
        6.97        32.78        12.43        20.55        19.50         4.31 
TCGA-BR-8680 TCGA-CD-8529 TCGA-CD-8536 TCGA-CG-4465 TCGA-CG-5733 TCGA-F1-6874 
       15.81         0.13         0.10         9.01        21.07        14.47 

$`DDX17 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69        12.26         9.60         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
       16.31         2.20        15.58         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.07         0.10         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
       12.03         0.00        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       16.24        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  DDX17 MUTATED DDX17 WILD-TYPE 
            0.1             0.0 
  DDX17 MUTATED DDX17 WILD-TYPE 
          32.78          105.07 
  DDX17 MUTATED DDX17 WILD-TYPE 
          13.45           12.62 
[1] "0.1 - 32.8 (13.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D122V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDX17 MUTATED         0        0        2        1         1         2
  DDX17 WILD-TYPE       1        9       25       25        30        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DDX17 MUTATED           0          2          0          1        3
  DDX17 WILD-TYPE         3         47         36         23       21
D122V3, multiclass
            clus
vv           DDX17 MUTATED DDX17 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               3              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDX17 MUTATED     0   3   4   6
  DDX17 WILD-TYPE  11  69 118  69
D122V4, multiclass
    clus
vv   DDX17 MUTATED DDX17 WILD-TYPE
  T1             0              11
  T2             3              69
  T3             4             118
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  DDX17 MUTATED    7  1  3  1
  DDX17 WILD-TYPE 86 80 47 52
D122V5, multiclass
    clus
vv   DDX17 MUTATED DDX17 WILD-TYPE
  N0             7              86
  N1             1              80
  N2             3              47
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V6, binary
                 cls
clus                0   1
  DDX17 MUTATED     8   3
  DDX17 WILD-TYPE 249  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      8    3
  DDX17 WILD-TYPE  249   15
   clus
vv  DDX17 MUTATED DDX17 WILD-TYPE
  0             8             249
  1             3              15
[1] 2 2
[1] FALSE
D122V7, binary
                 cls
clus                0   1
  DDX17 MUTATED     7   6
  DDX17 WILD-TYPE 103 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      7    6
  DDX17 WILD-TYPE  103  173
        clus
vv       DDX17 MUTATED DDX17 WILD-TYPE
  FEMALE             7             103
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DDX17 MUTATED                                       1
  DDX17 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DDX17 MUTATED                                                        7
  DDX17 WILD-TYPE                                                    128
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DDX17 MUTATED                                                                   3
  DDX17 WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DDX17 MUTATED                                                  1
  DDX17 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DDX17 MUTATED                                                          1
  DDX17 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DDX17 MUTATED                                                           0
  DDX17 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DDX17 MUTATED                                          0
  DDX17 WILD-TYPE                                        3
D122V8, multiclass
                                                                   clus
vv                                                                  DDX17 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  DDX17 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V9, binary
                 cls
clus                0   1
  DDX17 MUTATED     0  13
  DDX17 WILD-TYPE   5 271
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      0   13
  DDX17 WILD-TYPE    5  271
     clus
vv    DDX17 MUTATED DDX17 WILD-TYPE
  NO              0               5
  YES            13             271
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DDX17 MUTATED    10   0   1   2
  DDX17 WILD-TYPE 217  10   9  22
D122V10, multiclass
    clus
vv   DDX17 MUTATED DDX17 WILD-TYPE
  R0            10             217
  R1             0              10
  R2             1               9
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDX17 MUTATED       3                         0     8
  DDX17 WILD-TYPE    73                         4   160
D122V12, multiclass
                           clus
vv                          DDX17 MUTATED DDX17 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 8             160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(123) Variable = C19ORF40 MUTATION ANALYSIS
D123V1, survival
                    sevent
clus2                  0   1
  C19ORF40 MUTATED     4   1
  C19ORF40 WILD-TYPE 177  79
  C19ORF40 MUTATED C19ORF40 WILD-TYPE 
                 5                256 
  C19ORF40 MUTATED C19ORF40 WILD-TYPE 
                 1                 79 
$`C19ORF40 MUTATED`
TCGA-BR-4184 TCGA-CD-8536 TCGA-CG-4444 TCGA-CG-5721 TCGA-HU-A4GX 
        6.97         0.10        47.05         6.02        10.19 

$`C19ORF40 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.13         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.25         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  C19ORF40 MUTATED C19ORF40 WILD-TYPE 
               0.1                0.0 
  C19ORF40 MUTATED C19ORF40 WILD-TYPE 
             47.05             105.07 
  C19ORF40 MUTATED C19ORF40 WILD-TYPE 
              6.97              12.71 
[1] "0.1 - 47.0 (7.0)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.4"
D123V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C19ORF40 MUTATED         0        0        0        1         0         0
  C19ORF40 WILD-TYPE       1        9       27       25        31        44
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C19ORF40 MUTATED           0          2          0          1        1
  C19ORF40 WILD-TYPE         3         47         36         23       23
D123V3, multiclass
            clus
vv           C19ORF40 MUTATED C19ORF40 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  0                 27
  STAGE II                  1                 25
  STAGE IIA                 0                 31
  STAGE IIB                 0                 44
  STAGE III                 0                  3
  STAGE IIIA                2                 47
  STAGE IIIB                0                 36
  STAGE IIIC                1                 23
  STAGE IV                  1                 23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C19ORF40 MUTATED     0   1   2   2
  C19ORF40 WILD-TYPE  11  71 120  73
D123V4, multiclass
    clus
vv   C19ORF40 MUTATED C19ORF40 WILD-TYPE
  T1                0                 11
  T2                1                 71
  T3                2                120
  T4                2                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  C19ORF40 MUTATED    1  2  2  0
  C19ORF40 WILD-TYPE 92 79 48 53
D123V5, multiclass
    clus
vv   C19ORF40 MUTATED C19ORF40 WILD-TYPE
  N0                1                 92
  N1                2                 79
  N2                2                 48
  N3                0                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V6, binary
                    cls
clus                   0   1
  C19ORF40 MUTATED     5   0
  C19ORF40 WILD-TYPE 252  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF40 MUTATED      5    0
  C19ORF40 WILD-TYPE  252   18
   clus
vv  C19ORF40 MUTATED C19ORF40 WILD-TYPE
  0                5                252
  1                0                 18
[1] 2 2
[1] FALSE
D123V7, binary
                    cls
clus                   0   1
  C19ORF40 MUTATED     2   4
  C19ORF40 WILD-TYPE 108 175
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF40 MUTATED      2    4
  C19ORF40 WILD-TYPE  108  175
        clus
vv       C19ORF40 MUTATED C19ORF40 WILD-TYPE
  FEMALE                2                108
  MALE                  4                175
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C19ORF40 MUTATED                                       2
  C19ORF40 WILD-TYPE                                    48
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C19ORF40 MUTATED                                                        3
  C19ORF40 WILD-TYPE                                                    132
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C19ORF40 MUTATED                                                                   1
  C19ORF40 WILD-TYPE                                                                39
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C19ORF40 MUTATED                                                  0
  C19ORF40 WILD-TYPE                                               38
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C19ORF40 MUTATED                                                          0
  C19ORF40 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C19ORF40 MUTATED                                                           0
  C19ORF40 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C19ORF40 MUTATED                                          0
  C19ORF40 WILD-TYPE                                        3
D123V8, multiclass
                                                                   clus
vv                                                                  C19ORF40 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  C19ORF40 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V9, binary
                    cls
clus                   0   1
  C19ORF40 MUTATED     0   6
  C19ORF40 WILD-TYPE   5 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF40 MUTATED      0    6
  C19ORF40 WILD-TYPE    5  278
     clus
vv    C19ORF40 MUTATED C19ORF40 WILD-TYPE
  NO                 0                  5
  YES                6                278
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C19ORF40 MUTATED     4   0   0   2
  C19ORF40 WILD-TYPE 223  10  10  22
D123V10, multiclass
    clus
vv   C19ORF40 MUTATED C19ORF40 WILD-TYPE
  R0                4                223
  R1                0                 10
  R2                0                 10
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C19ORF40 MUTATED       2                         0     2
  C19ORF40 WILD-TYPE    74                         4   166
D123V12, multiclass
                           clus
vv                          C19ORF40 MUTATED C19ORF40 WILD-TYPE
  ASIAN                                    2                 74
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    2                166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(124) Variable = ABCC4 MUTATION ANALYSIS
D124V1, survival
                 sevent
clus2               0   1
  ABCC4 MUTATED    10   5
  ABCC4 WILD-TYPE 171  75
  ABCC4 MUTATED ABCC4 WILD-TYPE 
             15             246 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
              5              75 
$`ABCC4 MUTATED`
TCGA-BR-6852 TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8680 
       32.94        14.43        20.55         4.31         1.12        15.81 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 
       15.95         1.02         9.01         6.02       105.07        28.96 
TCGA-CG-5728 TCGA-CG-5734 TCGA-D7-A4YY 
       65.10         7.99        13.78 

$`ABCC4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        30.90        31.20        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 
       17.49         0.69        12.26         9.60         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 
        0.10        12.62        20.02         3.02        27.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       19.07        12.03         0.00        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5577 
       12.03        79.07         4.01        69.04        21.07        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 
       20.91        14.27        16.44         5.92        15.16        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  ABCC4 MUTATED ABCC4 WILD-TYPE 
           1.02            0.00 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
         105.07           79.07 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
         14.430          12.575 
[1] "1.0 - 105.1 (14.4)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.4"
D124V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCC4 MUTATED         0        1        2        2         2         1
  ABCC4 WILD-TYPE       1        8       25       24        29        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ABCC4 MUTATED           1          2          1          0        4
  ABCC4 WILD-TYPE         2         47         35         24       20
D124V3, multiclass
            clus
vv           ABCC4 MUTATED ABCC4 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               2              25
  STAGE II               2              24
  STAGE IIA              2              29
  STAGE IIB              1              43
  STAGE III              1               2
  STAGE IIIA             2              47
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               4              20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCC4 MUTATED     1   4   6   6
  ABCC4 WILD-TYPE  10  68 116  69
D124V4, multiclass
    clus
vv   ABCC4 MUTATED ABCC4 WILD-TYPE
  T1             1              10
  T2             4              68
  T3             6             116
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ABCC4 MUTATED    7  5  2  2
  ABCC4 WILD-TYPE 86 76 48 51
D124V5, multiclass
    clus
vv   ABCC4 MUTATED ABCC4 WILD-TYPE
  N0             7              86
  N1             5              76
  N2             2              48
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V6, binary
                 cls
clus                0   1
  ABCC4 MUTATED    13   3
  ABCC4 WILD-TYPE 244  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED     13    3
  ABCC4 WILD-TYPE  244   15
   clus
vv  ABCC4 MUTATED ABCC4 WILD-TYPE
  0            13             244
  1             3              15
[1] 2 2
[1] FALSE
D124V7, binary
                 cls
clus                0   1
  ABCC4 MUTATED     7  10
  ABCC4 WILD-TYPE 103 169
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED      7   10
  ABCC4 WILD-TYPE  103  169
        clus
vv       ABCC4 MUTATED ABCC4 WILD-TYPE
  FEMALE             7             103
  MALE              10             169
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ABCC4 MUTATED                                       1
  ABCC4 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ABCC4 MUTATED                                                       10
  ABCC4 WILD-TYPE                                                    125
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ABCC4 MUTATED                                                                   5
  ABCC4 WILD-TYPE                                                                35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ABCC4 MUTATED                                                  1
  ABCC4 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ABCC4 MUTATED                                                          0
  ABCC4 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ABCC4 MUTATED                                                           0
  ABCC4 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ABCC4 MUTATED                                          0
  ABCC4 WILD-TYPE                                        3
D124V8, multiclass
                                                                   clus
vv                                                                  ABCC4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ABCC4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V9, binary
                 cls
clus                0   1
  ABCC4 MUTATED     0  17
  ABCC4 WILD-TYPE   5 267
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED      0   17
  ABCC4 WILD-TYPE    5  267
     clus
vv    ABCC4 MUTATED ABCC4 WILD-TYPE
  NO              0               5
  YES            17             267
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ABCC4 MUTATED    13   0   2   2
  ABCC4 WILD-TYPE 214  10   8  22
D124V10, multiclass
    clus
vv   ABCC4 MUTATED ABCC4 WILD-TYPE
  R0            13             214
  R1             0              10
  R2             2               8
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ABCC4 MUTATED       1                         0     8
  ABCC4 WILD-TYPE    75                         4   160
D124V12, multiclass
                           clus
vv                          ABCC4 MUTATED ABCC4 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 8             160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(125) Variable = ZFC3H1 MUTATION ANALYSIS
D125V1, survival
                  sevent
clus2                0   1
  ZFC3H1 MUTATED    10   3
  ZFC3H1 WILD-TYPE 171  77
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
              13              248 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
               3               77 
$`ZFC3H1 MUTATED`
TCGA-BR-4187 TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4IY 
        4.64        34.68        19.50         1.12        15.81        12.89 
TCGA-CD-8530 TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-4475 TCGA-CG-5721 TCGA-HU-A4GN 
        0.16         6.58         1.02        22.98         6.02        29.98 
TCGA-HU-A4GX 
       10.19 

$`ZFC3H1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         6.97         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 
       22.26         1.48        13.41        13.51         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77         8.98         0.10         6.51         6.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
            0.16             0.00 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
           34.68           105.07 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
           10.19            12.64 
[1] "0.2 - 34.7 (10.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D125V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZFC3H1 MUTATED         0        0        1        1         4         2
  ZFC3H1 WILD-TYPE       1        9       26       25        27        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFC3H1 MUTATED           0          1          0          2        3
  ZFC3H1 WILD-TYPE         3         48         36         22       21
D125V3, multiclass
            clus
vv           ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                1               25
  STAGE IIA               4               27
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              2               22
  STAGE IV                3               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZFC3H1 MUTATED     0   2   6   6
  ZFC3H1 WILD-TYPE  11  70 116  69
D125V4, multiclass
    clus
vv   ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  T1              0               11
  T2              2               70
  T3              6              116
  T4              6               69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZFC3H1 MUTATED    7  3  4  0
  ZFC3H1 WILD-TYPE 86 78 46 53
D125V5, multiclass
    clus
vv   ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  N0              7               86
  N1              3               78
  N2              4               46
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V6, binary
                  cls
clus                 0   1
  ZFC3H1 MUTATED    13   2
  ZFC3H1 WILD-TYPE 244  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZFC3H1 MUTATED     13    2
  ZFC3H1 WILD-TYPE  244   16
   clus
vv  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  0             13              244
  1              2               16
[1] 2 2
[1] FALSE
D125V7, binary
                  cls
clus                 0   1
  ZFC3H1 MUTATED     6   9
  ZFC3H1 WILD-TYPE 104 170
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZFC3H1 MUTATED      6    9
  ZFC3H1 WILD-TYPE  104  170
        clus
vv       ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  FEMALE              6              104
  MALE                9              170
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZFC3H1 MUTATED                                       3
  ZFC3H1 WILD-TYPE                                    47
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZFC3H1 MUTATED                                                        8
  ZFC3H1 WILD-TYPE                                                    127
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZFC3H1 MUTATED                                                                   1
  ZFC3H1 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZFC3H1 MUTATED                                                  2
  ZFC3H1 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZFC3H1 MUTATED                                                          0
  ZFC3H1 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZFC3H1 MUTATED                                                           0
  ZFC3H1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZFC3H1 MUTATED                                          0
  ZFC3H1 WILD-TYPE                                        3
D125V8, multiclass
                                                                   clus
vv                                                                  ZFC3H1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ZFC3H1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V9, binary
                  cls
clus                 0   1
  ZFC3H1 MUTATED     0  15
  ZFC3H1 WILD-TYPE   5 269
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZFC3H1 MUTATED      0   15
  ZFC3H1 WILD-TYPE    5  269
     clus
vv    ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  NO               0                5
  YES             15              269
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZFC3H1 MUTATED    11   0   1   2
  ZFC3H1 WILD-TYPE 216  10   9  22
D125V10, multiclass
    clus
vv   ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  R0             11              216
  R1              0               10
  R2              1                9
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZFC3H1 MUTATED       6                         0     6
  ZFC3H1 WILD-TYPE    70                         4   162
D125V12, multiclass
                           clus
vv                          ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  ASIAN                                  6               70
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(126) Variable = ZKSCAN5 MUTATION ANALYSIS
D126V1, survival
                   sevent
clus2                 0   1
  ZKSCAN5 MUTATED     8   0
  ZKSCAN5 WILD-TYPE 173  80
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
                8               253 
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
                0                80 
$`ZKSCAN5 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-7851 TCGA-BR-8078 TCGA-CD-8529 TCGA-CG-5721 
       26.70        34.68        12.43        12.26         0.13         6.02 
TCGA-HU-A4GX TCGA-HU-A4H8 
       10.19         8.88 

$`ZKSCAN5 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.10         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        9.67        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
             0.13              0.00 
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
            34.68            105.07 
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
           11.225            12.760 
[1] "0.1 - 34.7 (11.2)"  "0.0 - 105.1 (12.8)"
[1] "hr="     "2.6e+07"
D126V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZKSCAN5 MUTATED         0        0        1        0         1         3
  ZKSCAN5 WILD-TYPE       1        9       26       26        30        41
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZKSCAN5 MUTATED           0          0          0          1        2
  ZKSCAN5 WILD-TYPE         3         49         36         23       22
D126V3, multiclass
            clus
vv           ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 0                26
  STAGE IIA                1                30
  STAGE IIB                3                41
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               0                36
  STAGE IIIC               1                23
  STAGE IV                 2                22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZKSCAN5 MUTATED     1   0   1   6
  ZKSCAN5 WILD-TYPE  10  72 121  69
D126V4, multiclass
    clus
vv   ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  T1               1                10
  T2               0                72
  T3               1               121
  T4               6                69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  ZKSCAN5 MUTATED    5  2  1  0
  ZKSCAN5 WILD-TYPE 88 79 49 53
D126V5, multiclass
    clus
vv   ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  N0               5                88
  N1               2                79
  N2               1                49
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V6, binary
                   cls
clus                  0   1
  ZKSCAN5 MUTATED     8   1
  ZKSCAN5 WILD-TYPE 249  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN5 MUTATED      8    1
  ZKSCAN5 WILD-TYPE  249   17
   clus
vv  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  0               8               249
  1               1                17
[1] 2 2
[1] FALSE
D126V7, binary
                   cls
clus                  0   1
  ZKSCAN5 MUTATED     5   4
  ZKSCAN5 WILD-TYPE 105 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN5 MUTATED      5    4
  ZKSCAN5 WILD-TYPE  105  175
        clus
vv       ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  FEMALE               5               105
  MALE                 4               175
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZKSCAN5 MUTATED                                       2
  ZKSCAN5 WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZKSCAN5 MUTATED                                                        3
  ZKSCAN5 WILD-TYPE                                                    132
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZKSCAN5 MUTATED                                                                   2
  ZKSCAN5 WILD-TYPE                                                                38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZKSCAN5 MUTATED                                                  1
  ZKSCAN5 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZKSCAN5 MUTATED                                                          1
  ZKSCAN5 WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZKSCAN5 MUTATED                                                           0
  ZKSCAN5 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZKSCAN5 MUTATED                                          0
  ZKSCAN5 WILD-TYPE                                        3
D126V8, multiclass
                                                                   clus
vv                                                                  ZKSCAN5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  ZKSCAN5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V9, binary
                   cls
clus                  0   1
  ZKSCAN5 MUTATED     0   9
  ZKSCAN5 WILD-TYPE   5 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN5 MUTATED      0    9
  ZKSCAN5 WILD-TYPE    5  275
     clus
vv    ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  NO                0                 5
  YES               9               275
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZKSCAN5 MUTATED     8   0   0   1
  ZKSCAN5 WILD-TYPE 219  10  10  23
D126V10, multiclass
    clus
vv   ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  R0               8               219
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZKSCAN5 MUTATED       3                         0     5
  ZKSCAN5 WILD-TYPE    73                         4   163
D126V12, multiclass
                           clus
vv                          ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  ASIAN                                   3                73
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   5               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(127) Variable = RABGAP1 MUTATION ANALYSIS
D127V1, survival
                   sevent
clus2                 0   1
  RABGAP1 MUTATED    16   2
  RABGAP1 WILD-TYPE 165  78
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
               18               243 
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
                2                78 
$`RABGAP1 MUTATED`
TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8361 
       34.68        23.93        12.43        12.26         6.18        19.50 
TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MJ TCGA-CG-4305 
        4.31         1.12        15.81        11.57        12.62        15.95 
TCGA-CG-5728 TCGA-CG-5733 TCGA-F1-A448 TCGA-FP-A4BE TCGA-HU-A4GQ TCGA-HU-A4GT 
       65.10        21.07        21.27        11.08         0.10         6.51 

$`RABGAP1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8364 
       16.31         2.20        15.58         7.40         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20         0.10        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        79.07         4.01        69.04         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
        5.03        13.58         0.56         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU 
       22.75        25.81        11.77        29.98         8.98         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
              0.1               0.0 
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
            65.10            105.07 
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
           12.525            12.660 
[1] "0.1 - 65.1 (12.5)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "3.2"
D127V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RABGAP1 MUTATED         0        0        5        1         5         2
  RABGAP1 WILD-TYPE       1        9       22       25        26        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RABGAP1 MUTATED           0          1          2          2        1
  RABGAP1 WILD-TYPE         3         48         34         22       23
D127V3, multiclass
            clus
vv           RABGAP1 MUTATED RABGAP1 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 5                22
  STAGE II                 1                25
  STAGE IIA                5                26
  STAGE IIB                2                42
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               2                34
  STAGE IIIC               2                22
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RABGAP1 MUTATED     0   7   7   5
  RABGAP1 WILD-TYPE  11  65 115  70
D127V4, multiclass
    clus
vv   RABGAP1 MUTATED RABGAP1 WILD-TYPE
  T1               0                11
  T2               7                65
  T3               7               115
  T4               5                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  RABGAP1 MUTATED   12  1  4  2
  RABGAP1 WILD-TYPE 81 80 46 51
D127V5, multiclass
    clus
vv   RABGAP1 MUTATED RABGAP1 WILD-TYPE
  N0              12                81
  N1               1                80
  N2               4                46
  N3               2                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V6, binary
                   cls
clus                  0   1
  RABGAP1 MUTATED    19   1
  RABGAP1 WILD-TYPE 238  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RABGAP1 MUTATED     19    1
  RABGAP1 WILD-TYPE  238   17
   clus
vv  RABGAP1 MUTATED RABGAP1 WILD-TYPE
  0              19               238
  1               1                17
[1] 2 2
[1] FALSE
D127V7, binary
                   cls
clus                  0   1
  RABGAP1 MUTATED    11   9
  RABGAP1 WILD-TYPE  99 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RABGAP1 MUTATED     11    9
  RABGAP1 WILD-TYPE   99  170
        clus
vv       RABGAP1 MUTATED RABGAP1 WILD-TYPE
  FEMALE              11                99
  MALE                 9               170
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RABGAP1 MUTATED                                       0
  RABGAP1 WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RABGAP1 MUTATED                                                       11
  RABGAP1 WILD-TYPE                                                    124
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RABGAP1 MUTATED                                                                   5
  RABGAP1 WILD-TYPE                                                                35
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RABGAP1 MUTATED                                                  3
  RABGAP1 WILD-TYPE                                               35
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RABGAP1 MUTATED                                                          1
  RABGAP1 WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RABGAP1 MUTATED                                                           0
  RABGAP1 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RABGAP1 MUTATED                                          0
  RABGAP1 WILD-TYPE                                        3
D127V8, multiclass
                                                                   clus
vv                                                                  RABGAP1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  RABGAP1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V9, binary
                   cls
clus                  0   1
  RABGAP1 MUTATED     0  20
  RABGAP1 WILD-TYPE   5 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RABGAP1 MUTATED      0   20
  RABGAP1 WILD-TYPE    5  264
     clus
vv    RABGAP1 MUTATED RABGAP1 WILD-TYPE
  NO                0                 5
  YES              20               264
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  RABGAP1 MUTATED    18   0   0   1
  RABGAP1 WILD-TYPE 209  10  10  23
D127V10, multiclass
    clus
vv   RABGAP1 MUTATED RABGAP1 WILD-TYPE
  R0              18               209
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RABGAP1 MUTATED       4                         1    11
  RABGAP1 WILD-TYPE    72                         3   157
D127V12, multiclass
                           clus
vv                          RABGAP1 MUTATED RABGAP1 WILD-TYPE
  ASIAN                                   4                72
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                  11               157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(128) Variable = RNF145 MUTATION ANALYSIS
D128V1, survival
                  sevent
clus2                0   1
  RNF145 MUTATED    12   3
  RNF145 WILD-TYPE 169  77
  RNF145 MUTATED RNF145 WILD-TYPE 
              15              246 
  RNF145 MUTATED RNF145 WILD-TYPE 
               3               77 
$`RNF145 MUTATED`
TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8382 TCGA-BR-A4QM TCGA-CD-A4MG 
       34.68        20.55         0.26        15.85         5.13         6.58 
TCGA-CD-A4MI TCGA-CG-4305 TCGA-CG-5721 TCGA-D7-6822 TCGA-EQ-5647 TCGA-HU-A4G9 
        0.10        15.95         6.02        12.33         0.62        24.20 
TCGA-HU-A4GN TCGA-HU-A4H4 TCGA-HU-A4H8 
       29.98        23.84         8.88 

$`RNF145 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       17.49        14.43         0.69        12.26         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        19.50        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        0.26         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        10.55        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-8122 
       16.44         5.92        15.16        13.78        14.76         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        11.84         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  RNF145 MUTATED RNF145 WILD-TYPE 
             0.1              0.0 
  RNF145 MUTATED RNF145 WILD-TYPE 
           34.68           105.07 
  RNF145 MUTATED RNF145 WILD-TYPE 
           12.33            12.64 
[1] "0.1 - 34.7 (12.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.5"
D128V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RNF145 MUTATED         0        1        3        1         3         2
  RNF145 WILD-TYPE       1        8       24       25        28        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF145 MUTATED           0          1          1          1        3
  RNF145 WILD-TYPE         3         48         35         23       21
D128V3, multiclass
            clus
vv           RNF145 MUTATED RNF145 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                3               24
  STAGE II                1               25
  STAGE IIA               3               28
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              1               23
  STAGE IV                3               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNF145 MUTATED     2   5   4   5
  RNF145 WILD-TYPE   9  67 118  70
D128V4, multiclass
    clus
vv   RNF145 MUTATED RNF145 WILD-TYPE
  T1              2                9
  T2              5               67
  T3              4              118
  T4              5               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  RNF145 MUTATED    6  6  3  2
  RNF145 WILD-TYPE 87 75 47 51
D128V5, multiclass
    clus
vv   RNF145 MUTATED RNF145 WILD-TYPE
  N0              6               87
  N1              6               75
  N2              3               47
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V6, binary
                  cls
clus                 0   1
  RNF145 MUTATED    17   1
  RNF145 WILD-TYPE 240  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF145 MUTATED     17    1
  RNF145 WILD-TYPE  240   17
   clus
vv  RNF145 MUTATED RNF145 WILD-TYPE
  0             17              240
  1              1               17
[1] 2 2
[1] FALSE
D128V7, binary
                  cls
clus                 0   1
  RNF145 MUTATED     9   9
  RNF145 WILD-TYPE 101 170
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF145 MUTATED      9    9
  RNF145 WILD-TYPE  101  170
        clus
vv       RNF145 MUTATED RNF145 WILD-TYPE
  FEMALE              9              101
  MALE                9              170
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RNF145 MUTATED                                       1
  RNF145 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RNF145 MUTATED                                                       11
  RNF145 WILD-TYPE                                                    124
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RNF145 MUTATED                                                                   1
  RNF145 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RNF145 MUTATED                                                  5
  RNF145 WILD-TYPE                                               33
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RNF145 MUTATED                                                          0
  RNF145 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RNF145 MUTATED                                                           0
  RNF145 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RNF145 MUTATED                                          0
  RNF145 WILD-TYPE                                        3
D128V8, multiclass
                                                                   clus
vv                                                                  RNF145 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  RNF145 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V9, binary
                  cls
clus                 0   1
  RNF145 MUTATED     0  18
  RNF145 WILD-TYPE   5 266
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF145 MUTATED      0   18
  RNF145 WILD-TYPE    5  266
     clus
vv    RNF145 MUTATED RNF145 WILD-TYPE
  NO               0                5
  YES             18              266
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RNF145 MUTATED    12   0   1   3
  RNF145 WILD-TYPE 215  10   9  21
D128V10, multiclass
    clus
vv   RNF145 MUTATED RNF145 WILD-TYPE
  R0             12              215
  R1              0               10
  R2              1                9
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RNF145 MUTATED       6                         0    10
  RNF145 WILD-TYPE    70                         4   158
D128V12, multiclass
                           clus
vv                          RNF145 MUTATED RNF145 WILD-TYPE
  ASIAN                                  6               70
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                 10              158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(129) Variable = SNAPC1 MUTATION ANALYSIS
D129V1, survival
                  sevent
clus2                0   1
  SNAPC1 MUTATED     5   2
  SNAPC1 WILD-TYPE 176  78
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
               7              254 
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
               2               78 
$`SNAPC1 MUTATED`
TCGA-B7-5816 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8487 TCGA-CG-5726 TCGA-D7-A4YV 
       26.70        12.26        19.50         1.12        28.96         5.92 
TCGA-HU-A4G9 
       24.20 

$`SNAPC1 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        11.84         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
            1.12             0.00 
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
           28.96           105.07 
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
          19.500           12.605 
[1] "1.1 - 29.0 (19.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D129V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SNAPC1 MUTATED         0        2        0        0         1         3
  SNAPC1 WILD-TYPE       1        7       27       26        30        41
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SNAPC1 MUTATED           0          0          0          1        0
  SNAPC1 WILD-TYPE         3         49         36         23       24
D129V3, multiclass
            clus
vv           SNAPC1 MUTATED SNAPC1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                2                7
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               3               41
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SNAPC1 MUTATED     2   0   2   3
  SNAPC1 WILD-TYPE   9  72 120  72
D129V4, multiclass
    clus
vv   SNAPC1 MUTATED SNAPC1 WILD-TYPE
  T1              2                9
  T2              0               72
  T3              2              120
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  SNAPC1 MUTATED    5  1  1  0
  SNAPC1 WILD-TYPE 88 80 49 53
D129V5, multiclass
    clus
vv   SNAPC1 MUTATED SNAPC1 WILD-TYPE
  N0              5               88
  N1              1               80
  N2              1               49
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V6, binary
                  cls
clus                 0   1
  SNAPC1 MUTATED     7   0
  SNAPC1 WILD-TYPE 250  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC1 MUTATED      7    0
  SNAPC1 WILD-TYPE  250   18
   clus
vv  SNAPC1 MUTATED SNAPC1 WILD-TYPE
  0              7              250
  1              0               18
[1] 2 2
[1] FALSE
D129V7, binary
                  cls
clus                 0   1
  SNAPC1 MUTATED     6   1
  SNAPC1 WILD-TYPE 104 178
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC1 MUTATED      6    1
  SNAPC1 WILD-TYPE  104  178
        clus
vv       SNAPC1 MUTATED SNAPC1 WILD-TYPE
  FEMALE              6              104
  MALE                1              178
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SNAPC1 MUTATED                                       1
  SNAPC1 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SNAPC1 MUTATED                                                        3
  SNAPC1 WILD-TYPE                                                    132
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SNAPC1 MUTATED                                                                   1
  SNAPC1 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SNAPC1 MUTATED                                                  2
  SNAPC1 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SNAPC1 MUTATED                                                          0
  SNAPC1 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SNAPC1 MUTATED                                                           0
  SNAPC1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SNAPC1 MUTATED                                          0
  SNAPC1 WILD-TYPE                                        3
D129V8, multiclass
                                                                   clus
vv                                                                  SNAPC1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  SNAPC1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V9, binary
                  cls
clus                 0   1
  SNAPC1 MUTATED     0   7
  SNAPC1 WILD-TYPE   5 277
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC1 MUTATED      0    7
  SNAPC1 WILD-TYPE    5  277
     clus
vv    SNAPC1 MUTATED SNAPC1 WILD-TYPE
  NO               0                5
  YES              7              277
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SNAPC1 MUTATED     7   0   0   0
  SNAPC1 WILD-TYPE 220  10  10  24
D129V10, multiclass
    clus
vv   SNAPC1 MUTATED SNAPC1 WILD-TYPE
  R0              7              220
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SNAPC1 MUTATED       1                         0     5
  SNAPC1 WILD-TYPE    75                         4   163
D129V12, multiclass
                           clus
vv                          SNAPC1 MUTATED SNAPC1 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  5              163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(130) Variable = CCDC153 MUTATION ANALYSIS
D130V1, survival
                   sevent
clus2                 0   1
  CCDC153 MUTATED     7   0
  CCDC153 WILD-TYPE 174  80
  CCDC153 MUTATED CCDC153 WILD-TYPE 
                7               254 
  CCDC153 MUTATED CCDC153 WILD-TYPE 
                0                80 
$`CCDC153 MUTATED`
TCGA-BR-8360 TCGA-BR-8591 TCGA-CD-A4MI TCGA-CG-5721 TCGA-F1-6874 TCGA-HU-A4GN 
        6.18        13.45         0.10         6.02        14.47        29.98 
TCGA-HU-A4H4 
       23.84 

$`CCDC153 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.99        16.24        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        19.36        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  CCDC153 MUTATED CCDC153 WILD-TYPE 
              0.1               0.0 
  CCDC153 MUTATED CCDC153 WILD-TYPE 
            29.98            105.07 
  CCDC153 MUTATED CCDC153 WILD-TYPE 
           13.450            12.605 
[1] "0.1 - 30.0 (13.4)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "2.5e+07"
D130V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC153 MUTATED         0        0        2        0         2         1
  CCDC153 WILD-TYPE       1        9       25       26        29        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC153 MUTATED           0          0          1          1        1
  CCDC153 WILD-TYPE         3         49         35         23       23
D130V3, multiclass
            clus
vv           CCDC153 MUTATED CCDC153 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 2                25
  STAGE II                 0                26
  STAGE IIA                2                29
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               1                35
  STAGE IIIC               1                23
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC153 MUTATED     0   4   2   2
  CCDC153 WILD-TYPE  11  68 120  73
D130V4, multiclass
    clus
vv   CCDC153 MUTATED CCDC153 WILD-TYPE
  T1               0                11
  T2               4                68
  T3               2               120
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  CCDC153 MUTATED    3  3  1  1
  CCDC153 WILD-TYPE 90 78 49 52
D130V5, multiclass
    clus
vv   CCDC153 MUTATED CCDC153 WILD-TYPE
  N0               3                90
  N1               3                78
  N2               1                49
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V6, binary
                   cls
clus                  0   1
  CCDC153 MUTATED     8   0
  CCDC153 WILD-TYPE 249  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC153 MUTATED      8    0
  CCDC153 WILD-TYPE  249   18
   clus
vv  CCDC153 MUTATED CCDC153 WILD-TYPE
  0               8               249
  1               0                18
[1] 2 2
[1] FALSE
D130V7, binary
                   cls
clus                  0   1
  CCDC153 MUTATED     1   7
  CCDC153 WILD-TYPE 109 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC153 MUTATED      1    7
  CCDC153 WILD-TYPE  109  172
        clus
vv       CCDC153 MUTATED CCDC153 WILD-TYPE
  FEMALE               1               109
  MALE                 7               172
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CCDC153 MUTATED                                       0
  CCDC153 WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CCDC153 MUTATED                                                        2
  CCDC153 WILD-TYPE                                                    133
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CCDC153 MUTATED                                                                   4
  CCDC153 WILD-TYPE                                                                36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CCDC153 MUTATED                                                  2
  CCDC153 WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CCDC153 MUTATED                                                          0
  CCDC153 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CCDC153 MUTATED                                                           0
  CCDC153 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CCDC153 MUTATED                                          0
  CCDC153 WILD-TYPE                                        3
D130V8, multiclass
                                                                   clus
vv                                                                  CCDC153 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  CCDC153 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V9, binary
                   cls
clus                  0   1
  CCDC153 MUTATED     0   8
  CCDC153 WILD-TYPE   5 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC153 MUTATED      0    8
  CCDC153 WILD-TYPE    5  276
     clus
vv    CCDC153 MUTATED CCDC153 WILD-TYPE
  NO                0                 5
  YES               8               276
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CCDC153 MUTATED     7   0   0   0
  CCDC153 WILD-TYPE 220  10  10  24
D130V10, multiclass
    clus
vv   CCDC153 MUTATED CCDC153 WILD-TYPE
  R0               7               220
  R1               0                10
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC153 MUTATED       3                         0     3
  CCDC153 WILD-TYPE    73                         4   165
D130V12, multiclass
                           clus
vv                          CCDC153 MUTATED CCDC153 WILD-TYPE
  ASIAN                                   3                73
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   3               165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(131) Variable = OPTN MUTATION ANALYSIS
D131V1, survival
                sevent
clus2              0   1
  OPTN MUTATED     4   2
  OPTN WILD-TYPE 177  78
  OPTN MUTATED OPTN WILD-TYPE 
             6            255 
  OPTN MUTATED OPTN WILD-TYPE 
             2             78 
$`OPTN MUTATED`
TCGA-BR-4201 TCGA-BR-7851 TCGA-CD-8529 TCGA-CG-5723 TCGA-CG-5726 TCGA-HU-A4GU 
       30.90        12.43         0.13       105.07        28.96         6.25 

$`OPTN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.10         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
        0.99        12.03        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  OPTN MUTATED OPTN WILD-TYPE 
          0.13           0.00 
  OPTN MUTATED OPTN WILD-TYPE 
        105.07          79.07 
  OPTN MUTATED OPTN WILD-TYPE 
        20.695         12.620 
[1] "0.1 - 105.1 (20.7)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.9"
D131V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OPTN MUTATED         1        1        1        1         0         2
  OPTN WILD-TYPE       0        8       26       25        31        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OPTN MUTATED           0          1          0          0        1
  OPTN WILD-TYPE         3         48         36         24       23
D131V3, multiclass
            clus
vv           OPTN MUTATED OPTN WILD-TYPE
  STAGE I               1              0
  STAGE IA              1              8
  STAGE IB              1             26
  STAGE II              1             25
  STAGE IIA             0             31
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  OPTN MUTATED     2   3   1   3
  OPTN WILD-TYPE   9  69 121  72
D131V4, multiclass
    clus
vv   OPTN MUTATED OPTN WILD-TYPE
  T1            2              9
  T2            3             69
  T3            1            121
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  OPTN MUTATED    5  3  0  0
  OPTN WILD-TYPE 88 78 50 53
D131V5, multiclass
    clus
vv   OPTN MUTATED OPTN WILD-TYPE
  N0            5             88
  N1            3             78
  N2            0             50
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V6, binary
                cls
clus               0   1
  OPTN MUTATED     7   1
  OPTN WILD-TYPE 250  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  OPTN MUTATED      7    1
  OPTN WILD-TYPE  250   17
   clus
vv  OPTN MUTATED OPTN WILD-TYPE
  0            7            250
  1            1             17
[1] 2 2
[1] FALSE
D131V7, binary
                cls
clus               0   1
  OPTN MUTATED     2   7
  OPTN WILD-TYPE 108 172
[1] "tbl2"
                cls
clus             [,1] [,2]
  OPTN MUTATED      2    7
  OPTN WILD-TYPE  108  172
        clus
vv       OPTN MUTATED OPTN WILD-TYPE
  FEMALE            2            108
  MALE              7            172
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  OPTN MUTATED                                       1
  OPTN WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OPTN MUTATED                                                        4
  OPTN WILD-TYPE                                                    131
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OPTN MUTATED                                                                   3
  OPTN WILD-TYPE                                                                37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  OPTN MUTATED                                                  0
  OPTN WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  OPTN MUTATED                                                          1
  OPTN WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  OPTN MUTATED                                                           0
  OPTN WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  OPTN MUTATED                                          0
  OPTN WILD-TYPE                                        3
D131V8, multiclass
                                                                   clus
vv                                                                  OPTN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  OPTN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V9, binary
                cls
clus               0   1
  OPTN MUTATED     0   9
  OPTN WILD-TYPE   5 275
[1] "tbl2"
                cls
clus             [,1] [,2]
  OPTN MUTATED      0    9
  OPTN WILD-TYPE    5  275
     clus
vv    OPTN MUTATED OPTN WILD-TYPE
  NO             0              5
  YES            9            275
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  OPTN MUTATED     7   0   0   2
  OPTN WILD-TYPE 220  10  10  22
D131V10, multiclass
    clus
vv   OPTN MUTATED OPTN WILD-TYPE
  R0            7            220
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OPTN MUTATED       2                         1     3
  OPTN WILD-TYPE    74                         3   165
D131V12, multiclass
                           clus
vv                          OPTN MUTATED OPTN WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                                3            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(132) Variable = PLEKHA5 MUTATION ANALYSIS
D132V1, survival
                   sevent
clus2                 0   1
  PLEKHA5 MUTATED    10   2
  PLEKHA5 WILD-TYPE 171  78
  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
               12               249 
  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
                2                78 
$`PLEKHA5 MUTATED`
TCGA-BR-4184 TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-A4QL 
        6.97         0.26        19.17        15.81        13.45        11.57 
TCGA-CD-A4MJ TCGA-CG-4305 TCGA-F1-6874 TCGA-HU-A4GN TCGA-HU-A4H4 TCGA-HU-A4H8 
       12.62        15.95        14.47        29.98        23.84         8.88 

$`PLEKHA5 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        19.50        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
       20.22         1.12        12.79         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
        0.10        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 
       14.76         0.62         7.99        16.24        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        11.77         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       19.36        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
             0.26              0.00 
  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
            29.98            105.07 
  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
            13.96             12.56 
[1] "0.3 - 30.0 (14.0)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.9"
D132V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLEKHA5 MUTATED         1        0        4        1         1         1
  PLEKHA5 WILD-TYPE       0        9       23       25        30        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHA5 MUTATED           0          1          2          2        0
  PLEKHA5 WILD-TYPE         3         48         34         22       24
D132V3, multiclass
            clus
vv           PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                 0                 9
  STAGE IB                 4                23
  STAGE II                 1                25
  STAGE IIA                1                30
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               2                34
  STAGE IIIC               2                22
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHA5 MUTATED     2   6   2   3
  PLEKHA5 WILD-TYPE   9  66 120  72
D132V4, multiclass
    clus
vv   PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  T1               2                 9
  T2               6                66
  T3               2               120
  T4               3                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  PLEKHA5 MUTATED    3  6  1  3
  PLEKHA5 WILD-TYPE 90 75 49 50
D132V5, multiclass
    clus
vv   PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  N0               3                90
  N1               6                75
  N2               1                49
  N3               3                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V6, binary
                   cls
clus                  0   1
  PLEKHA5 MUTATED    13   0
  PLEKHA5 WILD-TYPE 244  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA5 MUTATED     13    0
  PLEKHA5 WILD-TYPE  244   18
   clus
vv  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  0              13               244
  1               0                18
[1] 2 2
[1] FALSE
D132V7, binary
                   cls
clus                  0   1
  PLEKHA5 MUTATED     5  10
  PLEKHA5 WILD-TYPE 105 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA5 MUTATED      5   10
  PLEKHA5 WILD-TYPE  105  169
        clus
vv       PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  FEMALE               5               105
  MALE                10               169
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PLEKHA5 MUTATED                                       0
  PLEKHA5 WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLEKHA5 MUTATED                                                       11
  PLEKHA5 WILD-TYPE                                                    124
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLEKHA5 MUTATED                                                                   1
  PLEKHA5 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PLEKHA5 MUTATED                                                  3
  PLEKHA5 WILD-TYPE                                               35
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PLEKHA5 MUTATED                                                          0
  PLEKHA5 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PLEKHA5 MUTATED                                                           0
  PLEKHA5 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PLEKHA5 MUTATED                                          0
  PLEKHA5 WILD-TYPE                                        3
D132V8, multiclass
                                                                   clus
vv                                                                  PLEKHA5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  PLEKHA5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V9, binary
                   cls
clus                  0   1
  PLEKHA5 MUTATED     0  15
  PLEKHA5 WILD-TYPE   5 269
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA5 MUTATED      0   15
  PLEKHA5 WILD-TYPE    5  269
     clus
vv    PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  NO                0                 5
  YES              15               269
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PLEKHA5 MUTATED    11   0   0   3
  PLEKHA5 WILD-TYPE 216  10  10  21
D132V10, multiclass
    clus
vv   PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  R0              11               216
  R1               0                10
  R2               0                10
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLEKHA5 MUTATED       4                         1     9
  PLEKHA5 WILD-TYPE    72                         3   159
D132V12, multiclass
                           clus
vv                          PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  ASIAN                                   4                72
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   9               159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(133) Variable = SREBF2 MUTATION ANALYSIS
D133V1, survival
                  sevent
clus2                0   1
  SREBF2 MUTATED     8   2
  SREBF2 WILD-TYPE 173  78
  SREBF2 MUTATED SREBF2 WILD-TYPE 
              10              251 
  SREBF2 MUTATED SREBF2 WILD-TYPE 
               2               78 
$`SREBF2 MUTATED`
TCGA-BR-4183 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-A4QL TCGA-CD-5802 TCGA-CD-A4MI 
        6.61        34.68        24.76        11.57         0.30         0.10 
TCGA-CG-4436 TCGA-CG-5721 TCGA-HJ-7597 TCGA-HU-A4GN 
        7.99         6.02        26.47        29.98 

$`SREBF2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 
       30.90        31.20        32.94        12.82         9.21        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 
        5.13         2.83         3.25        13.15        13.18         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        11.77         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  SREBF2 MUTATED SREBF2 WILD-TYPE 
             0.1              0.0 
  SREBF2 MUTATED SREBF2 WILD-TYPE 
           34.68           105.07 
  SREBF2 MUTATED SREBF2 WILD-TYPE 
            9.78            12.66 
[1] "0.1 - 34.7 (9.8)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.7"
D133V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SREBF2 MUTATED         0        1        2        1         2         0
  SREBF2 WILD-TYPE       1        8       25       25        29        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SREBF2 MUTATED           0          1          2          0        1
  SREBF2 WILD-TYPE         3         48         34         24       23
D133V3, multiclass
            clus
vv           SREBF2 MUTATED SREBF2 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                2               25
  STAGE II                1               25
  STAGE IIA               2               29
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              2               34
  STAGE IIIC              0               24
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SREBF2 MUTATED     1   3   5   1
  SREBF2 WILD-TYPE  10  69 117  74
D133V4, multiclass
    clus
vv   SREBF2 MUTATED SREBF2 WILD-TYPE
  T1              1               10
  T2              3               69
  T3              5              117
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  SREBF2 MUTATED    5  4  0  1
  SREBF2 WILD-TYPE 88 77 50 52
D133V5, multiclass
    clus
vv   SREBF2 MUTATED SREBF2 WILD-TYPE
  N0              5               88
  N1              4               77
  N2              0               50
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V6, binary
                  cls
clus                 0   1
  SREBF2 MUTATED     9   0
  SREBF2 WILD-TYPE 248  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SREBF2 MUTATED      9    0
  SREBF2 WILD-TYPE  248   18
   clus
vv  SREBF2 MUTATED SREBF2 WILD-TYPE
  0              9              248
  1              0               18
[1] 2 2
[1] FALSE
D133V7, binary
                  cls
clus                 0   1
  SREBF2 MUTATED     4   6
  SREBF2 WILD-TYPE 106 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SREBF2 MUTATED      4    6
  SREBF2 WILD-TYPE  106  173
        clus
vv       SREBF2 MUTATED SREBF2 WILD-TYPE
  FEMALE              4              106
  MALE                6              173
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SREBF2 MUTATED                                       0
  SREBF2 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SREBF2 MUTATED                                                        5
  SREBF2 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SREBF2 MUTATED                                                                   2
  SREBF2 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SREBF2 MUTATED                                                  1
  SREBF2 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SREBF2 MUTATED                                                          0
  SREBF2 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SREBF2 MUTATED                                                           1
  SREBF2 WILD-TYPE                                                         5
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SREBF2 MUTATED                                          1
  SREBF2 WILD-TYPE                                        2
D133V8, multiclass
                                                                   clus
vv                                                                  SREBF2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       1
                                                                   clus
vv                                                                  SREBF2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V9, binary
                  cls
clus                 0   1
  SREBF2 MUTATED     0  10
  SREBF2 WILD-TYPE   5 274
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SREBF2 MUTATED      0   10
  SREBF2 WILD-TYPE    5  274
     clus
vv    SREBF2 MUTATED SREBF2 WILD-TYPE
  NO               0                5
  YES             10              274
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SREBF2 MUTATED     7   0   0   1
  SREBF2 WILD-TYPE 220  10  10  23
D133V10, multiclass
    clus
vv   SREBF2 MUTATED SREBF2 WILD-TYPE
  R0              7              220
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SREBF2 MUTATED       3                         0     5
  SREBF2 WILD-TYPE    73                         4   163
D133V12, multiclass
                           clus
vv                          SREBF2 MUTATED SREBF2 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  5              163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(134) Variable = FASTKD1 MUTATION ANALYSIS
D134V1, survival
                   sevent
clus2                 0   1
  FASTKD1 MUTATED     9   2
  FASTKD1 WILD-TYPE 172  78
  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
               11               250 
  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
                2                78 
$`FASTKD1 MUTATED`
TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8589 TCGA-BR-A4QL TCGA-CD-8527 TCGA-CG-5721 
       20.55         4.31        15.81        11.57         0.07         6.02 
TCGA-CG-5726 TCGA-D7-A4YV TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 
       28.96         5.92         6.51        10.19        19.36 

$`FASTKD1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22         1.12        12.79         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 
        0.07         0.39         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10         6.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
             0.07              0.00 
  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
            28.96            105.07 
  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
            10.19             12.71 
[1] "0.1 - 29.0 (10.2)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.4"
D134V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FASTKD1 MUTATED         0        1        1        1         1         2
  FASTKD1 WILD-TYPE       1        8       26       25        30        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FASTKD1 MUTATED           0          0          2          2        1
  FASTKD1 WILD-TYPE         3         49         34         22       23
D134V3, multiclass
            clus
vv           FASTKD1 MUTATED FASTKD1 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 1                 8
  STAGE IB                 1                26
  STAGE II                 1                25
  STAGE IIA                1                30
  STAGE IIB                2                42
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               2                34
  STAGE IIIC               2                22
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FASTKD1 MUTATED     1   2   3   5
  FASTKD1 WILD-TYPE  10  70 119  70
D134V4, multiclass
    clus
vv   FASTKD1 MUTATED FASTKD1 WILD-TYPE
  T1               1                10
  T2               2                70
  T3               3               119
  T4               5                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  FASTKD1 MUTATED    4  4  1  2
  FASTKD1 WILD-TYPE 89 77 49 51
D134V5, multiclass
    clus
vv   FASTKD1 MUTATED FASTKD1 WILD-TYPE
  N0               4                89
  N1               4                77
  N2               1                49
  N3               2                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V6, binary
                   cls
clus                  0   1
  FASTKD1 MUTATED    11   0
  FASTKD1 WILD-TYPE 246  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FASTKD1 MUTATED     11    0
  FASTKD1 WILD-TYPE  246   18
   clus
vv  FASTKD1 MUTATED FASTKD1 WILD-TYPE
  0              11               246
  1               0                18
[1] 2 2
[1] FALSE
D134V7, binary
                   cls
clus                  0   1
  FASTKD1 MUTATED     8   3
  FASTKD1 WILD-TYPE 102 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FASTKD1 MUTATED      8    3
  FASTKD1 WILD-TYPE  102  176
        clus
vv       FASTKD1 MUTATED FASTKD1 WILD-TYPE
  FEMALE               8               102
  MALE                 3               176
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FASTKD1 MUTATED                                       2
  FASTKD1 WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FASTKD1 MUTATED                                                        4
  FASTKD1 WILD-TYPE                                                    131
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FASTKD1 MUTATED                                                                   3
  FASTKD1 WILD-TYPE                                                                37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FASTKD1 MUTATED                                                  2
  FASTKD1 WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FASTKD1 MUTATED                                                          0
  FASTKD1 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FASTKD1 MUTATED                                                           0
  FASTKD1 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FASTKD1 MUTATED                                          0
  FASTKD1 WILD-TYPE                                        3
D134V8, multiclass
                                                                   clus
vv                                                                  FASTKD1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  FASTKD1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V9, binary
                   cls
clus                  0   1
  FASTKD1 MUTATED     0  11
  FASTKD1 WILD-TYPE   5 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FASTKD1 MUTATED      0   11
  FASTKD1 WILD-TYPE    5  273
     clus
vv    FASTKD1 MUTATED FASTKD1 WILD-TYPE
  NO                0                 5
  YES              11               273
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FASTKD1 MUTATED    11   0   0   0
  FASTKD1 WILD-TYPE 216  10  10  24
D134V10, multiclass
    clus
vv   FASTKD1 MUTATED FASTKD1 WILD-TYPE
  R0              11               216
  R1               0                10
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FASTKD1 MUTATED       4                         0     5
  FASTKD1 WILD-TYPE    72                         4   163
D134V12, multiclass
                           clus
vv                          FASTKD1 MUTATED FASTKD1 WILD-TYPE
  ASIAN                                   4                72
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   5               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(135) Variable = MAP7D1 MUTATION ANALYSIS
D135V1, survival
                  sevent
clus2                0   1
  MAP7D1 MUTATED     8   3
  MAP7D1 WILD-TYPE 173  77
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
              11              250 
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
               3               77 
$`MAP7D1 MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-A4J1 TCGA-CD-5800 
       34.68        12.26         0.26         4.31         0.72        13.15 
TCGA-CD-8536 TCGA-CD-A4MJ TCGA-CG-5721 TCGA-F1-A448 TCGA-HU-A4GQ 
        0.10        12.62         6.02        21.27         0.10 

$`MAP7D1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        19.50        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        8.98        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        2.83         3.25        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
        0.16         0.10         0.10         0.13         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        0.62         7.99        16.24        14.47        72.23         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        11.77        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
             0.1              0.0 
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
           34.68           105.07 
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
           6.020           12.775 
[1] "0.1 - 34.7 (6.0)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.3"
D135V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAP7D1 MUTATED         0        0        3        2         1         1
  MAP7D1 WILD-TYPE       1        9       24       24        30        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP7D1 MUTATED           0          1          1          1        1
  MAP7D1 WILD-TYPE         3         48         35         23       23
D135V3, multiclass
            clus
vv           MAP7D1 MUTATED MAP7D1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                3               24
  STAGE II                2               24
  STAGE IIA               1               30
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              1               23
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAP7D1 MUTATED     0   3   4   4
  MAP7D1 WILD-TYPE  11  69 118  71
D135V4, multiclass
    clus
vv   MAP7D1 MUTATED MAP7D1 WILD-TYPE
  T1              0               11
  T2              3               69
  T3              4              118
  T4              4               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  MAP7D1 MUTATED    7  3  1  1
  MAP7D1 WILD-TYPE 86 78 49 52
D135V5, multiclass
    clus
vv   MAP7D1 MUTATED MAP7D1 WILD-TYPE
  N0              7               86
  N1              3               78
  N2              1               49
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V6, binary
                  cls
clus                 0   1
  MAP7D1 MUTATED    12   0
  MAP7D1 WILD-TYPE 245  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D1 MUTATED     12    0
  MAP7D1 WILD-TYPE  245   18
   clus
vv  MAP7D1 MUTATED MAP7D1 WILD-TYPE
  0             12              245
  1              0               18
[1] 2 2
[1] FALSE
D135V7, binary
                  cls
clus                 0   1
  MAP7D1 MUTATED     5   7
  MAP7D1 WILD-TYPE 105 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D1 MUTATED      5    7
  MAP7D1 WILD-TYPE  105  172
        clus
vv       MAP7D1 MUTATED MAP7D1 WILD-TYPE
  FEMALE              5              105
  MALE                7              172
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MAP7D1 MUTATED                                       0
  MAP7D1 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MAP7D1 MUTATED                                                        8
  MAP7D1 WILD-TYPE                                                    127
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MAP7D1 MUTATED                                                                   1
  MAP7D1 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MAP7D1 MUTATED                                                  1
  MAP7D1 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MAP7D1 MUTATED                                                          1
  MAP7D1 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MAP7D1 MUTATED                                                           1
  MAP7D1 WILD-TYPE                                                         5
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MAP7D1 MUTATED                                          0
  MAP7D1 WILD-TYPE                                        3
D135V8, multiclass
                                                                   clus
vv                                                                  MAP7D1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  MAP7D1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V9, binary
                  cls
clus                 0   1
  MAP7D1 MUTATED     0  12
  MAP7D1 WILD-TYPE   5 272
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D1 MUTATED      0   12
  MAP7D1 WILD-TYPE    5  272
     clus
vv    MAP7D1 MUTATED MAP7D1 WILD-TYPE
  NO               0                5
  YES             12              272
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MAP7D1 MUTATED    10   0   0   1
  MAP7D1 WILD-TYPE 217  10  10  23
D135V10, multiclass
    clus
vv   MAP7D1 MUTATED MAP7D1 WILD-TYPE
  R0             10              217
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAP7D1 MUTATED       5                         0     6
  MAP7D1 WILD-TYPE    71                         4   162
D135V12, multiclass
                           clus
vv                          MAP7D1 MUTATED MAP7D1 WILD-TYPE
  ASIAN                                  5               71
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(136) Variable = SLC27A3 MUTATION ANALYSIS
D136V1, survival
                   sevent
clus2                 0   1
  SLC27A3 MUTATED     3   2
  SLC27A3 WILD-TYPE 178  78
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
                5               256 
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
                2                78 
$`SLC27A3 MUTATED`
TCGA-BR-8059 TCGA-BR-8382 TCGA-BR-A4QL TCGA-CG-4465 TCGA-FP-A4BE 
       14.43        15.85        11.57         9.01        11.08 

$`SLC27A3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       19.17        14.79         0.26         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
       12.03         0.00        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
             9.01              0.00 
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
            15.85            105.07 
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
            11.57             12.64 
[1] "9.0 - 15.8 (11.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.6"
D136V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC27A3 MUTATED         1        0        1        1         1         0
  SLC27A3 WILD-TYPE       0        9       26       25        30        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC27A3 MUTATED           1          0          1          1        1
  SLC27A3 WILD-TYPE         2         49         35         23       23
D136V3, multiclass
            clus
vv           SLC27A3 MUTATED SLC27A3 WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 1                25
  STAGE IIA                1                30
  STAGE IIB                0                44
  STAGE III                1                 2
  STAGE IIIA               0                49
  STAGE IIIB               1                35
  STAGE IIIC               1                23
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC27A3 MUTATED     2   2   2   3
  SLC27A3 WILD-TYPE   9  70 120  72
D136V4, multiclass
    clus
vv   SLC27A3 MUTATED SLC27A3 WILD-TYPE
  T1               2                 9
  T2               2                70
  T3               2               120
  T4               3                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  SLC27A3 MUTATED    2  3  0  3
  SLC27A3 WILD-TYPE 91 78 50 50
D136V5, multiclass
    clus
vv   SLC27A3 MUTATED SLC27A3 WILD-TYPE
  N0               2                91
  N1               3                78
  N2               0                50
  N3               3                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V6, binary
                   cls
clus                  0   1
  SLC27A3 MUTATED     7   1
  SLC27A3 WILD-TYPE 250  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A3 MUTATED      7    1
  SLC27A3 WILD-TYPE  250   17
   clus
vv  SLC27A3 MUTATED SLC27A3 WILD-TYPE
  0               7               250
  1               1                17
[1] 2 2
[1] FALSE
D136V7, binary
                   cls
clus                  0   1
  SLC27A3 MUTATED     4   5
  SLC27A3 WILD-TYPE 106 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A3 MUTATED      4    5
  SLC27A3 WILD-TYPE  106  174
        clus
vv       SLC27A3 MUTATED SLC27A3 WILD-TYPE
  FEMALE               4               106
  MALE                 5               174
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SLC27A3 MUTATED                                       1
  SLC27A3 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC27A3 MUTATED                                                        5
  SLC27A3 WILD-TYPE                                                    130
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC27A3 MUTATED                                                                   2
  SLC27A3 WILD-TYPE                                                                38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SLC27A3 MUTATED                                                  0
  SLC27A3 WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SLC27A3 MUTATED                                                          1
  SLC27A3 WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SLC27A3 MUTATED                                                           0
  SLC27A3 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SLC27A3 MUTATED                                          0
  SLC27A3 WILD-TYPE                                        3
D136V8, multiclass
                                                                   clus
vv                                                                  SLC27A3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  SLC27A3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V9, binary
                   cls
clus                  0   1
  SLC27A3 MUTATED     1   8
  SLC27A3 WILD-TYPE   4 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A3 MUTATED      1    8
  SLC27A3 WILD-TYPE    4  276
     clus
vv    SLC27A3 MUTATED SLC27A3 WILD-TYPE
  NO                1                 4
  YES               8               276
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC27A3 MUTATED     7   0   1   1
  SLC27A3 WILD-TYPE 220  10   9  23
D136V10, multiclass
    clus
vv   SLC27A3 MUTATED SLC27A3 WILD-TYPE
  R0               7               220
  R1               0                10
  R2               1                 9
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC27A3 MUTATED       0                         2     4
  SLC27A3 WILD-TYPE    76                         2   164
D136V12, multiclass
                           clus
vv                          SLC27A3 MUTATED SLC27A3 WILD-TYPE
  ASIAN                                   0                76
  BLACK OR AFRICAN AMERICAN               2                 2
  WHITE                                   4               164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(137) Variable = INF2 MUTATION ANALYSIS
D137V1, survival
                sevent
clus2              0   1
  INF2 MUTATED     6   3
  INF2 WILD-TYPE 175  77
  INF2 MUTATED INF2 WILD-TYPE 
             9            252 
  INF2 MUTATED INF2 WILD-TYPE 
             3             77 
$`INF2 MUTATED`
TCGA-B7-5816 TCGA-BR-7901 TCGA-BR-8487 TCGA-CG-4465 TCGA-CG-5723 TCGA-CG-5726 
       26.70         3.45         1.12         9.01       105.07        28.96 
TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4H3 
       11.41        11.84        19.36 

$`INF2 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73        12.43         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
       12.03         0.00        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  INF2 MUTATED INF2 WILD-TYPE 
          1.12           0.00 
  INF2 MUTATED INF2 WILD-TYPE 
        105.07          79.07 
  INF2 MUTATED INF2 WILD-TYPE 
         11.84          12.64 
[1] "1.1 - 105.1 (11.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.5"
D137V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  INF2 MUTATED         0        1        0        2         1         4
  INF2 WILD-TYPE       1        8       27       24        30        40
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  INF2 MUTATED           0          1          0          1        1
  INF2 WILD-TYPE         3         48         36         23       23
D137V3, multiclass
            clus
vv           INF2 MUTATED INF2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              0             27
  STAGE II              2             24
  STAGE IIA             1             30
  STAGE IIB             4             40
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            1             23
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  INF2 MUTATED     1   2   3   5
  INF2 WILD-TYPE  10  70 119  70
D137V4, multiclass
    clus
vv   INF2 MUTATED INF2 WILD-TYPE
  T1            1             10
  T2            2             70
  T3            3            119
  T4            5             70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  INF2 MUTATED    5  4  0  2
  INF2 WILD-TYPE 88 77 50 51
D137V5, multiclass
    clus
vv   INF2 MUTATED INF2 WILD-TYPE
  N0            5             88
  N1            4             77
  N2            0             50
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V6, binary
                cls
clus               0   1
  INF2 MUTATED    10   1
  INF2 WILD-TYPE 247  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  INF2 MUTATED     10    1
  INF2 WILD-TYPE  247   17
   clus
vv  INF2 MUTATED INF2 WILD-TYPE
  0           10            247
  1            1             17
[1] 2 2
[1] FALSE
D137V7, binary
                cls
clus               0   1
  INF2 MUTATED     7   4
  INF2 WILD-TYPE 103 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  INF2 MUTATED      7    4
  INF2 WILD-TYPE  103  175
        clus
vv       INF2 MUTATED INF2 WILD-TYPE
  FEMALE            7            103
  MALE              4            175
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  INF2 MUTATED                                       5
  INF2 WILD-TYPE                                    45
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  INF2 MUTATED                                                        4
  INF2 WILD-TYPE                                                    131
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  INF2 MUTATED                                                                   1
  INF2 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  INF2 MUTATED                                                  0
  INF2 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  INF2 MUTATED                                                          1
  INF2 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  INF2 MUTATED                                                           0
  INF2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  INF2 MUTATED                                          0
  INF2 WILD-TYPE                                        3
D137V8, multiclass
                                                                   clus
vv                                                                  INF2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  INF2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V9, binary
                cls
clus               0   1
  INF2 MUTATED     1  10
  INF2 WILD-TYPE   4 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  INF2 MUTATED      1   10
  INF2 WILD-TYPE    4  274
     clus
vv    INF2 MUTATED INF2 WILD-TYPE
  NO             1              4
  YES           10            274
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  INF2 MUTATED     8   0   1   1
  INF2 WILD-TYPE 219  10   9  23
D137V10, multiclass
    clus
vv   INF2 MUTATED INF2 WILD-TYPE
  R0            8            219
  R1            0             10
  R2            1              9
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  INF2 MUTATED       3                         0     4
  INF2 WILD-TYPE    73                         4   164
D137V12, multiclass
                           clus
vv                          INF2 MUTATED INF2 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                4            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(138) Variable = C13ORF33 MUTATION ANALYSIS
D138V1, survival
                    sevent
clus2                  0   1
  C13ORF33 MUTATED     5   1
  C13ORF33 WILD-TYPE 176  79
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
                 6                255 
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
                 1                 79 
$`C13ORF33 MUTATED`
TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8591 TCGA-BR-A4QL TCGA-HU-A4GQ TCGA-HU-A4H3 
       12.26        19.50        13.45        11.57         0.10        19.36 

$`C13ORF33 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        11.77        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.25        10.19         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
               0.1                0.0 
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
             19.50             105.07 
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
            12.855             12.620 
[1] "0.1 - 19.5 (12.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.7"
D138V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C13ORF33 MUTATED         0        0        0        1         0         1
  C13ORF33 WILD-TYPE       1        9       27       25        31        43
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C13ORF33 MUTATED           0          0          1          4        0
  C13ORF33 WILD-TYPE         3         49         35         20       24
D138V3, multiclass
            clus
vv           C13ORF33 MUTATED C13ORF33 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  0                 27
  STAGE II                  1                 25
  STAGE IIA                 0                 31
  STAGE IIB                 1                 43
  STAGE III                 0                  3
  STAGE IIIA                0                 49
  STAGE IIIB                1                 35
  STAGE IIIC                4                 20
  STAGE IV                  0                 24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C13ORF33 MUTATED     0   1   1   5
  C13ORF33 WILD-TYPE  11  71 121  70
D138V4, multiclass
    clus
vv   C13ORF33 MUTATED C13ORF33 WILD-TYPE
  T1                0                 11
  T2                1                 71
  T3                1                121
  T4                5                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  C13ORF33 MUTATED    1  1  2  3
  C13ORF33 WILD-TYPE 92 80 48 50
D138V5, multiclass
    clus
vv   C13ORF33 MUTATED C13ORF33 WILD-TYPE
  N0                1                 92
  N1                1                 80
  N2                2                 48
  N3                3                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V6, binary
                    cls
clus                   0   1
  C13ORF33 MUTATED     7   0
  C13ORF33 WILD-TYPE 250  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF33 MUTATED      7    0
  C13ORF33 WILD-TYPE  250   18
   clus
vv  C13ORF33 MUTATED C13ORF33 WILD-TYPE
  0                7                250
  1                0                 18
[1] 2 2
[1] FALSE
D138V7, binary
                    cls
clus                   0   1
  C13ORF33 MUTATED     4   3
  C13ORF33 WILD-TYPE 106 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF33 MUTATED      4    3
  C13ORF33 WILD-TYPE  106  176
        clus
vv       C13ORF33 MUTATED C13ORF33 WILD-TYPE
  FEMALE                4                106
  MALE                  3                176
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C13ORF33 MUTATED                                       1
  C13ORF33 WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C13ORF33 MUTATED                                                        4
  C13ORF33 WILD-TYPE                                                    131
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C13ORF33 MUTATED                                                                   0
  C13ORF33 WILD-TYPE                                                                40
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C13ORF33 MUTATED                                                  1
  C13ORF33 WILD-TYPE                                               37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C13ORF33 MUTATED                                                          1
  C13ORF33 WILD-TYPE                                                       15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C13ORF33 MUTATED                                                           0
  C13ORF33 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C13ORF33 MUTATED                                          0
  C13ORF33 WILD-TYPE                                        3
D138V8, multiclass
                                                                   clus
vv                                                                  C13ORF33 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  C13ORF33 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V9, binary
                    cls
clus                   0   1
  C13ORF33 MUTATED     1   6
  C13ORF33 WILD-TYPE   4 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF33 MUTATED      1    6
  C13ORF33 WILD-TYPE    4  278
     clus
vv    C13ORF33 MUTATED C13ORF33 WILD-TYPE
  NO                 1                  4
  YES                6                278
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C13ORF33 MUTATED     7   0   0   0
  C13ORF33 WILD-TYPE 220  10  10  24
D138V10, multiclass
    clus
vv   C13ORF33 MUTATED C13ORF33 WILD-TYPE
  R0                7                220
  R1                0                 10
  R2                0                 10
  RX                0                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C13ORF33 MUTATED       2                         0     4
  C13ORF33 WILD-TYPE    74                         4   164
D138V12, multiclass
                           clus
vv                          C13ORF33 MUTATED C13ORF33 WILD-TYPE
  ASIAN                                    2                 74
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    4                164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(139) Variable = AKAP13 MUTATION ANALYSIS
D139V1, survival
                  sevent
clus2                0   1
  AKAP13 MUTATED    15   7
  AKAP13 WILD-TYPE 166  73
  AKAP13 MUTATED AKAP13 WILD-TYPE 
              22              239 
  AKAP13 MUTATED AKAP13 WILD-TYPE 
               7               73 
$`AKAP13 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-7703 TCGA-BR-7716 TCGA-BR-7717 
        6.97        34.68        30.90        24.76        28.01        18.15 
TCGA-BR-8360 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-8527 TCGA-CD-8536 TCGA-CD-A4MG 
        6.18         1.12        15.81         0.07         0.10         6.58 
TCGA-CG-4306 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5721 
        1.02        54.08        14.01         7.07        30.97         6.02 
TCGA-CG-5726 TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4HD 
       28.96         6.25        23.84        27.42 

$`AKAP13 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 
       31.20        32.94        12.82         9.21        23.93        15.42 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        7.99         8.05         4.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5717 
       12.03         0.00         9.01        18.97        22.98         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        19.36        12.30         9.67         8.88 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  AKAP13 MUTATED AKAP13 WILD-TYPE 
            0.07             0.00 
  AKAP13 MUTATED AKAP13 WILD-TYPE 
           54.08           105.07 
  AKAP13 MUTATED AKAP13 WILD-TYPE 
           14.91            12.59 
[1] "0.1 - 54.1 (14.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D139V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AKAP13 MUTATED         1        2        1        3         4         3
  AKAP13 WILD-TYPE       0        7       26       23        27        41
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AKAP13 MUTATED           0          4          0          0        7
  AKAP13 WILD-TYPE         3         45         36         24       17
D139V3, multiclass
            clus
vv           AKAP13 MUTATED AKAP13 WILD-TYPE
  STAGE I                 1                0
  STAGE IA                2                7
  STAGE IB                1               26
  STAGE II                3               23
  STAGE IIA               4               27
  STAGE IIB               3               41
  STAGE III               0                3
  STAGE IIIA              4               45
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                7               17
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  AKAP13 MUTATED     4   5  12   5
  AKAP13 WILD-TYPE   7  67 110  70
D139V4, multiclass
    clus
vv   AKAP13 MUTATED AKAP13 WILD-TYPE
  T1              4                7
  T2              5               67
  T3             12              110
  T4              5               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  AKAP13 MUTATED    8  9  8  1
  AKAP13 WILD-TYPE 85 72 42 52
D139V5, multiclass
    clus
vv   AKAP13 MUTATED AKAP13 WILD-TYPE
  N0              8               85
  N1              9               72
  N2              8               42
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V6, binary
                  cls
clus                 0   1
  AKAP13 MUTATED    24   2
  AKAP13 WILD-TYPE 233  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP13 MUTATED     24    2
  AKAP13 WILD-TYPE  233   16
   clus
vv  AKAP13 MUTATED AKAP13 WILD-TYPE
  0             24              233
  1              2               16
[1] 2 2
[1] FALSE
D139V7, binary
                  cls
clus                 0   1
  AKAP13 MUTATED    10  18
  AKAP13 WILD-TYPE 100 161
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP13 MUTATED     10   18
  AKAP13 WILD-TYPE  100  161
        clus
vv       AKAP13 MUTATED AKAP13 WILD-TYPE
  FEMALE             10              100
  MALE               18              161
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AKAP13 MUTATED                                       2
  AKAP13 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AKAP13 MUTATED                                                       13
  AKAP13 WILD-TYPE                                                    122
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AKAP13 MUTATED                                                                   8
  AKAP13 WILD-TYPE                                                                32
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AKAP13 MUTATED                                                  3
  AKAP13 WILD-TYPE                                               35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AKAP13 MUTATED                                                          1
  AKAP13 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AKAP13 MUTATED                                                           1
  AKAP13 WILD-TYPE                                                         5
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AKAP13 MUTATED                                          0
  AKAP13 WILD-TYPE                                        3
D139V8, multiclass
                                                                   clus
vv                                                                  AKAP13 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        13
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  AKAP13 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         122
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V9, binary
                  cls
clus                 0   1
  AKAP13 MUTATED     1  27
  AKAP13 WILD-TYPE   4 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP13 MUTATED      1   27
  AKAP13 WILD-TYPE    4  257
     clus
vv    AKAP13 MUTATED AKAP13 WILD-TYPE
  NO               1                4
  YES             27              257
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  AKAP13 MUTATED    20   1   1   5
  AKAP13 WILD-TYPE 207   9   9  19
D139V10, multiclass
    clus
vv   AKAP13 MUTATED AKAP13 WILD-TYPE
  R0             20              207
  R1              1                9
  R2              1                9
  RX              5               19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AKAP13 MUTATED       7                         1    12
  AKAP13 WILD-TYPE    69                         3   156
D139V12, multiclass
                           clus
vv                          AKAP13 MUTATED AKAP13 WILD-TYPE
  ASIAN                                  7               69
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                 12              156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(140) Variable = DYRK4 MUTATION ANALYSIS
D140V1, survival
                 sevent
clus2               0   1
  DYRK4 MUTATED     5   1
  DYRK4 WILD-TYPE 176  79
  DYRK4 MUTATED DYRK4 WILD-TYPE 
              6             255 
  DYRK4 MUTATED DYRK4 WILD-TYPE 
              1              79 
$`DYRK4 MUTATED`
TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8680 TCGA-D7-A4YV TCGA-HU-8602 TCGA-HU-A4H3 
       12.26        19.50        15.81         5.92        11.41        19.36 

$`DYRK4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       14.27        16.44        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.25        10.19         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  DYRK4 MUTATED DYRK4 WILD-TYPE 
           5.92            0.00 
  DYRK4 MUTATED DYRK4 WILD-TYPE 
          19.50          105.07 
  DYRK4 MUTATED DYRK4 WILD-TYPE 
         14.035          12.620 
[1] "5.9 - 19.5 (14.0)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.8"
D140V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DYRK4 MUTATED         0        0        0        1         0         3
  DYRK4 WILD-TYPE       1        9       27       25        31        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DYRK4 MUTATED           0          0          0          2        1
  DYRK4 WILD-TYPE         3         49         36         22       23
D140V3, multiclass
            clus
vv           DYRK4 MUTATED DYRK4 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              0              31
  STAGE IIB              3              41
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             2              22
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DYRK4 MUTATED     1   1   1   5
  DYRK4 WILD-TYPE  10  71 121  70
D140V4, multiclass
    clus
vv   DYRK4 MUTATED DYRK4 WILD-TYPE
  T1             1              10
  T2             1              71
  T3             1             121
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  DYRK4 MUTATED    2  3  2  1
  DYRK4 WILD-TYPE 91 78 48 52
D140V5, multiclass
    clus
vv   DYRK4 MUTATED DYRK4 WILD-TYPE
  N0             2              91
  N1             3              78
  N2             2              48
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V6, binary
                 cls
clus                0   1
  DYRK4 MUTATED     8   1
  DYRK4 WILD-TYPE 249  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK4 MUTATED      8    1
  DYRK4 WILD-TYPE  249   17
   clus
vv  DYRK4 MUTATED DYRK4 WILD-TYPE
  0             8             249
  1             1              17
[1] 2 2
[1] FALSE
D140V7, binary
                 cls
clus                0   1
  DYRK4 MUTATED     6   3
  DYRK4 WILD-TYPE 104 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK4 MUTATED      6    3
  DYRK4 WILD-TYPE  104  176
        clus
vv       DYRK4 MUTATED DYRK4 WILD-TYPE
  FEMALE             6             104
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DYRK4 MUTATED                                       2
  DYRK4 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DYRK4 MUTATED                                                        4
  DYRK4 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DYRK4 MUTATED                                                                   0
  DYRK4 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DYRK4 MUTATED                                                  2
  DYRK4 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DYRK4 MUTATED                                                          1
  DYRK4 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DYRK4 MUTATED                                                           0
  DYRK4 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DYRK4 MUTATED                                          0
  DYRK4 WILD-TYPE                                        3
D140V8, multiclass
                                                                   clus
vv                                                                  DYRK4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  DYRK4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V9, binary
                 cls
clus                0   1
  DYRK4 MUTATED     1   8
  DYRK4 WILD-TYPE   4 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK4 MUTATED      1    8
  DYRK4 WILD-TYPE    4  276
     clus
vv    DYRK4 MUTATED DYRK4 WILD-TYPE
  NO              1               4
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DYRK4 MUTATED     7   0   0   2
  DYRK4 WILD-TYPE 220  10  10  22
D140V10, multiclass
    clus
vv   DYRK4 MUTATED DYRK4 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DYRK4 MUTATED       3                         0     5
  DYRK4 WILD-TYPE    73                         4   163
D140V12, multiclass
                           clus
vv                          DYRK4 MUTATED DYRK4 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(141) Variable = FOXN3 MUTATION ANALYSIS
D141V1, survival
                 sevent
clus2               0   1
  FOXN3 MUTATED     5   2
  FOXN3 WILD-TYPE 176  78
  FOXN3 MUTATED FOXN3 WILD-TYPE 
              7             254 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
              2              78 
$`FOXN3 MUTATED`
TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-8360 TCGA-CD-A4MG TCGA-D7-A4YV 
       32.78        23.93        12.43         6.18         6.58         5.92 
TCGA-HU-A4GT 
        6.51 

$`FOXN3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        2.66        16.31         2.20        15.58         7.40        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         0.10         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  FOXN3 MUTATED FOXN3 WILD-TYPE 
           5.92            0.00 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
          32.78          105.07 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
           6.58           12.71 
[1] "5.9 - 32.8 (6.6)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1"  
D141V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FOXN3 MUTATED         0        0        1        0         4         2
  FOXN3 WILD-TYPE       1        9       26       26        27        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FOXN3 MUTATED           0          0          0          0        0
  FOXN3 WILD-TYPE         3         49         36         24       24
D141V3, multiclass
            clus
vv           FOXN3 MUTATED FOXN3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              4              27
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FOXN3 MUTATED     0   1   5   1
  FOXN3 WILD-TYPE  11  71 117  74
D141V4, multiclass
    clus
vv   FOXN3 MUTATED FOXN3 WILD-TYPE
  T1             0              11
  T2             1              71
  T3             5             117
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  FOXN3 MUTATED    6  1  0  0
  FOXN3 WILD-TYPE 87 80 50 53
D141V5, multiclass
    clus
vv   FOXN3 MUTATED FOXN3 WILD-TYPE
  N0             6              87
  N1             1              80
  N2             0              50
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V6, binary
                 cls
clus                0   1
  FOXN3 MUTATED     8   0
  FOXN3 WILD-TYPE 249  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXN3 MUTATED      8    0
  FOXN3 WILD-TYPE  249   18
   clus
vv  FOXN3 MUTATED FOXN3 WILD-TYPE
  0             8             249
  1             0              18
[1] 2 2
[1] FALSE
D141V7, binary
                 cls
clus                0   1
  FOXN3 MUTATED     5   3
  FOXN3 WILD-TYPE 105 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXN3 MUTATED      5    3
  FOXN3 WILD-TYPE  105  176
        clus
vv       FOXN3 MUTATED FOXN3 WILD-TYPE
  FEMALE             5             105
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FOXN3 MUTATED                                       1
  FOXN3 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FOXN3 MUTATED                                                        3
  FOXN3 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FOXN3 MUTATED                                                                   2
  FOXN3 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FOXN3 MUTATED                                                  2
  FOXN3 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FOXN3 MUTATED                                                          0
  FOXN3 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FOXN3 MUTATED                                                           0
  FOXN3 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FOXN3 MUTATED                                          0
  FOXN3 WILD-TYPE                                        3
D141V8, multiclass
                                                                   clus
vv                                                                  FOXN3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  FOXN3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V9, binary
                 cls
clus                0   1
  FOXN3 MUTATED     0   8
  FOXN3 WILD-TYPE   5 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXN3 MUTATED      0    8
  FOXN3 WILD-TYPE    5  276
     clus
vv    FOXN3 MUTATED FOXN3 WILD-TYPE
  NO              0               5
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FOXN3 MUTATED     6   0   0   1
  FOXN3 WILD-TYPE 221  10  10  23
D141V10, multiclass
    clus
vv   FOXN3 MUTATED FOXN3 WILD-TYPE
  R0             6             221
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FOXN3 MUTATED       2                         0     6
  FOXN3 WILD-TYPE    74                         4   162
D141V12, multiclass
                           clus
vv                          FOXN3 MUTATED FOXN3 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(142) Variable = SLC16A1 MUTATION ANALYSIS
D142V1, survival
                   sevent
clus2                 0   1
  SLC16A1 MUTATED     5   1
  SLC16A1 WILD-TYPE 176  79
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                6               255 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                1                79 
$`SLC16A1 MUTATED`
TCGA-BR-6852 TCGA-BR-7707 TCGA-CG-4306 TCGA-CG-5721 TCGA-FP-A4BE TCGA-HU-A4H5 
       32.94        23.93         1.02         6.02        11.08        12.30 

$`SLC16A1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        30.90        31.20        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
             1.02              0.00 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
            32.94            105.07 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
            11.69             12.66 
[1] "1.0 - 32.9 (11.7)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "2"  
D142V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC16A1 MUTATED         0        0        2        0         2         0
  SLC16A1 WILD-TYPE       1        9       25       26        29        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC16A1 MUTATED           0          1          0          0        2
  SLC16A1 WILD-TYPE         3         48         36         24       22
D142V3, multiclass
            clus
vv           SLC16A1 MUTATED SLC16A1 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 2                25
  STAGE II                 0                26
  STAGE IIA                2                29
  STAGE IIB                0                44
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               0                36
  STAGE IIIC               0                24
  STAGE IV                 2                22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC16A1 MUTATED     0   2   3   2
  SLC16A1 WILD-TYPE  11  70 119  73
D142V4, multiclass
    clus
vv   SLC16A1 MUTATED SLC16A1 WILD-TYPE
  T1               0                11
  T2               2                70
  T3               3               119
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  SLC16A1 MUTATED    5  1  1  0
  SLC16A1 WILD-TYPE 88 80 49 53
D142V5, multiclass
    clus
vv   SLC16A1 MUTATED SLC16A1 WILD-TYPE
  N0               5                88
  N1               1                80
  N2               1                49
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V6, binary
                   cls
clus                  0   1
  SLC16A1 MUTATED     6   1
  SLC16A1 WILD-TYPE 251  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      6    1
  SLC16A1 WILD-TYPE  251   17
   clus
vv  SLC16A1 MUTATED SLC16A1 WILD-TYPE
  0               6               251
  1               1                17
[1] 2 2
[1] FALSE
D142V7, binary
                   cls
clus                  0   1
  SLC16A1 MUTATED     3   4
  SLC16A1 WILD-TYPE 107 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      3    4
  SLC16A1 WILD-TYPE  107  175
        clus
vv       SLC16A1 MUTATED SLC16A1 WILD-TYPE
  FEMALE               3               107
  MALE                 4               175
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SLC16A1 MUTATED                                       0
  SLC16A1 WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC16A1 MUTATED                                                        5
  SLC16A1 WILD-TYPE                                                    130
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC16A1 MUTATED                                                                   1
  SLC16A1 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SLC16A1 MUTATED                                                  0
  SLC16A1 WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SLC16A1 MUTATED                                                          0
  SLC16A1 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SLC16A1 MUTATED                                                           1
  SLC16A1 WILD-TYPE                                                         5
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SLC16A1 MUTATED                                          0
  SLC16A1 WILD-TYPE                                        3
D142V8, multiclass
                                                                   clus
vv                                                                  SLC16A1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  SLC16A1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V9, binary
                   cls
clus                  0   1
  SLC16A1 MUTATED     0   7
  SLC16A1 WILD-TYPE   5 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      0    7
  SLC16A1 WILD-TYPE    5  277
     clus
vv    SLC16A1 MUTATED SLC16A1 WILD-TYPE
  NO                0                 5
  YES               7               277
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC16A1 MUTATED     5   0   1   1
  SLC16A1 WILD-TYPE 222  10   9  23
D142V10, multiclass
    clus
vv   SLC16A1 MUTATED SLC16A1 WILD-TYPE
  R0               5               222
  R1               0                10
  R2               1                 9
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC16A1 MUTATED       1                         1     3
  SLC16A1 WILD-TYPE    75                         3   165
D142V12, multiclass
                           clus
vv                          SLC16A1 MUTATED SLC16A1 WILD-TYPE
  ASIAN                                   1                75
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   3               165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(143) Variable = TNFRSF9 MUTATION ANALYSIS
D143V1, survival
                   sevent
clus2                 0   1
  TNFRSF9 MUTATED     7   2
  TNFRSF9 WILD-TYPE 174  78
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
                9               252 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
                2                78 
$`TNFRSF9 MUTATED`
TCGA-BR-4184 TCGA-BR-6802 TCGA-BR-7707 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QI 
        6.97        30.90        23.93        13.45        15.81        13.64 
TCGA-CG-4441 TCGA-CG-5721 TCGA-HU-A4H3 
       14.01         6.02        19.36 

$`TNFRSF9 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
        1.02         7.99         8.05        54.08         4.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
             6.02              0.00 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
            30.90            105.07 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
           14.010            12.495 
[1] "6.0 - 30.9 (14.0)"  "0.0 - 105.1 (12.5)"
[1] "hr=" "1.6"
D143V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TNFRSF9 MUTATED         0        0        1        0         1         0
  TNFRSF9 WILD-TYPE       1        9       26       26        30        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNFRSF9 MUTATED           0          3          0          2        2
  TNFRSF9 WILD-TYPE         3         46         36         22       22
D143V3, multiclass
            clus
vv           TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 0                26
  STAGE IIA                1                30
  STAGE IIB                0                44
  STAGE III                0                 3
  STAGE IIIA               3                46
  STAGE IIIB               0                36
  STAGE IIIC               2                22
  STAGE IV                 2                22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TNFRSF9 MUTATED     0   2   3   4
  TNFRSF9 WILD-TYPE  11  70 119  71
D143V4, multiclass
    clus
vv   TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  T1               0                11
  T2               2                70
  T3               3               119
  T4               4                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  TNFRSF9 MUTATED    2  3  3  2
  TNFRSF9 WILD-TYPE 91 78 47 51
D143V5, multiclass
    clus
vv   TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  N0               2                91
  N1               3                78
  N2               3                47
  N3               2                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V6, binary
                   cls
clus                  0   1
  TNFRSF9 MUTATED     8   1
  TNFRSF9 WILD-TYPE 249  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFRSF9 MUTATED      8    1
  TNFRSF9 WILD-TYPE  249   17
   clus
vv  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  0               8               249
  1               1                17
[1] 2 2
[1] FALSE
D143V7, binary
                   cls
clus                  0   1
  TNFRSF9 MUTATED     3   7
  TNFRSF9 WILD-TYPE 107 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFRSF9 MUTATED      3    7
  TNFRSF9 WILD-TYPE  107  172
        clus
vv       TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  FEMALE               3               107
  MALE                 7               172
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TNFRSF9 MUTATED                                       1
  TNFRSF9 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TNFRSF9 MUTATED                                                        6
  TNFRSF9 WILD-TYPE                                                    129
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TNFRSF9 MUTATED                                                                   2
  TNFRSF9 WILD-TYPE                                                                38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TNFRSF9 MUTATED                                                  1
  TNFRSF9 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TNFRSF9 MUTATED                                                          0
  TNFRSF9 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TNFRSF9 MUTATED                                                           0
  TNFRSF9 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TNFRSF9 MUTATED                                          0
  TNFRSF9 WILD-TYPE                                        3
D143V8, multiclass
                                                                   clus
vv                                                                  TNFRSF9 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  TNFRSF9 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V9, binary
                   cls
clus                  0   1
  TNFRSF9 MUTATED     0  10
  TNFRSF9 WILD-TYPE   5 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFRSF9 MUTATED      0   10
  TNFRSF9 WILD-TYPE    5  274
     clus
vv    TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  NO                0                 5
  YES              10               274
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TNFRSF9 MUTATED     8   0   0   2
  TNFRSF9 WILD-TYPE 219  10  10  22
D143V10, multiclass
    clus
vv   TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  R0               8               219
  R1               0                10
  R2               0                10
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TNFRSF9 MUTATED       2                         0     6
  TNFRSF9 WILD-TYPE    74                         4   162
D143V12, multiclass
                           clus
vv                          TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  ASIAN                                   2                74
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   6               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(144) Variable = RHOQ MUTATION ANALYSIS
D144V1, survival
                sevent
clus2              0   1
  RHOQ MUTATED     3   1
  RHOQ WILD-TYPE 178  79
  RHOQ MUTATED RHOQ WILD-TYPE 
             4            257 
  RHOQ MUTATED RHOQ WILD-TYPE 
             1             79 
$`RHOQ MUTATED`
TCGA-BR-8487 TCGA-CG-4306 TCGA-HU-8602 TCGA-HU-A4H8 
        1.12         1.02        11.41         8.88 

$`RHOQ WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       26.47         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
       12.95        19.36        23.84        12.30         9.67        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  RHOQ MUTATED RHOQ WILD-TYPE 
          1.02           0.00 
  RHOQ MUTATED RHOQ WILD-TYPE 
         11.41         105.07 
  RHOQ MUTATED RHOQ WILD-TYPE 
          5.00          12.76 
[1] "1.0 - 11.4 (5.0)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "2.2"
D144V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RHOQ MUTATED         0        0        1        0         1         1
  RHOQ WILD-TYPE       1        9       26       26        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RHOQ MUTATED           0          0          0          0        2
  RHOQ WILD-TYPE         3         49         36         24       22
D144V3, multiclass
            clus
vv           RHOQ MUTATED RHOQ WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RHOQ MUTATED     1   0   2   2
  RHOQ WILD-TYPE  10  72 120  73
D144V4, multiclass
    clus
vv   RHOQ MUTATED RHOQ WILD-TYPE
  T1            1             10
  T2            0             72
  T3            2            120
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  RHOQ MUTATED    2  1  2  0
  RHOQ WILD-TYPE 91 80 48 53
D144V5, multiclass
    clus
vv   RHOQ MUTATED RHOQ WILD-TYPE
  N0            2             91
  N1            1             80
  N2            2             48
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V6, binary
                cls
clus               0   1
  RHOQ MUTATED     4   1
  RHOQ WILD-TYPE 253  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOQ MUTATED      4    1
  RHOQ WILD-TYPE  253   17
   clus
vv  RHOQ MUTATED RHOQ WILD-TYPE
  0            4            253
  1            1             17
[1] 2 2
[1] FALSE
D144V7, binary
                cls
clus               0   1
  RHOQ MUTATED     3   2
  RHOQ WILD-TYPE 107 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOQ MUTATED      3    2
  RHOQ WILD-TYPE  107  177
        clus
vv       RHOQ MUTATED RHOQ WILD-TYPE
  FEMALE            3            107
  MALE              2            177
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RHOQ MUTATED                                       1
  RHOQ WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RHOQ MUTATED                                                        3
  RHOQ WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RHOQ MUTATED                                                                   0
  RHOQ WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RHOQ MUTATED                                                  1
  RHOQ WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RHOQ MUTATED                                                          0
  RHOQ WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RHOQ MUTATED                                                           0
  RHOQ WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RHOQ MUTATED                                          0
  RHOQ WILD-TYPE                                        3
D144V8, multiclass
                                                                   clus
vv                                                                  RHOQ MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  RHOQ WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V9, binary
                cls
clus               0   1
  RHOQ MUTATED     0   5
  RHOQ WILD-TYPE   5 279
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOQ MUTATED      0    5
  RHOQ WILD-TYPE    5  279
     clus
vv    RHOQ MUTATED RHOQ WILD-TYPE
  NO             0              5
  YES            5            279
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RHOQ MUTATED     3   0   1   1
  RHOQ WILD-TYPE 224  10   9  23
D144V10, multiclass
    clus
vv   RHOQ MUTATED RHOQ WILD-TYPE
  R0            3            224
  R1            0             10
  R2            1              9
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RHOQ MUTATED       2                         0     2
  RHOQ WILD-TYPE    74                         4   166
D144V12, multiclass
                           clus
vv                          RHOQ MUTATED RHOQ WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                2            166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(145) Variable = PRPF40B MUTATION ANALYSIS
D145V1, survival
                   sevent
clus2                 0   1
  PRPF40B MUTATED    10   3
  PRPF40B WILD-TYPE 171  77
  PRPF40B MUTATED PRPF40B WILD-TYPE 
               13               248 
  PRPF40B MUTATED PRPF40B WILD-TYPE 
                3                77 
$`PRPF40B MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-8360 TCGA-BR-8680 
       26.70        30.90        34.68        30.90         6.18        15.81 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4306 TCGA-D7-6815 TCGA-F1-6874 TCGA-HU-A4GN 
        0.10        12.62         1.02        15.98        14.47        29.98 
TCGA-HU-A4GQ 
        0.10 

$`PRPF40B WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       25.61        18.05        19.89         8.98        21.11        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
       16.31         2.20        15.58         7.40        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
       17.85        13.35        17.19        10.26        15.22        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.99        16.24        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       25.81        11.77         8.98         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  PRPF40B MUTATED PRPF40B WILD-TYPE 
              0.1               0.0 
  PRPF40B MUTATED PRPF40B WILD-TYPE 
            34.68            105.07 
  PRPF40B MUTATED PRPF40B WILD-TYPE 
           15.810            12.495 
[1] "0.1 - 34.7 (15.8)"  "0.0 - 105.1 (12.5)"
[1] "hr=" "1.9"
D145V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRPF40B MUTATED         0        0        2        0         3         2
  PRPF40B WILD-TYPE       1        9       25       26        28        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRPF40B MUTATED           0          1          1          1        2
  PRPF40B WILD-TYPE         3         48         35         23       22
D145V3, multiclass
            clus
vv           PRPF40B MUTATED PRPF40B WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 2                25
  STAGE II                 0                26
  STAGE IIA                3                28
  STAGE IIB                2                42
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               1                35
  STAGE IIIC               1                23
  STAGE IV                 2                22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PRPF40B MUTATED     0   5   5   3
  PRPF40B WILD-TYPE  11  67 117  72
D145V4, multiclass
    clus
vv   PRPF40B MUTATED PRPF40B WILD-TYPE
  T1               0                11
  T2               5                67
  T3               5               117
  T4               3                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  PRPF40B MUTATED    5  3  5  0
  PRPF40B WILD-TYPE 88 78 45 53
D145V5, multiclass
    clus
vv   PRPF40B MUTATED PRPF40B WILD-TYPE
  N0               5                88
  N1               3                78
  N2               5                45
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V6, binary
                   cls
clus                  0   1
  PRPF40B MUTATED    12   2
  PRPF40B WILD-TYPE 245  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRPF40B MUTATED     12    2
  PRPF40B WILD-TYPE  245   16
   clus
vv  PRPF40B MUTATED PRPF40B WILD-TYPE
  0              12               245
  1               2                16
[1] 2 2
[1] FALSE
D145V7, binary
                   cls
clus                  0   1
  PRPF40B MUTATED     4  10
  PRPF40B WILD-TYPE 106 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRPF40B MUTATED      4   10
  PRPF40B WILD-TYPE  106  169
        clus
vv       PRPF40B MUTATED PRPF40B WILD-TYPE
  FEMALE               4               106
  MALE                10               169
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PRPF40B MUTATED                                       1
  PRPF40B WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PRPF40B MUTATED                                                        7
  PRPF40B WILD-TYPE                                                    128
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PRPF40B MUTATED                                                                   2
  PRPF40B WILD-TYPE                                                                38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PRPF40B MUTATED                                                  4
  PRPF40B WILD-TYPE                                               34
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PRPF40B MUTATED                                                          0
  PRPF40B WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PRPF40B MUTATED                                                           0
  PRPF40B WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PRPF40B MUTATED                                          0
  PRPF40B WILD-TYPE                                        3
D145V8, multiclass
                                                                   clus
vv                                                                  PRPF40B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  PRPF40B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V9, binary
                   cls
clus                  0   1
  PRPF40B MUTATED     0  14
  PRPF40B WILD-TYPE   5 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRPF40B MUTATED      0   14
  PRPF40B WILD-TYPE    5  270
     clus
vv    PRPF40B MUTATED PRPF40B WILD-TYPE
  NO                0                 5
  YES              14               270
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PRPF40B MUTATED     9   0   1   2
  PRPF40B WILD-TYPE 218  10   9  22
D145V10, multiclass
    clus
vv   PRPF40B MUTATED PRPF40B WILD-TYPE
  R0               9               218
  R1               0                10
  R2               1                 9
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRPF40B MUTATED       5                         0     8
  PRPF40B WILD-TYPE    71                         4   160
D145V12, multiclass
                           clus
vv                          PRPF40B MUTATED PRPF40B WILD-TYPE
  ASIAN                                   5                71
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   8               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(146) Variable = STAT5B MUTATION ANALYSIS
D146V1, survival
                  sevent
clus2                0   1
  STAT5B MUTATED     8   4
  STAT5B WILD-TYPE 173  76
  STAT5B MUTATED STAT5B WILD-TYPE 
              12              249 
  STAT5B MUTATED STAT5B WILD-TYPE 
               4               76 
$`STAT5B MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8361 
        6.97        30.90        32.78        30.90        32.94        19.50 
TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-5728 TCGA-CG-5732 TCGA-HU-A4GQ TCGA-HU-A4H8 
        1.12        15.81        65.10        69.04         0.10         8.88 

$`STAT5B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       25.61        18.05        19.89         8.98        21.11        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       12.82         9.21        24.76        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        20.55         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
        2.20        15.58         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        11.77        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  STAT5B MUTATED STAT5B WILD-TYPE 
             0.1              0.0 
  STAT5B MUTATED STAT5B WILD-TYPE 
           69.04           105.07 
  STAT5B MUTATED STAT5B WILD-TYPE 
           25.20            12.56 
[1] "0.1 - 69.0 (25.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.9"
D146V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  STAT5B MUTATED         0        0        2        0         3         0
  STAT5B WILD-TYPE       1        9       25       26        28        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STAT5B MUTATED           0          2          0          2        2
  STAT5B WILD-TYPE         3         47         36         22       22
D146V3, multiclass
            clus
vv           STAT5B MUTATED STAT5B WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                2               25
  STAGE II                0               26
  STAGE IIA               3               28
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              0               36
  STAGE IIIC              2               22
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  STAT5B MUTATED     1   3   5   3
  STAT5B WILD-TYPE  10  69 117  72
D146V4, multiclass
    clus
vv   STAT5B MUTATED STAT5B WILD-TYPE
  T1              1               10
  T2              3               69
  T3              5              117
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  STAT5B MUTATED    4  2  4  1
  STAT5B WILD-TYPE 89 79 46 52
D146V5, multiclass
    clus
vv   STAT5B MUTATED STAT5B WILD-TYPE
  N0              4               89
  N1              2               79
  N2              4               46
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V6, binary
                  cls
clus                 0   1
  STAT5B MUTATED    10   1
  STAT5B WILD-TYPE 247  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STAT5B MUTATED     10    1
  STAT5B WILD-TYPE  247   17
   clus
vv  STAT5B MUTATED STAT5B WILD-TYPE
  0             10              247
  1              1               17
[1] 2 2
[1] FALSE
D146V7, binary
                  cls
clus                 0   1
  STAT5B MUTATED     6   6
  STAT5B WILD-TYPE 104 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STAT5B MUTATED      6    6
  STAT5B WILD-TYPE  104  173
        clus
vv       STAT5B MUTATED STAT5B WILD-TYPE
  FEMALE              6              104
  MALE                6              173
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  STAT5B MUTATED                                       0
  STAT5B WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  STAT5B MUTATED                                                        7
  STAT5B WILD-TYPE                                                    128
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  STAT5B MUTATED                                                                   2
  STAT5B WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  STAT5B MUTATED                                                  3
  STAT5B WILD-TYPE                                               35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  STAT5B MUTATED                                                          0
  STAT5B WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  STAT5B MUTATED                                                           0
  STAT5B WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  STAT5B MUTATED                                          0
  STAT5B WILD-TYPE                                        3
D146V8, multiclass
                                                                   clus
vv                                                                  STAT5B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  STAT5B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V9, binary
                  cls
clus                 0   1
  STAT5B MUTATED     0  12
  STAT5B WILD-TYPE   5 272
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STAT5B MUTATED      0   12
  STAT5B WILD-TYPE    5  272
     clus
vv    STAT5B MUTATED STAT5B WILD-TYPE
  NO               0                5
  YES             12              272
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  STAT5B MUTATED    10   0   0   2
  STAT5B WILD-TYPE 217  10  10  22
D146V10, multiclass
    clus
vv   STAT5B MUTATED STAT5B WILD-TYPE
  R0             10              217
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STAT5B MUTATED       3                         0     7
  STAT5B WILD-TYPE    73                         4   161
D146V12, multiclass
                           clus
vv                          STAT5B MUTATED STAT5B WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  7              161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(147) Variable = CFI MUTATION ANALYSIS
D147V1, survival
               sevent
clus2             0   1
  CFI MUTATED    10   0
  CFI WILD-TYPE 171  80
  CFI MUTATED CFI WILD-TYPE 
           10           251 
  CFI MUTATED CFI WILD-TYPE 
            0            80 
$`CFI MUTATED`
TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-7715 TCGA-BR-7851 TCGA-BR-8487 TCGA-BR-8680 
       34.68        30.90        15.42        12.43         1.12        15.81 
TCGA-CD-8529 TCGA-CG-4305 TCGA-HU-A4GU TCGA-HU-A4H3 
        0.13        15.95         6.25        19.36 

$`CFI WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       23.93        28.01        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
        0.07         0.07         0.07         0.07         0.10         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       12.95        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  CFI MUTATED CFI WILD-TYPE 
         0.13          0.00 
  CFI MUTATED CFI WILD-TYPE 
        34.68        105.07 
  CFI MUTATED CFI WILD-TYPE 
       15.615        12.590 
[1] "0.1 - 34.7 (15.6)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "2.6e+07"
D147V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CFI MUTATED         0        0        0        1         3         2
  CFI WILD-TYPE       1        9       27       25        28        42
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CFI MUTATED           0          1          0          1        2
  CFI WILD-TYPE         3         48         36         23       22
D147V3, multiclass
            clus
vv           CFI MUTATED CFI WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             9
  STAGE IB             0            27
  STAGE II             1            25
  STAGE IIA            3            28
  STAGE IIB            2            42
  STAGE III            0             3
  STAGE IIIA           1            48
  STAGE IIIB           0            36
  STAGE IIIC           1            23
  STAGE IV             2            22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CFI MUTATED     0   1   5   4
  CFI WILD-TYPE  11  71 117  71
D147V4, multiclass
    clus
vv   CFI MUTATED CFI WILD-TYPE
  T1           0            11
  T2           1            71
  T3           5           117
  T4           4            71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  CFI MUTATED    5  4  2  1
  CFI WILD-TYPE 88 77 48 52
D147V5, multiclass
    clus
vv   CFI MUTATED CFI WILD-TYPE
  N0           5            88
  N1           4            77
  N2           2            48
  N3           1            52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V6, binary
               cls
clus              0   1
  CFI MUTATED    10   2
  CFI WILD-TYPE 247  16
[1] "tbl2"
               cls
clus            [,1] [,2]
  CFI MUTATED     10    2
  CFI WILD-TYPE  247   16
   clus
vv  CFI MUTATED CFI WILD-TYPE
  0          10           247
  1           2            16
[1] 2 2
[1] FALSE
D147V7, binary
               cls
clus              0   1
  CFI MUTATED     4   8
  CFI WILD-TYPE 106 171
[1] "tbl2"
               cls
clus            [,1] [,2]
  CFI MUTATED      4    8
  CFI WILD-TYPE  106  171
        clus
vv       CFI MUTATED CFI WILD-TYPE
  FEMALE           4           106
  MALE             8           171
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CFI MUTATED                                       2
  CFI WILD-TYPE                                    48
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CFI MUTATED                                                        7
  CFI WILD-TYPE                                                    128
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CFI MUTATED                                                                   1
  CFI WILD-TYPE                                                                39
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CFI MUTATED                                                  1
  CFI WILD-TYPE                                               37
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CFI MUTATED                                                          1
  CFI WILD-TYPE                                                       15
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CFI MUTATED                                                           0
  CFI WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CFI MUTATED                                          0
  CFI WILD-TYPE                                        3
D147V8, multiclass
                                                                   clus
vv                                                                  CFI MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  CFI WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V9, binary
               cls
clus              0   1
  CFI MUTATED     0  12
  CFI WILD-TYPE   5 272
[1] "tbl2"
               cls
clus            [,1] [,2]
  CFI MUTATED      0   12
  CFI WILD-TYPE    5  272
     clus
vv    CFI MUTATED CFI WILD-TYPE
  NO            0             5
  YES          12           272
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  CFI MUTATED    10   0   0   2
  CFI WILD-TYPE 217  10  10  22
D147V10, multiclass
    clus
vv   CFI MUTATED CFI WILD-TYPE
  R0          10           217
  R1           0            10
  R2           0            10
  RX           2            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CFI MUTATED       4                         0     7
  CFI WILD-TYPE    72                         4   161
D147V12, multiclass
                           clus
vv                          CFI MUTATED CFI WILD-TYPE
  ASIAN                               4            72
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                               7           161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(148) Variable = FERMT2 MUTATION ANALYSIS
D148V1, survival
                  sevent
clus2                0   1
  FERMT2 MUTATED     5   0
  FERMT2 WILD-TYPE 176  80
  FERMT2 MUTATED FERMT2 WILD-TYPE 
               5              256 
  FERMT2 MUTATED FERMT2 WILD-TYPE 
               0               80 
$`FERMT2 MUTATED`
TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-A4QL TCGA-HU-8602 
       19.50         1.12        13.45        11.57        11.41 

$`FERMT2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  FERMT2 MUTATED FERMT2 WILD-TYPE 
            1.12             0.00 
  FERMT2 MUTATED FERMT2 WILD-TYPE 
           19.50           105.07 
  FERMT2 MUTATED FERMT2 WILD-TYPE 
           11.57            12.64 
[1] "1.1 - 19.5 (11.6)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "9200000"
D148V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FERMT2 MUTATED         0        0        0        0         1         1
  FERMT2 WILD-TYPE       1        9       27       26        30        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FERMT2 MUTATED           0          1          1          2        0
  FERMT2 WILD-TYPE         3         48         35         22       24
D148V3, multiclass
            clus
vv           FERMT2 MUTATED FERMT2 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              2               22
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FERMT2 MUTATED     0   0   3   4
  FERMT2 WILD-TYPE  11  72 119  71
D148V4, multiclass
    clus
vv   FERMT2 MUTATED FERMT2 WILD-TYPE
  T1              0               11
  T2              0               72
  T3              3              119
  T4              4               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  FERMT2 MUTATED    3  0  1  2
  FERMT2 WILD-TYPE 90 81 49 51
D148V5, multiclass
    clus
vv   FERMT2 MUTATED FERMT2 WILD-TYPE
  N0              3               90
  N1              0               81
  N2              1               49
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D148V6, binary
                  cls
clus                 0   1
  FERMT2 MUTATED     6   0
  FERMT2 WILD-TYPE 251  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FERMT2 MUTATED      6    0
  FERMT2 WILD-TYPE  251   18
   clus
vv  FERMT2 MUTATED FERMT2 WILD-TYPE
  0              6              251
  1              0               18
[1] 2 2
[1] FALSE
D148V7, binary
                  cls
clus                 0   1
  FERMT2 MUTATED     6   1
  FERMT2 WILD-TYPE 104 178
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FERMT2 MUTATED      6    1
  FERMT2 WILD-TYPE  104  178
        clus
vv       FERMT2 MUTATED FERMT2 WILD-TYPE
  FEMALE              6              104
  MALE                1              178
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FERMT2 MUTATED                                       1
  FERMT2 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FERMT2 MUTATED                                                        6
  FERMT2 WILD-TYPE                                                    129
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FERMT2 MUTATED                                                                   0
  FERMT2 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FERMT2 MUTATED                                                  0
  FERMT2 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FERMT2 MUTATED                                                          0
  FERMT2 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FERMT2 MUTATED                                                           0
  FERMT2 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FERMT2 MUTATED                                          0
  FERMT2 WILD-TYPE                                        3
D148V8, multiclass
                                                                   clus
vv                                                                  FERMT2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  FERMT2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D148V9, binary
                  cls
clus                 0   1
  FERMT2 MUTATED     0   7
  FERMT2 WILD-TYPE   5 277
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FERMT2 MUTATED      0    7
  FERMT2 WILD-TYPE    5  277
     clus
vv    FERMT2 MUTATED FERMT2 WILD-TYPE
  NO               0                5
  YES              7              277
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FERMT2 MUTATED     5   0   0   2
  FERMT2 WILD-TYPE 222  10  10  22
D148V10, multiclass
    clus
vv   FERMT2 MUTATED FERMT2 WILD-TYPE
  R0              5              222
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D148V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FERMT2 MUTATED       1                         0     6
  FERMT2 WILD-TYPE    75                         4   162
D148V12, multiclass
                           clus
vv                          FERMT2 MUTATED FERMT2 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(149) Variable = ALDH3A1 MUTATION ANALYSIS
D149V1, survival
                   sevent
clus2                 0   1
  ALDH3A1 MUTATED     5   2
  ALDH3A1 WILD-TYPE 176  78
  ALDH3A1 MUTATED ALDH3A1 WILD-TYPE 
                7               254 
  ALDH3A1 MUTATED ALDH3A1 WILD-TYPE 
                2                78 
$`ALDH3A1 MUTATED`
TCGA-BR-7851 TCGA-BR-8361 TCGA-BR-8372 TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5723 
       12.43        19.50        19.17         6.58         1.02       105.07 
TCGA-F1-A448 
       21.27 

$`ALDH3A1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        72.23         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  ALDH3A1 MUTATED ALDH3A1 WILD-TYPE 
             1.02              0.00 
  ALDH3A1 MUTATED ALDH3A1 WILD-TYPE 
           105.07             79.07 
  ALDH3A1 MUTATED ALDH3A1 WILD-TYPE 
           19.170            12.605 
[1] "1.0 - 105.1 (19.2)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.8"
D149V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ALDH3A1 MUTATED         0        0        0        1         1         1
  ALDH3A1 WILD-TYPE       1        9       27       25        30        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ALDH3A1 MUTATED           0          0          1          2        1
  ALDH3A1 WILD-TYPE         3         49         35         22       23
D149V3, multiclass
            clus
vv           ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 0                27
  STAGE II                 1                25
  STAGE IIA                1                30
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               1                35
  STAGE IIIC               2                22
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ALDH3A1 MUTATED     0   1   3   3
  ALDH3A1 WILD-TYPE  11  71 119  72
D149V4, multiclass
    clus
vv   ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  T1               0                11
  T2               1                71
  T3               3               119
  T4               3                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  ALDH3A1 MUTATED    2  2  2  2
  ALDH3A1 WILD-TYPE 91 79 48 51
D149V5, multiclass
    clus
vv   ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  N0               2                91
  N1               2                79
  N2               2                48
  N3               2                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D149V6, binary
                   cls
clus                  0   1
  ALDH3A1 MUTATED     9   1
  ALDH3A1 WILD-TYPE 248  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH3A1 MUTATED      9    1
  ALDH3A1 WILD-TYPE  248   17
   clus
vv  ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  0               9               248
  1               1                17
[1] 2 2
[1] FALSE
D149V7, binary
                   cls
clus                  0   1
  ALDH3A1 MUTATED     4   6
  ALDH3A1 WILD-TYPE 106 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH3A1 MUTATED      4    6
  ALDH3A1 WILD-TYPE  106  173
        clus
vv       ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  FEMALE               4               106
  MALE                 6               173
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ALDH3A1 MUTATED                                       1
  ALDH3A1 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ALDH3A1 MUTATED                                                        7
  ALDH3A1 WILD-TYPE                                                    128
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ALDH3A1 MUTATED                                                                   1
  ALDH3A1 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ALDH3A1 MUTATED                                                  0
  ALDH3A1 WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ALDH3A1 MUTATED                                                          1
  ALDH3A1 WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ALDH3A1 MUTATED                                                           0
  ALDH3A1 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ALDH3A1 MUTATED                                          0
  ALDH3A1 WILD-TYPE                                        3
D149V8, multiclass
                                                                   clus
vv                                                                  ALDH3A1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  ALDH3A1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D149V9, binary
                   cls
clus                  0   1
  ALDH3A1 MUTATED     0  10
  ALDH3A1 WILD-TYPE   5 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH3A1 MUTATED      0   10
  ALDH3A1 WILD-TYPE    5  274
     clus
vv    ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  NO                0                 5
  YES              10               274
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ALDH3A1 MUTATED     5   0   1   3
  ALDH3A1 WILD-TYPE 222  10   9  21
D149V10, multiclass
    clus
vv   ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  R0               5               222
  R1               0                10
  R2               1                 9
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D149V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ALDH3A1 MUTATED       1                         0     7
  ALDH3A1 WILD-TYPE    75                         4   161
D149V12, multiclass
                           clus
vv                          ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  ASIAN                                   1                75
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   7               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(150) Variable = GCC2 MUTATION ANALYSIS
D150V1, survival
                sevent
clus2              0   1
  GCC2 MUTATED     6   1
  GCC2 WILD-TYPE 175  79
  GCC2 MUTATED GCC2 WILD-TYPE 
             7            254 
  GCC2 MUTATED GCC2 WILD-TYPE 
             1             79 
$`GCC2 MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-8382 TCGA-BR-8589 TCGA-BR-8680 TCGA-CG-5721 
       26.70        30.90        15.85        15.81        15.81         6.02 
TCGA-HU-A4H3 
       19.36 

$`GCC2 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        12.79         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  GCC2 MUTATED GCC2 WILD-TYPE 
          6.02           0.00 
  GCC2 MUTATED GCC2 WILD-TYPE 
         30.90         105.07 
  GCC2 MUTATED GCC2 WILD-TYPE 
        15.850         12.495 
[1] "6.0 - 30.9 (15.8)"  "0.0 - 105.1 (12.5)"
[1] "hr=" "3.2"
D150V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GCC2 MUTATED         0        0        0        0         0         1
  GCC2 WILD-TYPE       1        9       27       26        31        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GCC2 MUTATED           0          1          1          2        2
  GCC2 WILD-TYPE         3         48         35         22       22
D150V3, multiclass
            clus
vv           GCC2 MUTATED GCC2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              0             26
  STAGE IIA             0             31
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            2             22
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GCC2 MUTATED     0   1   0   7
  GCC2 WILD-TYPE  11  71 122  68
D150V4, multiclass
    clus
vv   GCC2 MUTATED GCC2 WILD-TYPE
  T1            0             11
  T2            1             71
  T3            0            122
  T4            7             68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  GCC2 MUTATED    2  3  1  2
  GCC2 WILD-TYPE 91 78 49 51
D150V5, multiclass
    clus
vv   GCC2 MUTATED GCC2 WILD-TYPE
  N0            2             91
  N1            3             78
  N2            1             49
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V6, binary
                cls
clus               0   1
  GCC2 MUTATED     9   1
  GCC2 WILD-TYPE 248  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCC2 MUTATED      9    1
  GCC2 WILD-TYPE  248   17
   clus
vv  GCC2 MUTATED GCC2 WILD-TYPE
  0            9            248
  1            1             17
[1] 2 2
[1] FALSE
D150V7, binary
                cls
clus               0   1
  GCC2 MUTATED     7   3
  GCC2 WILD-TYPE 103 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCC2 MUTATED      7    3
  GCC2 WILD-TYPE  103  176
        clus
vv       GCC2 MUTATED GCC2 WILD-TYPE
  FEMALE            7            103
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GCC2 MUTATED                                       2
  GCC2 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GCC2 MUTATED                                                        6
  GCC2 WILD-TYPE                                                    129
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GCC2 MUTATED                                                                   1
  GCC2 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GCC2 MUTATED                                                  1
  GCC2 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GCC2 MUTATED                                                          0
  GCC2 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GCC2 MUTATED                                                           0
  GCC2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GCC2 MUTATED                                          0
  GCC2 WILD-TYPE                                        3
D150V8, multiclass
                                                                   clus
vv                                                                  GCC2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  GCC2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V9, binary
                cls
clus               0   1
  GCC2 MUTATED     0  10
  GCC2 WILD-TYPE   5 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCC2 MUTATED      0   10
  GCC2 WILD-TYPE    5  274
     clus
vv    GCC2 MUTATED GCC2 WILD-TYPE
  NO             0              5
  YES           10            274
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GCC2 MUTATED     6   0   0   4
  GCC2 WILD-TYPE 221  10  10  20
D150V10, multiclass
    clus
vv   GCC2 MUTATED GCC2 WILD-TYPE
  R0            6            221
  R1            0             10
  R2            0             10
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GCC2 MUTATED       2                         0     7
  GCC2 WILD-TYPE    74                         4   161
D150V12, multiclass
                           clus
vv                          GCC2 MUTATED GCC2 WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                7            161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(151) Variable = NOX5 MUTATION ANALYSIS
D151V1, survival
                sevent
clus2              0   1
  NOX5 MUTATED     9   3
  NOX5 WILD-TYPE 172  77
  NOX5 MUTATED NOX5 WILD-TYPE 
            12            249 
  NOX5 MUTATED NOX5 WILD-TYPE 
             3             77 
$`NOX5 MUTATED`
TCGA-BR-4184 TCGA-BR-6458 TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8680 TCGA-BR-A4QL 
        6.97        19.33        20.55        19.50        15.81        11.57 
TCGA-CG-4305 TCGA-CG-5721 TCGA-D7-A4YV TCGA-F1-6874 TCGA-HU-A4GX TCGA-HU-A4H8 
       15.95         6.02         5.92        14.47        10.19         8.88 

$`NOX5 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69        12.26         9.60         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
        0.10        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        0.62         7.99        16.24        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.25         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  NOX5 MUTATED NOX5 WILD-TYPE 
          5.92           0.00 
  NOX5 MUTATED NOX5 WILD-TYPE 
         20.55         105.07 
  NOX5 MUTATED NOX5 WILD-TYPE 
         13.02          12.62 
[1] "5.9 - 20.6 (13.0)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D151V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NOX5 MUTATED         0        0        2        1         0         3
  NOX5 WILD-TYPE       1        9       25       25        31        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NOX5 MUTATED           0          1          1          3        2
  NOX5 WILD-TYPE         3         48         35         21       22
D151V3, multiclass
            clus
vv           NOX5 MUTATED NOX5 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              1             25
  STAGE IIA             0             31
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            3             21
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NOX5 MUTATED     1   2   4   6
  NOX5 WILD-TYPE  10  70 118  69
D151V4, multiclass
    clus
vv   NOX5 MUTATED NOX5 WILD-TYPE
  T1            1             10
  T2            2             70
  T3            4            118
  T4            6             69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  NOX5 MUTATED    2  6  3  2
  NOX5 WILD-TYPE 91 75 47 51
D151V5, multiclass
    clus
vv   NOX5 MUTATED NOX5 WILD-TYPE
  N0            2             91
  N1            6             75
  N2            3             47
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D151V6, binary
                cls
clus               0   1
  NOX5 MUTATED    12   1
  NOX5 WILD-TYPE 245  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED     12    1
  NOX5 WILD-TYPE  245   17
   clus
vv  NOX5 MUTATED NOX5 WILD-TYPE
  0           12            245
  1            1             17
[1] 2 2
[1] FALSE
D151V7, binary
                cls
clus               0   1
  NOX5 MUTATED     7   7
  NOX5 WILD-TYPE 103 172
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED      7    7
  NOX5 WILD-TYPE  103  172
        clus
vv       NOX5 MUTATED NOX5 WILD-TYPE
  FEMALE            7            103
  MALE              7            172
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NOX5 MUTATED                                       1
  NOX5 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NOX5 MUTATED                                                        8
  NOX5 WILD-TYPE                                                    127
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NOX5 MUTATED                                                                   2
  NOX5 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NOX5 MUTATED                                                  3
  NOX5 WILD-TYPE                                               35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NOX5 MUTATED                                                          0
  NOX5 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NOX5 MUTATED                                                           0
  NOX5 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NOX5 MUTATED                                          0
  NOX5 WILD-TYPE                                        3
D151V8, multiclass
                                                                   clus
vv                                                                  NOX5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  NOX5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D151V9, binary
                cls
clus               0   1
  NOX5 MUTATED     0  14
  NOX5 WILD-TYPE   5 270
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED      0   14
  NOX5 WILD-TYPE    5  270
     clus
vv    NOX5 MUTATED NOX5 WILD-TYPE
  NO             0              5
  YES           14            270
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NOX5 MUTATED    11   1   0   2
  NOX5 WILD-TYPE 216   9  10  22
D151V10, multiclass
    clus
vv   NOX5 MUTATED NOX5 WILD-TYPE
  R0           11            216
  R1            1              9
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D151V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NOX5 MUTATED       3                         0     9
  NOX5 WILD-TYPE    73                         4   159
D151V12, multiclass
                           clus
vv                          NOX5 MUTATED NOX5 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                9            159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(152) Variable = KIF13A MUTATION ANALYSIS
D152V1, survival
                  sevent
clus2                0   1
  KIF13A MUTATED    11   6
  KIF13A WILD-TYPE 170  74
  KIF13A MUTATED KIF13A WILD-TYPE 
              17              244 
  KIF13A MUTATED KIF13A WILD-TYPE 
               6               74 
$`KIF13A MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8289 TCGA-BR-8363 TCGA-BR-8372 
       26.70        30.90        34.68         2.66         0.26        19.17 
TCGA-BR-8589 TCGA-CD-A486 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4465 
       15.81         3.42         6.58        12.62        15.95         9.01 
TCGA-CG-5721 TCGA-FP-A4BE TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H4 
        6.02        11.08         0.10         6.51        23.84 

$`KIF13A WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.13         0.10         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       12.43        11.61        12.20         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       19.36        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  KIF13A MUTATED KIF13A WILD-TYPE 
             0.1              0.0 
  KIF13A MUTATED KIF13A WILD-TYPE 
           34.68           105.07 
  KIF13A MUTATED KIF13A WILD-TYPE 
           11.08            12.71 
[1] "0.1 - 34.7 (11.1)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.2"
D152V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIF13A MUTATED         0        0        3        1         5         2
  KIF13A WILD-TYPE       1        9       24       25        26        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIF13A MUTATED           0          1          1          2        3
  KIF13A WILD-TYPE         3         48         35         22       21
D152V3, multiclass
            clus
vv           KIF13A MUTATED KIF13A WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                3               24
  STAGE II                1               25
  STAGE IIA               5               26
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              2               22
  STAGE IV                3               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KIF13A MUTATED     0   6   5   8
  KIF13A WILD-TYPE  11  66 117  67
D152V4, multiclass
    clus
vv   KIF13A MUTATED KIF13A WILD-TYPE
  T1              0               11
  T2              6               66
  T3              5              117
  T4              8               67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  KIF13A MUTATED   10  4  2  3
  KIF13A WILD-TYPE 83 77 48 50
D152V5, multiclass
    clus
vv   KIF13A MUTATED KIF13A WILD-TYPE
  N0             10               83
  N1              4               77
  N2              2               48
  N3              3               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V6, binary
                  cls
clus                 0   1
  KIF13A MUTATED    18   2
  KIF13A WILD-TYPE 239  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF13A MUTATED     18    2
  KIF13A WILD-TYPE  239   16
   clus
vv  KIF13A MUTATED KIF13A WILD-TYPE
  0             18              239
  1              2               16
[1] 2 2
[1] FALSE
D152V7, binary
                  cls
clus                 0   1
  KIF13A MUTATED     8  12
  KIF13A WILD-TYPE 102 167
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF13A MUTATED      8   12
  KIF13A WILD-TYPE  102  167
        clus
vv       KIF13A MUTATED KIF13A WILD-TYPE
  FEMALE              8              102
  MALE               12              167
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KIF13A MUTATED                                       3
  KIF13A WILD-TYPE                                    47
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIF13A MUTATED                                                       11
  KIF13A WILD-TYPE                                                    124
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIF13A MUTATED                                                                   3
  KIF13A WILD-TYPE                                                                37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KIF13A MUTATED                                                  3
  KIF13A WILD-TYPE                                               35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KIF13A MUTATED                                                          0
  KIF13A WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KIF13A MUTATED                                                           0
  KIF13A WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KIF13A MUTATED                                          0
  KIF13A WILD-TYPE                                        3
D152V8, multiclass
                                                                   clus
vv                                                                  KIF13A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  KIF13A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V9, binary
                  cls
clus                 0   1
  KIF13A MUTATED     0  20
  KIF13A WILD-TYPE   5 264
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF13A MUTATED      0   20
  KIF13A WILD-TYPE    5  264
     clus
vv    KIF13A MUTATED KIF13A WILD-TYPE
  NO               0                5
  YES             20              264
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  KIF13A MUTATED    13   0   1   3
  KIF13A WILD-TYPE 214  10   9  21
D152V10, multiclass
    clus
vv   KIF13A MUTATED KIF13A WILD-TYPE
  R0             13              214
  R1              0               10
  R2              1                9
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIF13A MUTATED       6                         1     9
  KIF13A WILD-TYPE    70                         3   159
D152V12, multiclass
                           clus
vv                          KIF13A MUTATED KIF13A WILD-TYPE
  ASIAN                                  6               70
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  9              159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(153) Variable = CR1L MUTATION ANALYSIS
D153V1, survival
                sevent
clus2              0   1
  CR1L MUTATED     8   2
  CR1L WILD-TYPE 173  78
  CR1L MUTATED CR1L WILD-TYPE 
            10            251 
  CR1L MUTATED CR1L WILD-TYPE 
             2             78 
$`CR1L MUTATED`
TCGA-B7-5816 TCGA-BR-8363 TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-5721 
       26.70         0.26         0.10         1.02         8.05         6.02 
TCGA-CG-5723 TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GU 
      105.07        24.20        11.77         6.25 

$`CR1L WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        19.50        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
        3.02        27.02        15.95         7.99        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
       36.00         1.02         0.99         0.99        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP 
       11.84         3.25        22.75        25.81        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  CR1L MUTATED CR1L WILD-TYPE 
           0.1            0.0 
  CR1L MUTATED CR1L WILD-TYPE 
        105.07          79.07 
  CR1L MUTATED CR1L WILD-TYPE 
          7.15          12.76 
[1] "0.1 - 105.1 (7.2)" "0.0 - 79.1 (12.8)"
[1] "hr=" "1.8"
D153V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CR1L MUTATED         1        2        1        2         0         2
  CR1L WILD-TYPE       0        7       26       24        31        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CR1L MUTATED           0          0          1          0        2
  CR1L WILD-TYPE         3         49         35         24       22
D153V3, multiclass
            clus
vv           CR1L MUTATED CR1L WILD-TYPE
  STAGE I               1              0
  STAGE IA              2              7
  STAGE IB              1             26
  STAGE II              2             24
  STAGE IIA             0             31
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            1             35
  STAGE IIIC            0             24
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CR1L MUTATED     3   3   3   2
  CR1L WILD-TYPE   8  69 119  73
D153V4, multiclass
    clus
vv   CR1L MUTATED CR1L WILD-TYPE
  T1            3              8
  T2            3             69
  T3            3            119
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  CR1L MUTATED    4  6  1  0
  CR1L WILD-TYPE 89 75 49 53
D153V5, multiclass
    clus
vv   CR1L MUTATED CR1L WILD-TYPE
  N0            4             89
  N1            6             75
  N2            1             49
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V6, binary
                cls
clus               0   1
  CR1L MUTATED     9   1
  CR1L WILD-TYPE 248  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  CR1L MUTATED      9    1
  CR1L WILD-TYPE  248   17
   clus
vv  CR1L MUTATED CR1L WILD-TYPE
  0            9            248
  1            1             17
[1] 2 2
[1] FALSE
D153V7, binary
                cls
clus               0   1
  CR1L MUTATED     3   8
  CR1L WILD-TYPE 107 171
[1] "tbl2"
                cls
clus             [,1] [,2]
  CR1L MUTATED      3    8
  CR1L WILD-TYPE  107  171
        clus
vv       CR1L MUTATED CR1L WILD-TYPE
  FEMALE            3            107
  MALE              8            171
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CR1L MUTATED                                       2
  CR1L WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CR1L MUTATED                                                        5
  CR1L WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CR1L MUTATED                                                                   2
  CR1L WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CR1L MUTATED                                                  2
  CR1L WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CR1L MUTATED                                                          0
  CR1L WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CR1L MUTATED                                                           0
  CR1L WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CR1L MUTATED                                          0
  CR1L WILD-TYPE                                        3
D153V8, multiclass
                                                                   clus
vv                                                                  CR1L MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  CR1L WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V9, binary
                cls
clus               0   1
  CR1L MUTATED     0  11
  CR1L WILD-TYPE   5 273
[1] "tbl2"
                cls
clus             [,1] [,2]
  CR1L MUTATED      0   11
  CR1L WILD-TYPE    5  273
     clus
vv    CR1L MUTATED CR1L WILD-TYPE
  NO             0              5
  YES           11            273
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CR1L MUTATED     9   0   1   0
  CR1L WILD-TYPE 218  10   9  24
D153V10, multiclass
    clus
vv   CR1L MUTATED CR1L WILD-TYPE
  R0            9            218
  R1            0             10
  R2            1              9
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CR1L MUTATED       4                         1     2
  CR1L WILD-TYPE    72                         3   166
D153V12, multiclass
                           clus
vv                          CR1L MUTATED CR1L WILD-TYPE
  ASIAN                                4             72
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                                2            166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(154) Variable = GALNTL1 MUTATION ANALYSIS
D154V1, survival
                   sevent
clus2                 0   1
  GALNTL1 MUTATED     4   6
  GALNTL1 WILD-TYPE 177  74
  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
               10               251 
  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
                6                74 
$`GALNTL1 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8591 TCGA-BR-A4QL 
        6.97        34.68         9.07        14.43        13.45        11.57 
TCGA-CG-5728 TCGA-F1-6875 TCGA-HJ-7597 TCGA-HU-A4GQ 
       65.10        72.23        26.47         0.10 

$`GALNTL1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 
       12.43         3.45        12.76        18.71        17.49         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        15.81         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
              0.1               0.0 
  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
            72.23            105.07 
  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
            13.94             12.59 
[1] "0.1 - 72.2 (13.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D154V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GALNTL1 MUTATED         0        1        2        0         1         0
  GALNTL1 WILD-TYPE       1        8       25       26        30        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GALNTL1 MUTATED           1          1          1          2        1
  GALNTL1 WILD-TYPE         2         48         35         22       23
D154V3, multiclass
            clus
vv           GALNTL1 MUTATED GALNTL1 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 1                 8
  STAGE IB                 2                25
  STAGE II                 0                26
  STAGE IIA                1                30
  STAGE IIB                0                44
  STAGE III                1                 2
  STAGE IIIA               1                48
  STAGE IIIB               1                35
  STAGE IIIC               2                22
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GALNTL1 MUTATED     0   3   4   3
  GALNTL1 WILD-TYPE  11  69 118  72
D154V4, multiclass
    clus
vv   GALNTL1 MUTATED GALNTL1 WILD-TYPE
  T1               0                11
  T2               3                69
  T3               4               118
  T4               3                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  GALNTL1 MUTATED    4  2  1  3
  GALNTL1 WILD-TYPE 89 79 49 50
D154V5, multiclass
    clus
vv   GALNTL1 MUTATED GALNTL1 WILD-TYPE
  N0               4                89
  N1               2                79
  N2               1                49
  N3               3                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V6, binary
                   cls
clus                  0   1
  GALNTL1 MUTATED     7   1
  GALNTL1 WILD-TYPE 250  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GALNTL1 MUTATED      7    1
  GALNTL1 WILD-TYPE  250   17
   clus
vv  GALNTL1 MUTATED GALNTL1 WILD-TYPE
  0               7               250
  1               1                17
[1] 2 2
[1] FALSE
D154V7, binary
                   cls
clus                  0   1
  GALNTL1 MUTATED     5   5
  GALNTL1 WILD-TYPE 105 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GALNTL1 MUTATED      5    5
  GALNTL1 WILD-TYPE  105  174
        clus
vv       GALNTL1 MUTATED GALNTL1 WILD-TYPE
  FEMALE               5               105
  MALE                 5               174
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GALNTL1 MUTATED                                       0
  GALNTL1 WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GALNTL1 MUTATED                                                        5
  GALNTL1 WILD-TYPE                                                    130
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GALNTL1 MUTATED                                                                   3
  GALNTL1 WILD-TYPE                                                                37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GALNTL1 MUTATED                                                  1
  GALNTL1 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GALNTL1 MUTATED                                                          0
  GALNTL1 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GALNTL1 MUTATED                                                           0
  GALNTL1 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GALNTL1 MUTATED                                          1
  GALNTL1 WILD-TYPE                                        2
D154V8, multiclass
                                                                   clus
vv                                                                  GALNTL1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  GALNTL1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V9, binary
                   cls
clus                  0   1
  GALNTL1 MUTATED     0  10
  GALNTL1 WILD-TYPE   5 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GALNTL1 MUTATED      0   10
  GALNTL1 WILD-TYPE    5  274
     clus
vv    GALNTL1 MUTATED GALNTL1 WILD-TYPE
  NO                0                 5
  YES              10               274
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  GALNTL1 MUTATED     9   0   0   1
  GALNTL1 WILD-TYPE 218  10  10  23
D154V10, multiclass
    clus
vv   GALNTL1 MUTATED GALNTL1 WILD-TYPE
  R0               9               218
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GALNTL1 MUTATED       1                         1     7
  GALNTL1 WILD-TYPE    75                         3   161
D154V12, multiclass
                           clus
vv                          GALNTL1 MUTATED GALNTL1 WILD-TYPE
  ASIAN                                   1                75
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   7               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(155) Variable = SCLT1 MUTATION ANALYSIS
D155V1, survival
                 sevent
clus2               0   1
  SCLT1 MUTATED     7   5
  SCLT1 WILD-TYPE 174  75
  SCLT1 MUTATED SCLT1 WILD-TYPE 
             12             249 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
              5              75 
$`SCLT1 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8484 TCGA-BR-8487 TCGA-CD-A48A 
        6.97        30.90        34.68        25.18         1.12        12.43 
TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5728 TCGA-HU-8602 TCGA-HU-A4GU TCGA-HU-A4GX 
        6.58         1.02        65.10        11.41         6.25        10.19 

$`SCLT1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        0.26        15.85         3.72         5.39         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        3.42         9.34        11.31        11.61        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  SCLT1 MUTATED SCLT1 WILD-TYPE 
           1.02            0.00 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
          65.10          105.07 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
          10.80           12.76 
[1] "1.0 - 65.1 (10.8)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.1"
D155V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SCLT1 MUTATED         0        0        2        1         4         2
  SCLT1 WILD-TYPE       1        9       25       25        27        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SCLT1 MUTATED           0          2          0          1        2
  SCLT1 WILD-TYPE         3         47         36         23       22
D155V3, multiclass
            clus
vv           SCLT1 MUTATED SCLT1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               1              25
  STAGE IIA              4              27
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SCLT1 MUTATED     0   4   7   4
  SCLT1 WILD-TYPE  11  68 115  71
D155V4, multiclass
    clus
vv   SCLT1 MUTATED SCLT1 WILD-TYPE
  T1             0              11
  T2             4              68
  T3             7             115
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  SCLT1 MUTATED    7  5  3  0
  SCLT1 WILD-TYPE 86 76 47 53
D155V5, multiclass
    clus
vv   SCLT1 MUTATED SCLT1 WILD-TYPE
  N0             7              86
  N1             5              76
  N2             3              47
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D155V6, binary
                 cls
clus                0   1
  SCLT1 MUTATED    14   1
  SCLT1 WILD-TYPE 243  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED     14    1
  SCLT1 WILD-TYPE  243   17
   clus
vv  SCLT1 MUTATED SCLT1 WILD-TYPE
  0            14             243
  1             1              17
[1] 2 2
[1] FALSE
D155V7, binary
                 cls
clus                0   1
  SCLT1 MUTATED     8   8
  SCLT1 WILD-TYPE 102 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED      8    8
  SCLT1 WILD-TYPE  102  171
        clus
vv       SCLT1 MUTATED SCLT1 WILD-TYPE
  FEMALE             8             102
  MALE               8             171
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SCLT1 MUTATED                                       4
  SCLT1 WILD-TYPE                                    46
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SCLT1 MUTATED                                                        9
  SCLT1 WILD-TYPE                                                    126
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SCLT1 MUTATED                                                                   2
  SCLT1 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SCLT1 MUTATED                                                  0
  SCLT1 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SCLT1 MUTATED                                                          1
  SCLT1 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SCLT1 MUTATED                                                           0
  SCLT1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SCLT1 MUTATED                                          0
  SCLT1 WILD-TYPE                                        3
D155V8, multiclass
                                                                   clus
vv                                                                  SCLT1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  SCLT1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D155V9, binary
                 cls
clus                0   1
  SCLT1 MUTATED     1  15
  SCLT1 WILD-TYPE   4 269
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED      1   15
  SCLT1 WILD-TYPE    4  269
     clus
vv    SCLT1 MUTATED SCLT1 WILD-TYPE
  NO              1               4
  YES            15             269
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SCLT1 MUTATED     9   0   1   4
  SCLT1 WILD-TYPE 218  10   9  20
D155V10, multiclass
    clus
vv   SCLT1 MUTATED SCLT1 WILD-TYPE
  R0             9             218
  R1             0              10
  R2             1               9
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D155V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SCLT1 MUTATED       5                         0     7
  SCLT1 WILD-TYPE    71                         4   161
D155V12, multiclass
                           clus
vv                          SCLT1 MUTATED SCLT1 WILD-TYPE
  ASIAN                                 5              71
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 7             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(156) Variable = STAB1 MUTATION ANALYSIS
D156V1, survival
                 sevent
clus2               0   1
  STAB1 MUTATED    19   6
  STAB1 WILD-TYPE 162  74
  STAB1 MUTATED STAB1 WILD-TYPE 
             25             236 
  STAB1 MUTATED STAB1 WILD-TYPE 
              6              74 
$`STAB1 MUTATED`
TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8078 
        6.97        18.35        34.68        32.78        23.93        12.26 
TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8590 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MI 
       19.50        19.17         9.34        15.81        11.57         0.10 
TCGA-CD-A4MJ TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-A4YV TCGA-D7-A4YY 
       12.62         6.02       105.07        21.07         5.92        13.78 
TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-A4GC TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.08        11.41        12.10         3.25         0.10         6.25 
TCGA-HU-A4H3 
       19.36 

$`STAB1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
       26.70        11.70         6.61         4.64         7.43        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       13.68        19.33        39.12        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 
       32.94        12.82         9.21        24.76        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 
       12.76        18.71        17.49        14.43         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 
        9.21        20.22         1.12        12.79        15.81        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        13.64         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.20        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99         0.99        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       16.44        15.16        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8608 
        5.52        26.47         5.92        12.59        14.17        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        11.77        29.98         8.98         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  STAB1 MUTATED STAB1 WILD-TYPE 
            0.1             0.0 
  STAB1 MUTATED STAB1 WILD-TYPE 
         105.07           79.07 
  STAB1 MUTATED STAB1 WILD-TYPE 
          12.26           12.71 
[1] "0.1 - 105.1 (12.3)" "0.0 - 79.1 (12.7)" 
[1] "hr=" "1.5"
D156V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  STAB1 MUTATED         0        0        3        1         4         4
  STAB1 WILD-TYPE       1        9       24       25        27        40
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STAB1 MUTATED           0          3          4          5        2
  STAB1 WILD-TYPE         3         46         32         19       22
D156V3, multiclass
            clus
vv           STAB1 MUTATED STAB1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               3              24
  STAGE II               1              25
  STAGE IIA              4              27
  STAGE IIB              4              40
  STAGE III              0               3
  STAGE IIIA             3              46
  STAGE IIIB             4              32
  STAGE IIIC             5              19
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STAB1 MUTATED     1   5  10  11
  STAB1 WILD-TYPE  10  67 112  64
D156V4, multiclass
    clus
vv   STAB1 MUTATED STAB1 WILD-TYPE
  T1             1              10
  T2             5              67
  T3            10             112
  T4            11              64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  STAB1 MUTATED   10  7  6  4
  STAB1 WILD-TYPE 83 74 44 49
D156V5, multiclass
    clus
vv   STAB1 MUTATED STAB1 WILD-TYPE
  N0            10              83
  N1             7              74
  N2             6              44
  N3             4              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D156V6, binary
                 cls
clus                0   1
  STAB1 MUTATED    26   1
  STAB1 WILD-TYPE 231  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAB1 MUTATED     26    1
  STAB1 WILD-TYPE  231   17
   clus
vv  STAB1 MUTATED STAB1 WILD-TYPE
  0            26             231
  1             1              17
[1] 2 2
[1] FALSE
D156V7, binary
                 cls
clus                0   1
  STAB1 MUTATED    13  15
  STAB1 WILD-TYPE  97 164
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAB1 MUTATED     13   15
  STAB1 WILD-TYPE   97  164
        clus
vv       STAB1 MUTATED STAB1 WILD-TYPE
  FEMALE            13              97
  MALE              15             164
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  STAB1 MUTATED                                       4
  STAB1 WILD-TYPE                                    46
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  STAB1 MUTATED                                                       17
  STAB1 WILD-TYPE                                                    118
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  STAB1 MUTATED                                                                   3
  STAB1 WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  STAB1 MUTATED                                                  4
  STAB1 WILD-TYPE                                               34
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  STAB1 MUTATED                                                          0
  STAB1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  STAB1 MUTATED                                                           0
  STAB1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  STAB1 MUTATED                                          0
  STAB1 WILD-TYPE                                        3
D156V8, multiclass
                                                                   clus
vv                                                                  STAB1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       17
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  STAB1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        118
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D156V9, binary
                 cls
clus                0   1
  STAB1 MUTATED     0  28
  STAB1 WILD-TYPE   5 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAB1 MUTATED      0   28
  STAB1 WILD-TYPE    5  256
     clus
vv    STAB1 MUTATED STAB1 WILD-TYPE
  NO              0               5
  YES            28             256
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  STAB1 MUTATED    22   0   0   4
  STAB1 WILD-TYPE 205  10  10  20
D156V10, multiclass
    clus
vv   STAB1 MUTATED STAB1 WILD-TYPE
  R0            22             205
  R1             0              10
  R2             0              10
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D156V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STAB1 MUTATED       9                         1    14
  STAB1 WILD-TYPE    67                         3   154
D156V12, multiclass
                           clus
vv                          STAB1 MUTATED STAB1 WILD-TYPE
  ASIAN                                 9              67
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                14             154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(157) Variable = TP53BP1 MUTATION ANALYSIS
D157V1, survival
                   sevent
clus2                 0   1
  TP53BP1 MUTATED    12   3
  TP53BP1 WILD-TYPE 169  77
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
               15               246 
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
                3                77 
$`TP53BP1 MUTATED`
TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-8370 TCGA-BR-8589 
       30.90         6.61        34.68        30.90         3.32        15.81 
TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-6522 TCGA-D7-6525 TCGA-HU-8610 
       15.95         6.02       105.07        18.61        13.35         0.76 
TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GT 
       11.84        29.98         6.51 

$`TP53BP1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       18.35         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       25.61        18.05        19.89         8.98        21.11        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
        0.10        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99         0.99        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6524 
       11.93        19.13        20.55        18.84        18.54        17.85 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        11.41        12.10        10.62        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
             0.76              0.00 
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
           105.07             79.07 
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
           15.810            12.575 
[1] "0.8 - 105.1 (15.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "2.5"
D157V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TP53BP1 MUTATED         0        1        1        2         3         1
  TP53BP1 WILD-TYPE       1        8       26       24        28        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TP53BP1 MUTATED           1          2          2          0        2
  TP53BP1 WILD-TYPE         2         47         34         24       22
D157V3, multiclass
            clus
vv           TP53BP1 MUTATED TP53BP1 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 1                 8
  STAGE IB                 1                26
  STAGE II                 2                24
  STAGE IIA                3                28
  STAGE IIB                1                43
  STAGE III                1                 2
  STAGE IIIA               2                47
  STAGE IIIB               2                34
  STAGE IIIC               0                24
  STAGE IV                 2                22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TP53BP1 MUTATED     1   7   5   3
  TP53BP1 WILD-TYPE  10  65 117  72
D157V4, multiclass
    clus
vv   TP53BP1 MUTATED TP53BP1 WILD-TYPE
  T1               1                10
  T2               7                65
  T3               5               117
  T4               3                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  TP53BP1 MUTATED    4  7  3  1
  TP53BP1 WILD-TYPE 89 74 47 52
D157V5, multiclass
    clus
vv   TP53BP1 MUTATED TP53BP1 WILD-TYPE
  N0               4                89
  N1               7                74
  N2               3                47
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V6, binary
                   cls
clus                  0   1
  TP53BP1 MUTATED    16   0
  TP53BP1 WILD-TYPE 241  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP1 MUTATED     16    0
  TP53BP1 WILD-TYPE  241   18
   clus
vv  TP53BP1 MUTATED TP53BP1 WILD-TYPE
  0              16               241
  1               0                18
[1] 2 2
[1] FALSE
D157V7, binary
                   cls
clus                  0   1
  TP53BP1 MUTATED     6  10
  TP53BP1 WILD-TYPE 104 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP1 MUTATED      6   10
  TP53BP1 WILD-TYPE  104  169
        clus
vv       TP53BP1 MUTATED TP53BP1 WILD-TYPE
  FEMALE               6               104
  MALE                10               169
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TP53BP1 MUTATED                                       4
  TP53BP1 WILD-TYPE                                    46
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TP53BP1 MUTATED                                                        8
  TP53BP1 WILD-TYPE                                                    127
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TP53BP1 MUTATED                                                                   1
  TP53BP1 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TP53BP1 MUTATED                                                  3
  TP53BP1 WILD-TYPE                                               35
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TP53BP1 MUTATED                                                          0
  TP53BP1 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TP53BP1 MUTATED                                                           0
  TP53BP1 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TP53BP1 MUTATED                                          0
  TP53BP1 WILD-TYPE                                        3
D157V8, multiclass
                                                                   clus
vv                                                                  TP53BP1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  TP53BP1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V9, binary
                   cls
clus                  0   1
  TP53BP1 MUTATED     0  16
  TP53BP1 WILD-TYPE   5 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP1 MUTATED      0   16
  TP53BP1 WILD-TYPE    5  268
     clus
vv    TP53BP1 MUTATED TP53BP1 WILD-TYPE
  NO                0                 5
  YES              16               268
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TP53BP1 MUTATED    12   0   0   3
  TP53BP1 WILD-TYPE 215  10  10  21
D157V10, multiclass
    clus
vv   TP53BP1 MUTATED TP53BP1 WILD-TYPE
  R0              12               215
  R1               0                10
  R2               0                10
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53BP1 MUTATED       4                         0     9
  TP53BP1 WILD-TYPE    72                         4   159
D157V12, multiclass
                           clus
vv                          TP53BP1 MUTATED TP53BP1 WILD-TYPE
  ASIAN                                   4                72
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   9               159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(158) Variable = IFRD1 MUTATION ANALYSIS
D158V1, survival
                 sevent
clus2               0   1
  IFRD1 MUTATED     1   4
  IFRD1 WILD-TYPE 180  76
  IFRD1 MUTATED IFRD1 WILD-TYPE 
              5             256 
  IFRD1 MUTATED IFRD1 WILD-TYPE 
              4              76 
$`IFRD1 MUTATED`
TCGA-BR-4201 TCGA-BR-6455 TCGA-BR-8078 TCGA-BR-8363 TCGA-CD-A4MG 
       30.90        13.87        12.26         0.26         6.58 

$`IFRD1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       19.50        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  IFRD1 MUTATED IFRD1 WILD-TYPE 
           0.26            0.00 
  IFRD1 MUTATED IFRD1 WILD-TYPE 
          30.90          105.07 
  IFRD1 MUTATED IFRD1 WILD-TYPE 
          12.26           12.64 
[1] "0.3 - 30.9 (12.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.8"
D158V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IFRD1 MUTATED         1        0        1        1         1         2
  IFRD1 WILD-TYPE       0        9       26       25        30        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IFRD1 MUTATED           0          0          0          0        0
  IFRD1 WILD-TYPE         3         49         36         24       24
D158V3, multiclass
            clus
vv           IFRD1 MUTATED IFRD1 WILD-TYPE
  STAGE I                1               0
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IFRD1 MUTATED     1   3   2   1
  IFRD1 WILD-TYPE  10  69 120  74
D158V4, multiclass
    clus
vv   IFRD1 MUTATED IFRD1 WILD-TYPE
  T1             1              10
  T2             3              69
  T3             2             120
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  IFRD1 MUTATED    3  4  0  0
  IFRD1 WILD-TYPE 90 77 50 53
D158V5, multiclass
    clus
vv   IFRD1 MUTATED IFRD1 WILD-TYPE
  N0             3              90
  N1             4              77
  N2             0              50
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D158V6, binary
                 cls
clus                0   1
  IFRD1 MUTATED     7   0
  IFRD1 WILD-TYPE 250  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFRD1 MUTATED      7    0
  IFRD1 WILD-TYPE  250   18
   clus
vv  IFRD1 MUTATED IFRD1 WILD-TYPE
  0             7             250
  1             0              18
[1] 2 2
[1] FALSE
D158V7, binary
                 cls
clus                0   1
  IFRD1 MUTATED     4   4
  IFRD1 WILD-TYPE 106 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFRD1 MUTATED      4    4
  IFRD1 WILD-TYPE  106  175
        clus
vv       IFRD1 MUTATED IFRD1 WILD-TYPE
  FEMALE             4             106
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  IFRD1 MUTATED                                       1
  IFRD1 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IFRD1 MUTATED                                                        6
  IFRD1 WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IFRD1 MUTATED                                                                   0
  IFRD1 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  IFRD1 MUTATED                                                  0
  IFRD1 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  IFRD1 MUTATED                                                          1
  IFRD1 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  IFRD1 MUTATED                                                           0
  IFRD1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  IFRD1 MUTATED                                          0
  IFRD1 WILD-TYPE                                        3
D158V8, multiclass
                                                                   clus
vv                                                                  IFRD1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  IFRD1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D158V9, binary
                 cls
clus                0   1
  IFRD1 MUTATED     1   7
  IFRD1 WILD-TYPE   4 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFRD1 MUTATED      1    7
  IFRD1 WILD-TYPE    4  277
     clus
vv    IFRD1 MUTATED IFRD1 WILD-TYPE
  NO              1               4
  YES             7             277
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IFRD1 MUTATED     5   0   0   2
  IFRD1 WILD-TYPE 222  10  10  22
D158V10, multiclass
    clus
vv   IFRD1 MUTATED IFRD1 WILD-TYPE
  R0             5             222
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D158V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IFRD1 MUTATED       1                         1     5
  IFRD1 WILD-TYPE    75                         3   163
D158V12, multiclass
                           clus
vv                          IFRD1 MUTATED IFRD1 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(159) Variable = SF3B2 MUTATION ANALYSIS
D159V1, survival
                 sevent
clus2               0   1
  SF3B2 MUTATED    11   4
  SF3B2 WILD-TYPE 170  76
  SF3B2 MUTATED SF3B2 WILD-TYPE 
             15             246 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
              4              76 
$`SF3B2 MUTATED`
TCGA-B7-5816 TCGA-BR-6565 TCGA-BR-8360 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8680 
       26.70         9.17         6.18         1.12        12.79        15.81 
TCGA-CG-4477 TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-A4YY TCGA-HJ-7597 TCGA-HU-8602 
       30.97         6.02        28.96        13.78        26.47        11.41 
TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GQ 
       11.84        29.98         0.10 

$`SF3B2 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       20.22        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        22.98         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 
        0.99         0.99       105.07        12.03        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 
       14.27        16.44         5.92        15.16        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56        11.08         5.52         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  SF3B2 MUTATED SF3B2 WILD-TYPE 
            0.1             0.0 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
          30.97          105.07 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
         12.790          12.605 
[1] "0.1 - 31.0 (12.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D159V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SF3B2 MUTATED         0        1        2        0         3         5
  SF3B2 WILD-TYPE       1        8       25       26        28        39
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SF3B2 MUTATED           0          0          1          1        2
  SF3B2 WILD-TYPE         3         49         35         23       22
D159V3, multiclass
            clus
vv           SF3B2 MUTATED SF3B2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              3              28
  STAGE IIB              5              39
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SF3B2 MUTATED     1   3   4   7
  SF3B2 WILD-TYPE  10  69 118  68
D159V4, multiclass
    clus
vv   SF3B2 MUTATED SF3B2 WILD-TYPE
  T1             1              10
  T2             3              69
  T3             4             118
  T4             7              68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  SF3B2 MUTATED    9  4  2  1
  SF3B2 WILD-TYPE 84 77 48 52
D159V5, multiclass
    clus
vv   SF3B2 MUTATED SF3B2 WILD-TYPE
  N0             9              84
  N1             4              77
  N2             2              48
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V6, binary
                 cls
clus                0   1
  SF3B2 MUTATED    15   1
  SF3B2 WILD-TYPE 242  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B2 MUTATED     15    1
  SF3B2 WILD-TYPE  242   17
   clus
vv  SF3B2 MUTATED SF3B2 WILD-TYPE
  0            15             242
  1             1              17
[1] 2 2
[1] FALSE
D159V7, binary
                 cls
clus                0   1
  SF3B2 MUTATED     9   8
  SF3B2 WILD-TYPE 101 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B2 MUTATED      9    8
  SF3B2 WILD-TYPE  101  171
        clus
vv       SF3B2 MUTATED SF3B2 WILD-TYPE
  FEMALE             9             101
  MALE               8             171
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SF3B2 MUTATED                                       3
  SF3B2 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SF3B2 MUTATED                                                        6
  SF3B2 WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SF3B2 MUTATED                                                                   4
  SF3B2 WILD-TYPE                                                                36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SF3B2 MUTATED                                                  3
  SF3B2 WILD-TYPE                                               35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SF3B2 MUTATED                                                          0
  SF3B2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SF3B2 MUTATED                                                           0
  SF3B2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SF3B2 MUTATED                                          1
  SF3B2 WILD-TYPE                                        2
D159V8, multiclass
                                                                   clus
vv                                                                  SF3B2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  SF3B2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V9, binary
                 cls
clus                0   1
  SF3B2 MUTATED     0  17
  SF3B2 WILD-TYPE   5 267
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B2 MUTATED      0   17
  SF3B2 WILD-TYPE    5  267
     clus
vv    SF3B2 MUTATED SF3B2 WILD-TYPE
  NO              0               5
  YES            17             267
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SF3B2 MUTATED    14   0   0   2
  SF3B2 WILD-TYPE 213  10  10  22
D159V10, multiclass
    clus
vv   SF3B2 MUTATED SF3B2 WILD-TYPE
  R0            14             213
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SF3B2 MUTATED       5                         0     9
  SF3B2 WILD-TYPE    71                         4   159
D159V12, multiclass
                           clus
vv                          SF3B2 MUTATED SF3B2 WILD-TYPE
  ASIAN                                 5              71
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 9             159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(160) Variable = FAM151A MUTATION ANALYSIS
D160V1, survival
                   sevent
clus2                 0   1
  FAM151A MUTATED     3   3
  FAM151A WILD-TYPE 178  77
  FAM151A MUTATED FAM151A WILD-TYPE 
                6               255 
  FAM151A MUTATED FAM151A WILD-TYPE 
                3                77 
$`FAM151A MUTATED`
TCGA-BR-8487 TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5726 TCGA-D7-6524 TCGA-HU-A4H3 
        1.12         6.58         1.02        28.96        17.85        19.36 

$`FAM151A WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6525 
       19.13        20.55        18.84        18.54        18.61        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.25        10.19         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  FAM151A MUTATED FAM151A WILD-TYPE 
             1.02              0.00 
  FAM151A MUTATED FAM151A WILD-TYPE 
            28.96            105.07 
  FAM151A MUTATED FAM151A WILD-TYPE 
           12.215            12.620 
[1] "1.0 - 29.0 (12.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.7"
D160V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM151A MUTATED         1        1        0        1         2         0
  FAM151A WILD-TYPE       0        8       27       25        29        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM151A MUTATED           0          1          0          1        1
  FAM151A WILD-TYPE         3         48         36         23       23
D160V3, multiclass
            clus
vv           FAM151A MUTATED FAM151A WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                 1                 8
  STAGE IB                 0                27
  STAGE II                 1                25
  STAGE IIA                2                29
  STAGE IIB                0                44
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               0                36
  STAGE IIIC               1                23
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM151A MUTATED     2   1   3   2
  FAM151A WILD-TYPE   9  71 119  73
D160V4, multiclass
    clus
vv   FAM151A MUTATED FAM151A WILD-TYPE
  T1               2                 9
  T2               1                71
  T3               3               119
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  FAM151A MUTATED    4  3  1  1
  FAM151A WILD-TYPE 89 78 49 52
D160V5, multiclass
    clus
vv   FAM151A MUTATED FAM151A WILD-TYPE
  N0               4                89
  N1               3                78
  N2               1                49
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V6, binary
                   cls
clus                  0   1
  FAM151A MUTATED     7   1
  FAM151A WILD-TYPE 250  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM151A MUTATED      7    1
  FAM151A WILD-TYPE  250   17
   clus
vv  FAM151A MUTATED FAM151A WILD-TYPE
  0               7               250
  1               1                17
[1] 2 2
[1] FALSE
D160V7, binary
                   cls
clus                  0   1
  FAM151A MUTATED     4   5
  FAM151A WILD-TYPE 106 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM151A MUTATED      4    5
  FAM151A WILD-TYPE  106  174
        clus
vv       FAM151A MUTATED FAM151A WILD-TYPE
  FEMALE               4               106
  MALE                 5               174
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FAM151A MUTATED                                       3
  FAM151A WILD-TYPE                                    47
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAM151A MUTATED                                                        5
  FAM151A WILD-TYPE                                                    130
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAM151A MUTATED                                                                   1
  FAM151A WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FAM151A MUTATED                                                  0
  FAM151A WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FAM151A MUTATED                                                          0
  FAM151A WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FAM151A MUTATED                                                           0
  FAM151A WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FAM151A MUTATED                                          0
  FAM151A WILD-TYPE                                        3
D160V8, multiclass
                                                                   clus
vv                                                                  FAM151A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  FAM151A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V9, binary
                   cls
clus                  0   1
  FAM151A MUTATED     0   9
  FAM151A WILD-TYPE   5 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM151A MUTATED      0    9
  FAM151A WILD-TYPE    5  275
     clus
vv    FAM151A MUTATED FAM151A WILD-TYPE
  NO                0                 5
  YES               9               275
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM151A MUTATED     4   1   1   2
  FAM151A WILD-TYPE 223   9   9  22
D160V10, multiclass
    clus
vv   FAM151A MUTATED FAM151A WILD-TYPE
  R0               4               223
  R1               1                 9
  R2               1                 9
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM151A MUTATED       2                         1     4
  FAM151A WILD-TYPE    74                         3   164
D160V12, multiclass
                           clus
vv                          FAM151A MUTATED FAM151A WILD-TYPE
  ASIAN                                   2                74
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   4               164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(161) Variable = FHDC1 MUTATION ANALYSIS
D161V1, survival
                 sevent
clus2               0   1
  FHDC1 MUTATED     7   4
  FHDC1 WILD-TYPE 174  76
  FHDC1 MUTATED FHDC1 WILD-TYPE 
             11             250 
  FHDC1 MUTATED FHDC1 WILD-TYPE 
              4              76 
$`FHDC1 MUTATED`
TCGA-BR-4201 TCGA-BR-7851 TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8382 TCGA-BR-8591 
       30.90        12.43        14.43        20.55        15.85        13.45 
TCGA-CD-A4MG TCGA-CG-4306 TCGA-D7-5577 TCGA-F1-6874 TCGA-HU-A4G8 
        6.58         1.02        12.36        14.47        11.84 

$`FHDC1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69        12.26         9.60         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        15.81         9.34         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 
       65.10         4.01        69.04        21.07         7.99        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        0.62         7.99        16.24        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  FHDC1 MUTATED FHDC1 WILD-TYPE 
           1.02            0.00 
  FHDC1 MUTATED FHDC1 WILD-TYPE 
          30.90          105.07 
  FHDC1 MUTATED FHDC1 WILD-TYPE 
         13.450          12.605 
[1] "1.0 - 30.9 (13.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D161V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FHDC1 MUTATED         0        0        1        1         1         3
  FHDC1 WILD-TYPE       1        9       26       25        30        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FHDC1 MUTATED           1          2          0          2        1
  FHDC1 WILD-TYPE         2         47         36         22       23
D161V3, multiclass
            clus
vv           FHDC1 MUTATED FHDC1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              3              41
  STAGE III              1               2
  STAGE IIIA             2              47
  STAGE IIIB             0              36
  STAGE IIIC             2              22
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FHDC1 MUTATED     0   4   3   6
  FHDC1 WILD-TYPE  11  68 119  69
D161V4, multiclass
    clus
vv   FHDC1 MUTATED FHDC1 WILD-TYPE
  T1             0              11
  T2             4              68
  T3             3             119
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  FHDC1 MUTATED    5  4  1  3
  FHDC1 WILD-TYPE 88 77 49 50
D161V5, multiclass
    clus
vv   FHDC1 MUTATED FHDC1 WILD-TYPE
  N0             5              88
  N1             4              77
  N2             1              49
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V6, binary
                 cls
clus                0   1
  FHDC1 MUTATED    14   1
  FHDC1 WILD-TYPE 243  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHDC1 MUTATED     14    1
  FHDC1 WILD-TYPE  243   17
   clus
vv  FHDC1 MUTATED FHDC1 WILD-TYPE
  0            14             243
  1             1              17
[1] 2 2
[1] FALSE
D161V7, binary
                 cls
clus                0   1
  FHDC1 MUTATED     7   8
  FHDC1 WILD-TYPE 103 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHDC1 MUTATED      7    8
  FHDC1 WILD-TYPE  103  171
        clus
vv       FHDC1 MUTATED FHDC1 WILD-TYPE
  FEMALE             7             103
  MALE               8             171
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FHDC1 MUTATED                                       2
  FHDC1 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FHDC1 MUTATED                                                        8
  FHDC1 WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FHDC1 MUTATED                                                                   3
  FHDC1 WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FHDC1 MUTATED                                                  1
  FHDC1 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FHDC1 MUTATED                                                          1
  FHDC1 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FHDC1 MUTATED                                                           0
  FHDC1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FHDC1 MUTATED                                          0
  FHDC1 WILD-TYPE                                        3
D161V8, multiclass
                                                                   clus
vv                                                                  FHDC1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  FHDC1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V9, binary
                 cls
clus                0   1
  FHDC1 MUTATED     1  14
  FHDC1 WILD-TYPE   4 270
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHDC1 MUTATED      1   14
  FHDC1 WILD-TYPE    4  270
     clus
vv    FHDC1 MUTATED FHDC1 WILD-TYPE
  NO              1               4
  YES            14             270
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FHDC1 MUTATED     8   0   1   4
  FHDC1 WILD-TYPE 219  10   9  20
D161V10, multiclass
    clus
vv   FHDC1 MUTATED FHDC1 WILD-TYPE
  R0             8             219
  R1             0              10
  R2             1               9
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FHDC1 MUTATED       2                         0    11
  FHDC1 WILD-TYPE    74                         4   157
D161V12, multiclass
                           clus
vv                          FHDC1 MUTATED FHDC1 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                11             157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(162) Variable = FAM46D MUTATION ANALYSIS
D162V1, survival
                  sevent
clus2                0   1
  FAM46D MUTATED     8   1
  FAM46D WILD-TYPE 173  79
  FAM46D MUTATED FAM46D WILD-TYPE 
               9              252 
  FAM46D MUTATED FAM46D WILD-TYPE 
               1               79 
$`FAM46D MUTATED`
TCGA-BR-6453 TCGA-BR-6563 TCGA-BR-8369 TCGA-BR-8485 TCGA-CD-A4MG TCGA-CG-4444 
       15.95        39.12        14.04         9.21         6.58        47.05 
TCGA-CG-5723 TCGA-D7-6822 TCGA-F1-6874 
      105.07        12.33        14.47 

$`FAM46D WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        19.33        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 
        0.26        15.85         3.72         5.39        25.18        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         6.02         0.99        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       15.22        15.98        12.79        10.55        11.31        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 
       14.76         0.62         7.99        16.24        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  FAM46D MUTATED FAM46D WILD-TYPE 
            6.58             0.00 
  FAM46D MUTATED FAM46D WILD-TYPE 
          105.07            79.07 
  FAM46D MUTATED FAM46D WILD-TYPE 
          14.470           12.575 
[1] "6.6 - 105.1 (14.5)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "5.6"
D162V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM46D MUTATED         0        0        2        1         2         1
  FAM46D WILD-TYPE       1        9       25       25        29        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM46D MUTATED           0          1          1          1        0
  FAM46D WILD-TYPE         3         48         35         23       24
D162V3, multiclass
            clus
vv           FAM46D MUTATED FAM46D WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                2               25
  STAGE II                1               25
  STAGE IIA               2               29
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              1               23
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM46D MUTATED     0   5   3   1
  FAM46D WILD-TYPE  11  67 119  74
D162V4, multiclass
    clus
vv   FAM46D MUTATED FAM46D WILD-TYPE
  T1              0               11
  T2              5               67
  T3              3              119
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  FAM46D MUTATED    3  3  1  2
  FAM46D WILD-TYPE 90 78 49 51
D162V5, multiclass
    clus
vv   FAM46D MUTATED FAM46D WILD-TYPE
  N0              3               90
  N1              3               78
  N2              1               49
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V6, binary
                  cls
clus                 0   1
  FAM46D MUTATED     9   0
  FAM46D WILD-TYPE 248  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM46D MUTATED      9    0
  FAM46D WILD-TYPE  248   18
   clus
vv  FAM46D MUTATED FAM46D WILD-TYPE
  0              9              248
  1              0               18
[1] 2 2
[1] FALSE
D162V7, binary
                  cls
clus                 0   1
  FAM46D MUTATED     2   7
  FAM46D WILD-TYPE 108 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM46D MUTATED      2    7
  FAM46D WILD-TYPE  108  172
        clus
vv       FAM46D MUTATED FAM46D WILD-TYPE
  FEMALE              2              108
  MALE                7              172
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FAM46D MUTATED                                       2
  FAM46D WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAM46D MUTATED                                                        5
  FAM46D WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAM46D MUTATED                                                                   1
  FAM46D WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FAM46D MUTATED                                                  1
  FAM46D WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FAM46D MUTATED                                                          0
  FAM46D WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FAM46D MUTATED                                                           0
  FAM46D WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FAM46D MUTATED                                          0
  FAM46D WILD-TYPE                                        3
D162V8, multiclass
                                                                   clus
vv                                                                  FAM46D MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  FAM46D WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V9, binary
                  cls
clus                 0   1
  FAM46D MUTATED     0   9
  FAM46D WILD-TYPE   5 275
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM46D MUTATED      0    9
  FAM46D WILD-TYPE    5  275
     clus
vv    FAM46D MUTATED FAM46D WILD-TYPE
  NO               0                5
  YES              9              275
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FAM46D MUTATED     8   0   0   0
  FAM46D WILD-TYPE 219  10  10  24
D162V10, multiclass
    clus
vv   FAM46D MUTATED FAM46D WILD-TYPE
  R0              8              219
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM46D MUTATED       1                         0     6
  FAM46D WILD-TYPE    75                         4   162
D162V12, multiclass
                           clus
vv                          FAM46D MUTATED FAM46D WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(163) Variable = TLE2 MUTATION ANALYSIS
D163V1, survival
                sevent
clus2              0   1
  TLE2 MUTATED    15   2
  TLE2 WILD-TYPE 166  78
  TLE2 MUTATED TLE2 WILD-TYPE 
            17            244 
  TLE2 MUTATED TLE2 WILD-TYPE 
             2             78 
$`TLE2 MUTATED`
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7851 
       34.68        32.78        32.94        24.76        23.93        12.43 
TCGA-BR-8366 TCGA-BR-A4QL TCGA-CD-A48A TCGA-CD-A4MG TCGA-CG-4305 TCGA-F1-A448 
        0.95        11.57        12.43         6.58        15.95        21.27 
TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.08        11.41        29.98         0.10         6.51 

$`TLE2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 
       30.90        31.20        12.82         9.21        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       16.24        14.47        72.23         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        5.52        26.47         5.92        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       24.20         3.25        22.75        25.81        11.77         8.98 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  TLE2 MUTATED TLE2 WILD-TYPE 
           0.1            0.0 
  TLE2 MUTATED TLE2 WILD-TYPE 
         34.68         105.07 
  TLE2 MUTATED TLE2 WILD-TYPE 
         12.43          12.64 
[1] "0.1 - 34.7 (12.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "3.5"
D163V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TLE2 MUTATED         0        1        1        1         9         2
  TLE2 WILD-TYPE       1        8       26       25        22        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TLE2 MUTATED           0          0          2          1        0
  TLE2 WILD-TYPE         3         49         34         23       24
D163V3, multiclass
            clus
vv           TLE2 MUTATED TLE2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              1             26
  STAGE II              1             25
  STAGE IIA             9             22
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            2             34
  STAGE IIIC            1             23
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TLE2 MUTATED     1   3  10   3
  TLE2 WILD-TYPE  10  69 112  72
D163V4, multiclass
    clus
vv   TLE2 MUTATED TLE2 WILD-TYPE
  T1            1             10
  T2            3             69
  T3           10            112
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  TLE2 MUTATED   12  3  1  2
  TLE2 WILD-TYPE 81 78 49 51
D163V5, multiclass
    clus
vv   TLE2 MUTATED TLE2 WILD-TYPE
  N0           12             81
  N1            3             78
  N2            1             49
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V6, binary
                cls
clus               0   1
  TLE2 MUTATED    19   0
  TLE2 WILD-TYPE 238  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLE2 MUTATED     19    0
  TLE2 WILD-TYPE  238   18
   clus
vv  TLE2 MUTATED TLE2 WILD-TYPE
  0           19            238
  1            0             18
[1] 2 2
[1] FALSE
D163V7, binary
                cls
clus               0   1
  TLE2 MUTATED     9  10
  TLE2 WILD-TYPE 101 169
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLE2 MUTATED      9   10
  TLE2 WILD-TYPE  101  169
        clus
vv       TLE2 MUTATED TLE2 WILD-TYPE
  FEMALE            9            101
  MALE             10            169
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TLE2 MUTATED                                       2
  TLE2 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TLE2 MUTATED                                                       11
  TLE2 WILD-TYPE                                                    124
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TLE2 MUTATED                                                                   1
  TLE2 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TLE2 MUTATED                                                  3
  TLE2 WILD-TYPE                                               35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TLE2 MUTATED                                                          1
  TLE2 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TLE2 MUTATED                                                           1
  TLE2 WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TLE2 MUTATED                                          0
  TLE2 WILD-TYPE                                        3
D163V8, multiclass
                                                                   clus
vv                                                                  TLE2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  TLE2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V9, binary
                cls
clus               0   1
  TLE2 MUTATED     0  19
  TLE2 WILD-TYPE   5 265
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLE2 MUTATED      0   19
  TLE2 WILD-TYPE    5  265
     clus
vv    TLE2 MUTATED TLE2 WILD-TYPE
  NO             0              5
  YES           19            265
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TLE2 MUTATED    15   0   0   2
  TLE2 WILD-TYPE 212  10  10  22
D163V10, multiclass
    clus
vv   TLE2 MUTATED TLE2 WILD-TYPE
  R0           15            212
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TLE2 MUTATED       6                         1    11
  TLE2 WILD-TYPE    70                         3   157
D163V12, multiclass
                           clus
vv                          TLE2 MUTATED TLE2 WILD-TYPE
  ASIAN                                6             70
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                               11            157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(164) Variable = HOXD8 MUTATION ANALYSIS
D164V1, survival
                 sevent
clus2               0   1
  HOXD8 MUTATED     4   3
  HOXD8 WILD-TYPE 177  77
  HOXD8 MUTATED HOXD8 WILD-TYPE 
              7             254 
  HOXD8 MUTATED HOXD8 WILD-TYPE 
              3              77 
$`HOXD8 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8360 TCGA-CG-4306 TCGA-CG-5721 
       30.90        34.68        32.94         6.18         1.02         6.02 
TCGA-IN-8663 
        3.39 

$`HOXD8 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       18.35         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        2.66        16.31         2.20        15.58         7.40        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IP-7968 
       18.81         2.53 

  HOXD8 MUTATED HOXD8 WILD-TYPE 
           1.02            0.00 
  HOXD8 MUTATED HOXD8 WILD-TYPE 
          34.68          105.07 
  HOXD8 MUTATED HOXD8 WILD-TYPE 
           6.18           12.64 
[1] "1.0 - 34.7 (6.2)"   "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D164V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HOXD8 MUTATED         0        0        0        0         3         1
  HOXD8 WILD-TYPE       1        9       27       26        28        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HOXD8 MUTATED           0          0          0          0        2
  HOXD8 WILD-TYPE         3         49         36         24       22
D164V3, multiclass
            clus
vv           HOXD8 MUTATED HOXD8 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              3              28
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HOXD8 MUTATED     0   2   4   1
  HOXD8 WILD-TYPE  11  70 118  74
D164V4, multiclass
    clus
vv   HOXD8 MUTATED HOXD8 WILD-TYPE
  T1             0              11
  T2             2              70
  T3             4             118
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  HOXD8 MUTATED    3  1  2  0
  HOXD8 WILD-TYPE 90 80 48 53
D164V5, multiclass
    clus
vv   HOXD8 MUTATED HOXD8 WILD-TYPE
  N0             3              90
  N1             1              80
  N2             2              48
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V6, binary
                 cls
clus                0   1
  HOXD8 MUTATED     6   1
  HOXD8 WILD-TYPE 251  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXD8 MUTATED      6    1
  HOXD8 WILD-TYPE  251   17
   clus
vv  HOXD8 MUTATED HOXD8 WILD-TYPE
  0             6             251
  1             1              17
[1] 2 2
[1] FALSE
D164V7, binary
                 cls
clus                0   1
  HOXD8 MUTATED     3   4
  HOXD8 WILD-TYPE 107 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXD8 MUTATED      3    4
  HOXD8 WILD-TYPE  107  175
        clus
vv       HOXD8 MUTATED HOXD8 WILD-TYPE
  FEMALE             3             107
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  HOXD8 MUTATED                                       0
  HOXD8 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HOXD8 MUTATED                                                        5
  HOXD8 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HOXD8 MUTATED                                                                   2
  HOXD8 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  HOXD8 MUTATED                                                  0
  HOXD8 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  HOXD8 MUTATED                                                          0
  HOXD8 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  HOXD8 MUTATED                                                           0
  HOXD8 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  HOXD8 MUTATED                                          0
  HOXD8 WILD-TYPE                                        3
D164V8, multiclass
                                                                   clus
vv                                                                  HOXD8 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  HOXD8 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V9, binary
                 cls
clus                0   1
  HOXD8 MUTATED     0   7
  HOXD8 WILD-TYPE   5 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXD8 MUTATED      0    7
  HOXD8 WILD-TYPE    5  277
     clus
vv    HOXD8 MUTATED HOXD8 WILD-TYPE
  NO              0               5
  YES             7             277
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HOXD8 MUTATED     5   0   1   1
  HOXD8 WILD-TYPE 222  10   9  23
D164V10, multiclass
    clus
vv   HOXD8 MUTATED HOXD8 WILD-TYPE
  R0             5             222
  R1             0              10
  R2             1               9
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HOXD8 MUTATED       0                         0     5
  HOXD8 WILD-TYPE    76                         4   163
D164V12, multiclass
                           clus
vv                          HOXD8 MUTATED HOXD8 WILD-TYPE
  ASIAN                                 0              76
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(165) Variable = ZIM3 MUTATION ANALYSIS
D165V1, survival
                sevent
clus2              0   1
  ZIM3 MUTATED     3   5
  ZIM3 WILD-TYPE 178  75
  ZIM3 MUTATED ZIM3 WILD-TYPE 
             8            253 
  ZIM3 MUTATED ZIM3 WILD-TYPE 
             5             75 
$`ZIM3 MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6802 TCGA-BR-8059 TCGA-BR-8284 TCGA-CG-5723 
        6.97         6.61        30.90        14.43         8.05       105.07 
TCGA-CG-5726 TCGA-HU-A4GH 
       28.96        11.77 

$`ZIM3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 
        3.45         9.07        12.76        18.71        17.49         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       12.26         9.60        20.55        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN 
       11.84        24.20         3.25        22.75        25.81        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  ZIM3 MUTATED ZIM3 WILD-TYPE 
          6.61           0.00 
  ZIM3 MUTATED ZIM3 WILD-TYPE 
        105.07          79.07 
  ZIM3 MUTATED ZIM3 WILD-TYPE 
         13.10          12.62 
[1] "6.6 - 105.1 (13.1)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.2"
D165V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZIM3 MUTATED         0        2        1        1         0         0
  ZIM3 WILD-TYPE       1        7       26       25        31        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZIM3 MUTATED           2          2          0          1        1
  ZIM3 WILD-TYPE         1         47         36         23       23
D165V3, multiclass
            clus
vv           ZIM3 MUTATED ZIM3 WILD-TYPE
  STAGE I               0              1
  STAGE IA              2              7
  STAGE IB              1             26
  STAGE II              1             25
  STAGE IIA             0             31
  STAGE IIB             0             44
  STAGE III             2              1
  STAGE IIIA            2             47
  STAGE IIIB            0             36
  STAGE IIIC            1             23
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ZIM3 MUTATED     2   3   2   3
  ZIM3 WILD-TYPE   9  69 120  72
D165V4, multiclass
    clus
vv   ZIM3 MUTATED ZIM3 WILD-TYPE
  T1            2              9
  T2            3             69
  T3            2            120
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  ZIM3 MUTATED    3  4  2  1
  ZIM3 WILD-TYPE 90 77 48 52
D165V5, multiclass
    clus
vv   ZIM3 MUTATED ZIM3 WILD-TYPE
  N0            3             90
  N1            4             77
  N2            2             48
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D165V6, binary
                cls
clus               0   1
  ZIM3 MUTATED     9   0
  ZIM3 WILD-TYPE 248  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZIM3 MUTATED      9    0
  ZIM3 WILD-TYPE  248   18
   clus
vv  ZIM3 MUTATED ZIM3 WILD-TYPE
  0            9            248
  1            0             18
[1] 2 2
[1] FALSE
D165V7, binary
                cls
clus               0   1
  ZIM3 MUTATED     3   7
  ZIM3 WILD-TYPE 107 172
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZIM3 MUTATED      3    7
  ZIM3 WILD-TYPE  107  172
        clus
vv       ZIM3 MUTATED ZIM3 WILD-TYPE
  FEMALE            3            107
  MALE              7            172
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZIM3 MUTATED                                       0
  ZIM3 WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZIM3 MUTATED                                                        5
  ZIM3 WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZIM3 MUTATED                                                                   4
  ZIM3 WILD-TYPE                                                                36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZIM3 MUTATED                                                  1
  ZIM3 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZIM3 MUTATED                                                          0
  ZIM3 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZIM3 MUTATED                                                           0
  ZIM3 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZIM3 MUTATED                                          0
  ZIM3 WILD-TYPE                                        3
D165V8, multiclass
                                                                   clus
vv                                                                  ZIM3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  ZIM3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D165V9, binary
                cls
clus               0   1
  ZIM3 MUTATED     0  10
  ZIM3 WILD-TYPE   5 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZIM3 MUTATED      0   10
  ZIM3 WILD-TYPE    5  274
     clus
vv    ZIM3 MUTATED ZIM3 WILD-TYPE
  NO             0              5
  YES           10            274
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ZIM3 MUTATED     7   0   0   3
  ZIM3 WILD-TYPE 220  10  10  21
D165V10, multiclass
    clus
vv   ZIM3 MUTATED ZIM3 WILD-TYPE
  R0            7            220
  R1            0             10
  R2            0             10
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D165V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZIM3 MUTATED       1                         0     6
  ZIM3 WILD-TYPE    75                         4   162
D165V12, multiclass
                           clus
vv                          ZIM3 MUTATED ZIM3 WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                6            162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(166) Variable = DDX60 MUTATION ANALYSIS
D166V1, survival
                 sevent
clus2               0   1
  DDX60 MUTATED     6   3
  DDX60 WILD-TYPE 175  77
  DDX60 MUTATED DDX60 WILD-TYPE 
              9             252 
  DDX60 MUTATED DDX60 WILD-TYPE 
              3              77 
$`DDX60 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8591 TCGA-BR-8680 TCGA-CG-5721 
        6.97        30.90        34.68        13.45        15.81         6.02 
TCGA-CG-5728 TCGA-HJ-7597 TCGA-HU-A4G9 
       65.10        26.47        24.20 

$`DDX60 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.52         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  DDX60 MUTATED DDX60 WILD-TYPE 
           6.02            0.00 
  DDX60 MUTATED DDX60 WILD-TYPE 
          65.10          105.07 
  DDX60 MUTATED DDX60 WILD-TYPE 
         24.200          12.495 
[1] "6.0 - 65.1 (24.2)"  "0.0 - 105.1 (12.5)"
[1] "hr=" "1.6"
D166V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDX60 MUTATED         0        1        2        0         1         0
  DDX60 WILD-TYPE       1        8       25       26        30        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DDX60 MUTATED           0          1          0          1        2
  DDX60 WILD-TYPE         3         48         36         23       22
D166V3, multiclass
            clus
vv           DDX60 MUTATED DDX60 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDX60 MUTATED     1   3   2   3
  DDX60 WILD-TYPE  10  69 120  72
D166V4, multiclass
    clus
vv   DDX60 MUTATED DDX60 WILD-TYPE
  T1             1              10
  T2             3              69
  T3             2             120
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  DDX60 MUTATED    4  2  1  1
  DDX60 WILD-TYPE 89 79 49 52
D166V5, multiclass
    clus
vv   DDX60 MUTATED DDX60 WILD-TYPE
  N0             4              89
  N1             2              79
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V6, binary
                 cls
clus                0   1
  DDX60 MUTATED     7   1
  DDX60 WILD-TYPE 250  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX60 MUTATED      7    1
  DDX60 WILD-TYPE  250   17
   clus
vv  DDX60 MUTATED DDX60 WILD-TYPE
  0             7             250
  1             1              17
[1] 2 2
[1] FALSE
D166V7, binary
                 cls
clus                0   1
  DDX60 MUTATED     6   4
  DDX60 WILD-TYPE 104 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX60 MUTATED      6    4
  DDX60 WILD-TYPE  104  175
        clus
vv       DDX60 MUTATED DDX60 WILD-TYPE
  FEMALE             6             104
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DDX60 MUTATED                                       0
  DDX60 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DDX60 MUTATED                                                        5
  DDX60 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DDX60 MUTATED                                                                   2
  DDX60 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DDX60 MUTATED                                                  2
  DDX60 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DDX60 MUTATED                                                          0
  DDX60 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DDX60 MUTATED                                                           0
  DDX60 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DDX60 MUTATED                                          1
  DDX60 WILD-TYPE                                        2
D166V8, multiclass
                                                                   clus
vv                                                                  DDX60 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  DDX60 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V9, binary
                 cls
clus                0   1
  DDX60 MUTATED     0  10
  DDX60 WILD-TYPE   5 274
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX60 MUTATED      0   10
  DDX60 WILD-TYPE    5  274
     clus
vv    DDX60 MUTATED DDX60 WILD-TYPE
  NO              0               5
  YES            10             274
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DDX60 MUTATED     7   0   0   3
  DDX60 WILD-TYPE 220  10  10  21
D166V10, multiclass
    clus
vv   DDX60 MUTATED DDX60 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDX60 MUTATED       2                         0     6
  DDX60 WILD-TYPE    74                         4   162
D166V12, multiclass
                           clus
vv                          DDX60 MUTATED DDX60 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(167) Variable = BEND3 MUTATION ANALYSIS
D167V1, survival
                 sevent
clus2               0   1
  BEND3 MUTATED     7   2
  BEND3 WILD-TYPE 174  78
  BEND3 MUTATED BEND3 WILD-TYPE 
              9             252 
  BEND3 MUTATED BEND3 WILD-TYPE 
              2              78 
$`BEND3 MUTATED`
TCGA-BR-8363 TCGA-BR-8487 TCGA-CD-8536 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5733 
        0.26         1.12         0.10         6.02       105.07        21.07 
TCGA-D7-5579 TCGA-D7-6528 TCGA-HU-A4GT 
       11.93        15.22         6.51 

$`BEND3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40         6.18        19.50        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        7.99        12.36        12.66        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  BEND3 MUTATED BEND3 WILD-TYPE 
            0.1             0.0 
  BEND3 MUTATED BEND3 WILD-TYPE 
         105.07           79.07 
  BEND3 MUTATED BEND3 WILD-TYPE 
           6.51           12.71 
[1] "0.1 - 105.1 (6.5)" "0.0 - 79.1 (12.7)"
[1] "hr=" "1.6"
D167V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BEND3 MUTATED         0        0        3        2         2         0
  BEND3 WILD-TYPE       1        9       24       24        29        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BEND3 MUTATED           0          2          0          0        2
  BEND3 WILD-TYPE         3         47         36         24       22
D167V3, multiclass
            clus
vv           BEND3 MUTATED BEND3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               3              24
  STAGE II               2              24
  STAGE IIA              2              29
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BEND3 MUTATED     0   5   4   2
  BEND3 WILD-TYPE  11  67 118  73
D167V4, multiclass
    clus
vv   BEND3 MUTATED BEND3 WILD-TYPE
  T1             0              11
  T2             5              67
  T3             4             118
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  BEND3 MUTATED    6  2  3  0
  BEND3 WILD-TYPE 87 79 47 53
D167V5, multiclass
    clus
vv   BEND3 MUTATED BEND3 WILD-TYPE
  N0             6              87
  N1             2              79
  N2             3              47
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D167V6, binary
                 cls
clus                0   1
  BEND3 MUTATED    12   0
  BEND3 WILD-TYPE 245  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND3 MUTATED     12    0
  BEND3 WILD-TYPE  245   18
   clus
vv  BEND3 MUTATED BEND3 WILD-TYPE
  0            12             245
  1             0              18
[1] 2 2
[1] FALSE
D167V7, binary
                 cls
clus                0   1
  BEND3 MUTATED     7   5
  BEND3 WILD-TYPE 103 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND3 MUTATED      7    5
  BEND3 WILD-TYPE  103  174
        clus
vv       BEND3 MUTATED BEND3 WILD-TYPE
  FEMALE             7             103
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  BEND3 MUTATED                                       0
  BEND3 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BEND3 MUTATED                                                        6
  BEND3 WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BEND3 MUTATED                                                                   3
  BEND3 WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  BEND3 MUTATED                                                  2
  BEND3 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  BEND3 MUTATED                                                          1
  BEND3 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  BEND3 MUTATED                                                           0
  BEND3 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  BEND3 MUTATED                                          0
  BEND3 WILD-TYPE                                        3
D167V8, multiclass
                                                                   clus
vv                                                                  BEND3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  BEND3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D167V9, binary
                 cls
clus                0   1
  BEND3 MUTATED     0  12
  BEND3 WILD-TYPE   5 272
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND3 MUTATED      0   12
  BEND3 WILD-TYPE    5  272
     clus
vv    BEND3 MUTATED BEND3 WILD-TYPE
  NO              0               5
  YES            12             272
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BEND3 MUTATED     9   1   0   2
  BEND3 WILD-TYPE 218   9  10  22
D167V10, multiclass
    clus
vv   BEND3 MUTATED BEND3 WILD-TYPE
  R0             9             218
  R1             1               9
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D167V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BEND3 MUTATED       2                         0     6
  BEND3 WILD-TYPE    74                         4   162
D167V12, multiclass
                           clus
vv                          BEND3 MUTATED BEND3 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(168) Variable = EIF4G3 MUTATION ANALYSIS
D168V1, survival
                  sevent
clus2                0   1
  EIF4G3 MUTATED    10   5
  EIF4G3 WILD-TYPE 171  75
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
              15              246 
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
               5               75 
$`EIF4G3 MUTATED`
TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8289 TCGA-BR-8363 TCGA-BR-8372 
       11.70        34.68        12.26         2.66         0.26        19.17 
TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4465 
        1.12        13.45        15.81        11.57         6.58         9.01 
TCGA-CG-5733 TCGA-FP-A4BE TCGA-HU-A4GH 
       21.07        11.08        11.77 

$`EIF4G3 WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        9.34         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       28.96        79.07        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        22.75        25.81        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
            0.26             0.00 
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
           34.68           105.07 
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
          11.700           12.775 
[1] "0.3 - 34.7 (11.7)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.3"
D168V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EIF4G3 MUTATED         0        1        2        0         4         1
  EIF4G3 WILD-TYPE       1        8       25       26        27        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF4G3 MUTATED           0          1          1          2        3
  EIF4G3 WILD-TYPE         3         48         35         22       21
D168V3, multiclass
            clus
vv           EIF4G3 MUTATED EIF4G3 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                2               25
  STAGE II                0               26
  STAGE IIA               4               27
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              2               22
  STAGE IV                3               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EIF4G3 MUTATED     1   3   5   6
  EIF4G3 WILD-TYPE  10  69 117  69
D168V4, multiclass
    clus
vv   EIF4G3 MUTATED EIF4G3 WILD-TYPE
  T1              1               10
  T2              3               69
  T3              5              117
  T4              6               69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  EIF4G3 MUTATED    8  0  2  5
  EIF4G3 WILD-TYPE 85 81 48 48
D168V5, multiclass
    clus
vv   EIF4G3 MUTATED EIF4G3 WILD-TYPE
  N0              8               85
  N1              0               81
  N2              2               48
  N3              5               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V6, binary
                  cls
clus                 0   1
  EIF4G3 MUTATED    12   3
  EIF4G3 WILD-TYPE 245  15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G3 MUTATED     12    3
  EIF4G3 WILD-TYPE  245   15
   clus
vv  EIF4G3 MUTATED EIF4G3 WILD-TYPE
  0             12              245
  1              3               15
[1] 2 2
[1] FALSE
D168V7, binary
                  cls
clus                 0   1
  EIF4G3 MUTATED     7   8
  EIF4G3 WILD-TYPE 103 171
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G3 MUTATED      7    8
  EIF4G3 WILD-TYPE  103  171
        clus
vv       EIF4G3 MUTATED EIF4G3 WILD-TYPE
  FEMALE              7              103
  MALE                8              171
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  EIF4G3 MUTATED                                       3
  EIF4G3 WILD-TYPE                                    47
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EIF4G3 MUTATED                                                        8
  EIF4G3 WILD-TYPE                                                    127
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EIF4G3 MUTATED                                                                   2
  EIF4G3 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  EIF4G3 MUTATED                                                  2
  EIF4G3 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  EIF4G3 MUTATED                                                          0
  EIF4G3 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  EIF4G3 MUTATED                                                           0
  EIF4G3 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  EIF4G3 MUTATED                                          0
  EIF4G3 WILD-TYPE                                        3
D168V8, multiclass
                                                                   clus
vv                                                                  EIF4G3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  EIF4G3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V9, binary
                  cls
clus                 0   1
  EIF4G3 MUTATED     0  15
  EIF4G3 WILD-TYPE   5 269
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G3 MUTATED      0   15
  EIF4G3 WILD-TYPE    5  269
     clus
vv    EIF4G3 MUTATED EIF4G3 WILD-TYPE
  NO               0                5
  YES             15              269
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  EIF4G3 MUTATED    13   0   1   0
  EIF4G3 WILD-TYPE 214  10   9  24
D168V10, multiclass
    clus
vv   EIF4G3 MUTATED EIF4G3 WILD-TYPE
  R0             13              214
  R1              0               10
  R2              1                9
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EIF4G3 MUTATED       3                         1     9
  EIF4G3 WILD-TYPE    73                         3   159
D168V12, multiclass
                           clus
vv                          EIF4G3 MUTATED EIF4G3 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  9              159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(169) Variable = MFRP MUTATION ANALYSIS
D169V1, survival
                sevent
clus2              0   1
  MFRP MUTATED     9   2
  MFRP WILD-TYPE 172  78
  MFRP MUTATED MFRP WILD-TYPE 
            11            250 
  MFRP MUTATED MFRP WILD-TYPE 
             2             78 
$`MFRP MUTATED`
TCGA-BR-6452 TCGA-BR-7851 TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8680 
       34.68        12.43        20.55        19.50         1.12        15.81 
TCGA-BR-A4J4 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4306 TCGA-HU-A4GU 
        0.53        11.57         6.58         1.02         6.25 

$`MFRP WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69        12.26         9.60         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       14.17         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  MFRP MUTATED MFRP WILD-TYPE 
          0.53           0.00 
  MFRP MUTATED MFRP WILD-TYPE 
         34.68         105.07 
  MFRP MUTATED MFRP WILD-TYPE 
         11.57          12.71 
[1] "0.5 - 34.7 (11.6)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.4"
D169V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MFRP MUTATED         0        0        0        0         3         3
  MFRP WILD-TYPE       1        9       27       26        28        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MFRP MUTATED           0          0          2          1        2
  MFRP WILD-TYPE         3         49         34         23       22
D169V3, multiclass
            clus
vv           MFRP MUTATED MFRP WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              0             26
  STAGE IIA             3             28
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            2             34
  STAGE IIIC            1             23
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MFRP MUTATED     0   0   6   5
  MFRP WILD-TYPE  11  72 116  70
D169V4, multiclass
    clus
vv   MFRP MUTATED MFRP WILD-TYPE
  T1            0             11
  T2            0             72
  T3            6            116
  T4            5             70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  MFRP MUTATED    5  1  4  1
  MFRP WILD-TYPE 88 80 46 52
D169V5, multiclass
    clus
vv   MFRP MUTATED MFRP WILD-TYPE
  N0            5             88
  N1            1             80
  N2            4             46
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D169V6, binary
                cls
clus               0   1
  MFRP MUTATED     9   2
  MFRP WILD-TYPE 248  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFRP MUTATED      9    2
  MFRP WILD-TYPE  248   16
   clus
vv  MFRP MUTATED MFRP WILD-TYPE
  0            9            248
  1            2             16
[1] 2 2
[1] FALSE
D169V7, binary
                cls
clus               0   1
  MFRP MUTATED     5   6
  MFRP WILD-TYPE 105 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFRP MUTATED      5    6
  MFRP WILD-TYPE  105  173
        clus
vv       MFRP MUTATED MFRP WILD-TYPE
  FEMALE            5            105
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MFRP MUTATED                                       2
  MFRP WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MFRP MUTATED                                                        7
  MFRP WILD-TYPE                                                    128
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MFRP MUTATED                                                                   1
  MFRP WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MFRP MUTATED                                                  1
  MFRP WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MFRP MUTATED                                                          0
  MFRP WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MFRP MUTATED                                                           0
  MFRP WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MFRP MUTATED                                          0
  MFRP WILD-TYPE                                        3
D169V8, multiclass
                                                                   clus
vv                                                                  MFRP MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  MFRP WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D169V9, binary
                cls
clus               0   1
  MFRP MUTATED     0  11
  MFRP WILD-TYPE   5 273
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFRP MUTATED      0   11
  MFRP WILD-TYPE    5  273
     clus
vv    MFRP MUTATED MFRP WILD-TYPE
  NO             0              5
  YES           11            273
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MFRP MUTATED     9   0   1   0
  MFRP WILD-TYPE 218  10   9  24
D169V10, multiclass
    clus
vv   MFRP MUTATED MFRP WILD-TYPE
  R0            9            218
  R1            0             10
  R2            1              9
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D169V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MFRP MUTATED       4                         0     6
  MFRP WILD-TYPE    72                         4   162
D169V12, multiclass
                           clus
vv                          MFRP MUTATED MFRP WILD-TYPE
  ASIAN                                4             72
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                6            162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(170) Variable = EIF5B MUTATION ANALYSIS
D170V1, survival
                 sevent
clus2               0   1
  EIF5B MUTATED    12   3
  EIF5B WILD-TYPE 169  77
  EIF5B MUTATED EIF5B WILD-TYPE 
             15             246 
  EIF5B MUTATED EIF5B WILD-TYPE 
              3              77 
$`EIF5B MUTATED`
TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8372 TCGA-BR-8589 TCGA-BR-8680 
        6.97        32.94        12.26        19.17        15.81        15.81 
TCGA-BR-A4QL TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-6525 TCGA-F1-6874 
       11.57         6.02        28.96        65.10        13.35        14.47 
TCGA-HU-8602 TCGA-HU-A4GT TCGA-HU-A4GX 
       11.41         6.51        10.19 

$`EIF5B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5730 
        0.99         0.99       105.07        12.03        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       16.24        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         0.10         6.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  EIF5B MUTATED EIF5B WILD-TYPE 
           6.02            0.00 
  EIF5B MUTATED EIF5B WILD-TYPE 
          65.10          105.07 
  EIF5B MUTATED EIF5B WILD-TYPE 
         13.350          12.605 
[1] "6.0 - 65.1 (13.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2"  
D170V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EIF5B MUTATED         0        1        2        0         2         2
  EIF5B WILD-TYPE       1        8       25       26        29        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF5B MUTATED           0          2          2          2        2
  EIF5B WILD-TYPE         3         47         34         22       22
D170V3, multiclass
            clus
vv           EIF5B MUTATED EIF5B WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             2              34
  STAGE IIIC             2              22
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EIF5B MUTATED     2   3   4   7
  EIF5B WILD-TYPE   9  69 118  68
D170V4, multiclass
    clus
vv   EIF5B MUTATED EIF5B WILD-TYPE
  T1             2               9
  T2             3              69
  T3             4             118
  T4             7              68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  EIF5B MUTATED    7  4  3  2
  EIF5B WILD-TYPE 86 77 47 51
D170V5, multiclass
    clus
vv   EIF5B MUTATED EIF5B WILD-TYPE
  N0             7              86
  N1             4              77
  N2             3              47
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D170V6, binary
                 cls
clus                0   1
  EIF5B MUTATED    16   1
  EIF5B WILD-TYPE 241  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED     16    1
  EIF5B WILD-TYPE  241   17
   clus
vv  EIF5B MUTATED EIF5B WILD-TYPE
  0            16             241
  1             1              17
[1] 2 2
[1] FALSE
D170V7, binary
                 cls
clus                0   1
  EIF5B MUTATED    10   8
  EIF5B WILD-TYPE 100 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED     10    8
  EIF5B WILD-TYPE  100  171
        clus
vv       EIF5B MUTATED EIF5B WILD-TYPE
  FEMALE            10             100
  MALE               8             171
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  EIF5B MUTATED                                       3
  EIF5B WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EIF5B MUTATED                                                        9
  EIF5B WILD-TYPE                                                    126
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EIF5B MUTATED                                                                   4
  EIF5B WILD-TYPE                                                                36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  EIF5B MUTATED                                                  2
  EIF5B WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  EIF5B MUTATED                                                          0
  EIF5B WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  EIF5B MUTATED                                                           0
  EIF5B WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  EIF5B MUTATED                                          0
  EIF5B WILD-TYPE                                        3
D170V8, multiclass
                                                                   clus
vv                                                                  EIF5B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  EIF5B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D170V9, binary
                 cls
clus                0   1
  EIF5B MUTATED     0  18
  EIF5B WILD-TYPE   5 266
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED      0   18
  EIF5B WILD-TYPE    5  266
     clus
vv    EIF5B MUTATED EIF5B WILD-TYPE
  NO              0               5
  YES            18             266
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EIF5B MUTATED    14   0   0   4
  EIF5B WILD-TYPE 213  10  10  20
D170V10, multiclass
    clus
vv   EIF5B MUTATED EIF5B WILD-TYPE
  R0            14             213
  R1             0              10
  R2             0              10
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D170V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EIF5B MUTATED       4                         0    11
  EIF5B WILD-TYPE    72                         4   157
D170V12, multiclass
                           clus
vv                          EIF5B MUTATED EIF5B WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                11             157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(171) Variable = FANCE MUTATION ANALYSIS
D171V1, survival
                 sevent
clus2               0   1
  FANCE MUTATED     4   2
  FANCE WILD-TYPE 177  78
  FANCE MUTATED FANCE WILD-TYPE 
              6             255 
  FANCE MUTATED FANCE WILD-TYPE 
              2              78 
$`FANCE MUTATED`
TCGA-BR-4184 TCGA-BR-8382 TCGA-CG-5723 TCGA-CG-5733 TCGA-FP-A4BE TCGA-HU-A4G8 
        6.97        15.85       105.07        21.07        11.08        11.84 

$`FANCE WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       19.17        14.79         0.26         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  FANCE MUTATED FANCE WILD-TYPE 
           6.97            0.00 
  FANCE MUTATED FANCE WILD-TYPE 
         105.07           79.07 
  FANCE MUTATED FANCE WILD-TYPE 
         13.845          12.620 
[1] "7.0 - 105.1 (13.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.6"
D171V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FANCE MUTATED         0        0        0        1         1         1
  FANCE WILD-TYPE       1        9       27       25        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FANCE MUTATED           0          3          0          1        0
  FANCE WILD-TYPE         3         46         36         23       24
D171V3, multiclass
            clus
vv           FANCE MUTATED FANCE WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             3              46
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FANCE MUTATED     0   2   3   2
  FANCE WILD-TYPE  11  70 119  73
D171V4, multiclass
    clus
vv   FANCE MUTATED FANCE WILD-TYPE
  T1             0              11
  T2             2              70
  T3             3             119
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  FANCE MUTATED    2  3  1  1
  FANCE WILD-TYPE 91 78 49 52
D171V5, multiclass
    clus
vv   FANCE MUTATED FANCE WILD-TYPE
  N0             2              91
  N1             3              78
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V6, binary
                 cls
clus                0   1
  FANCE MUTATED     6   0
  FANCE WILD-TYPE 251  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANCE MUTATED      6    0
  FANCE WILD-TYPE  251   18
   clus
vv  FANCE MUTATED FANCE WILD-TYPE
  0             6             251
  1             0              18
[1] 2 2
[1] FALSE
D171V7, binary
                 cls
clus                0   1
  FANCE MUTATED     4   3
  FANCE WILD-TYPE 106 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANCE MUTATED      4    3
  FANCE WILD-TYPE  106  176
        clus
vv       FANCE MUTATED FANCE WILD-TYPE
  FEMALE             4             106
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FANCE MUTATED                                       1
  FANCE WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FANCE MUTATED                                                        5
  FANCE WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FANCE MUTATED                                                                   1
  FANCE WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FANCE MUTATED                                                  0
  FANCE WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FANCE MUTATED                                                          0
  FANCE WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FANCE MUTATED                                                           0
  FANCE WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FANCE MUTATED                                          0
  FANCE WILD-TYPE                                        3
D171V8, multiclass
                                                                   clus
vv                                                                  FANCE MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  FANCE WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V9, binary
                 cls
clus                0   1
  FANCE MUTATED     0   7
  FANCE WILD-TYPE   5 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANCE MUTATED      0    7
  FANCE WILD-TYPE    5  277
     clus
vv    FANCE MUTATED FANCE WILD-TYPE
  NO              0               5
  YES             7             277
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FANCE MUTATED     4   0   0   2
  FANCE WILD-TYPE 223  10  10  22
D171V10, multiclass
    clus
vv   FANCE MUTATED FANCE WILD-TYPE
  R0             4             223
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FANCE MUTATED       1                         1     3
  FANCE WILD-TYPE    75                         3   165
D171V12, multiclass
                           clus
vv                          FANCE MUTATED FANCE WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(172) Variable = PALB2 MUTATION ANALYSIS
D172V1, survival
                 sevent
clus2               0   1
  PALB2 MUTATED     8   1
  PALB2 WILD-TYPE 173  79
  PALB2 MUTATED PALB2 WILD-TYPE 
              9             252 
  PALB2 MUTATED PALB2 WILD-TYPE 
              1              79 
$`PALB2 MUTATED`
TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8591 TCGA-BR-A4QL 
       32.78        32.94        20.55        19.50        13.45        11.57 
TCGA-CG-5721 TCGA-CG-5723 TCGA-HU-A4GQ 
        6.02       105.07         0.10 

$`PALB2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69        12.26         9.60         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        15.81         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        1.02         0.99         0.99        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  PALB2 MUTATED PALB2 WILD-TYPE 
            0.1             0.0 
  PALB2 MUTATED PALB2 WILD-TYPE 
         105.07           79.07 
  PALB2 MUTATED PALB2 WILD-TYPE 
         19.500          12.575 
[1] "0.1 - 105.1 (19.5)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "5.3"
D172V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PALB2 MUTATED         0        0        0        1         2         1
  PALB2 WILD-TYPE       1        9       27       25        29        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PALB2 MUTATED           0          0          1          3        1
  PALB2 WILD-TYPE         3         49         35         21       23
D172V3, multiclass
            clus
vv           PALB2 MUTATED PALB2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              2              29
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             3              21
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PALB2 MUTATED     0   1   3   5
  PALB2 WILD-TYPE  11  71 119  70
D172V4, multiclass
    clus
vv   PALB2 MUTATED PALB2 WILD-TYPE
  T1             0              11
  T2             1              71
  T3             3             119
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PALB2 MUTATED    3  2  2  2
  PALB2 WILD-TYPE 90 79 48 51
D172V5, multiclass
    clus
vv   PALB2 MUTATED PALB2 WILD-TYPE
  N0             3              90
  N1             2              79
  N2             2              48
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V6, binary
                 cls
clus                0   1
  PALB2 MUTATED     9   0
  PALB2 WILD-TYPE 248  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALB2 MUTATED      9    0
  PALB2 WILD-TYPE  248   18
   clus
vv  PALB2 MUTATED PALB2 WILD-TYPE
  0             9             248
  1             0              18
[1] 2 2
[1] FALSE
D172V7, binary
                 cls
clus                0   1
  PALB2 MUTATED     5   4
  PALB2 WILD-TYPE 105 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALB2 MUTATED      5    4
  PALB2 WILD-TYPE  105  175
        clus
vv       PALB2 MUTATED PALB2 WILD-TYPE
  FEMALE             5             105
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PALB2 MUTATED                                       0
  PALB2 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PALB2 MUTATED                                                        7
  PALB2 WILD-TYPE                                                    128
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PALB2 MUTATED                                                                   1
  PALB2 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PALB2 MUTATED                                                  1
  PALB2 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PALB2 MUTATED                                                          0
  PALB2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PALB2 MUTATED                                                           0
  PALB2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PALB2 MUTATED                                          0
  PALB2 WILD-TYPE                                        3
D172V8, multiclass
                                                                   clus
vv                                                                  PALB2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  PALB2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V9, binary
                 cls
clus                0   1
  PALB2 MUTATED     0   9
  PALB2 WILD-TYPE   5 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALB2 MUTATED      0    9
  PALB2 WILD-TYPE    5  275
     clus
vv    PALB2 MUTATED PALB2 WILD-TYPE
  NO              0               5
  YES             9             275
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PALB2 MUTATED     9   0   0   0
  PALB2 WILD-TYPE 218  10  10  24
D172V10, multiclass
    clus
vv   PALB2 MUTATED PALB2 WILD-TYPE
  R0             9             218
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PALB2 MUTATED       1                         0     6
  PALB2 WILD-TYPE    75                         4   162
D172V12, multiclass
                           clus
vv                          PALB2 MUTATED PALB2 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(173) Variable = ISG20L2 MUTATION ANALYSIS
D173V1, survival
                   sevent
clus2                 0   1
  ISG20L2 MUTATED     5   1
  ISG20L2 WILD-TYPE 176  79
  ISG20L2 MUTATED ISG20L2 WILD-TYPE 
                6               255 
  ISG20L2 MUTATED ISG20L2 WILD-TYPE 
                1                79 
$`ISG20L2 MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8368 TCGA-CG-5721 TCGA-CG-5733 TCGA-HU-A4GX 
       34.68        12.26         4.31         6.02        21.07        10.19 

$`ISG20L2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  ISG20L2 MUTATED ISG20L2 WILD-TYPE 
             4.31              0.00 
  ISG20L2 MUTATED ISG20L2 WILD-TYPE 
            34.68            105.07 
  ISG20L2 MUTATED ISG20L2 WILD-TYPE 
           11.225            12.660 
[1] "4.3 - 34.7 (11.2)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "2"  
D173V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ISG20L2 MUTATED         0        0        1        1         1         1
  ISG20L2 WILD-TYPE       1        9       26       25        30        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ISG20L2 MUTATED           0          1          0          1        1
  ISG20L2 WILD-TYPE         3         48         36         23       23
D173V3, multiclass
            clus
vv           ISG20L2 MUTATED ISG20L2 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 1                25
  STAGE IIA                1                30
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               0                36
  STAGE IIIC               1                23
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ISG20L2 MUTATED     0   3   1   3
  ISG20L2 WILD-TYPE  11  69 121  72
D173V4, multiclass
    clus
vv   ISG20L2 MUTATED ISG20L2 WILD-TYPE
  T1               0                11
  T2               3                69
  T3               1               121
  T4               3                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  ISG20L2 MUTATED    3  2  2  0
  ISG20L2 WILD-TYPE 90 79 48 53
D173V5, multiclass
    clus
vv   ISG20L2 MUTATED ISG20L2 WILD-TYPE
  N0               3                90
  N1               2                79
  N2               2                48
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V6, binary
                   cls
clus                  0   1
  ISG20L2 MUTATED     7   0
  ISG20L2 WILD-TYPE 250  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ISG20L2 MUTATED      7    0
  ISG20L2 WILD-TYPE  250   18
   clus
vv  ISG20L2 MUTATED ISG20L2 WILD-TYPE
  0               7               250
  1               0                18
[1] 2 2
[1] FALSE
D173V7, binary
                   cls
clus                  0   1
  ISG20L2 MUTATED     5   2
  ISG20L2 WILD-TYPE 105 177
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ISG20L2 MUTATED      5    2
  ISG20L2 WILD-TYPE  105  177
        clus
vv       ISG20L2 MUTATED ISG20L2 WILD-TYPE
  FEMALE               5               105
  MALE                 2               177
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ISG20L2 MUTATED                                       1
  ISG20L2 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ISG20L2 MUTATED                                                        3
  ISG20L2 WILD-TYPE                                                    132
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ISG20L2 MUTATED                                                                   2
  ISG20L2 WILD-TYPE                                                                38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ISG20L2 MUTATED                                                  0
  ISG20L2 WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ISG20L2 MUTATED                                                          1
  ISG20L2 WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ISG20L2 MUTATED                                                           0
  ISG20L2 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ISG20L2 MUTATED                                          0
  ISG20L2 WILD-TYPE                                        3
D173V8, multiclass
                                                                   clus
vv                                                                  ISG20L2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  ISG20L2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V9, binary
                   cls
clus                  0   1
  ISG20L2 MUTATED     1   6
  ISG20L2 WILD-TYPE   4 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ISG20L2 MUTATED      1    6
  ISG20L2 WILD-TYPE    4  278
     clus
vv    ISG20L2 MUTATED ISG20L2 WILD-TYPE
  NO                1                 4
  YES               6               278
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ISG20L2 MUTATED     7   0   0   0
  ISG20L2 WILD-TYPE 220  10  10  24
D173V10, multiclass
    clus
vv   ISG20L2 MUTATED ISG20L2 WILD-TYPE
  R0               7               220
  R1               0                10
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ISG20L2 MUTATED       1                         0     3
  ISG20L2 WILD-TYPE    75                         4   165
D173V12, multiclass
                           clus
vv                          ISG20L2 MUTATED ISG20L2 WILD-TYPE
  ASIAN                                   1                75
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   3               165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(174) Variable = ITGA6 MUTATION ANALYSIS
D174V1, survival
                 sevent
clus2               0   1
  ITGA6 MUTATED     3   2
  ITGA6 WILD-TYPE 178  78
  ITGA6 MUTATED ITGA6 WILD-TYPE 
              5             256 
  ITGA6 MUTATED ITGA6 WILD-TYPE 
              2              78 
$`ITGA6 MUTATED`
TCGA-BR-4280 TCGA-CD-A4MG TCGA-CG-5723 TCGA-D7-8573 TCGA-HU-8602 
        6.61         6.58       105.07        19.50        11.41 

$`ITGA6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  ITGA6 MUTATED ITGA6 WILD-TYPE 
           6.58            0.00 
  ITGA6 MUTATED ITGA6 WILD-TYPE 
         105.07           79.07 
  ITGA6 MUTATED ITGA6 WILD-TYPE 
          11.41           12.64 
[1] "6.6 - 105.1 (11.4)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.3"
D174V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ITGA6 MUTATED         0        0        1        1         2         1
  ITGA6 WILD-TYPE       1        9       26       25        29        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ITGA6 MUTATED           1          0          0          0        0
  ITGA6 WILD-TYPE         2         49         36         24       24
D174V3, multiclass
            clus
vv           ITGA6 MUTATED ITGA6 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              2              29
  STAGE IIB              1              43
  STAGE III              1               2
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITGA6 MUTATED     0   3   2   1
  ITGA6 WILD-TYPE  11  69 120  74
D174V4, multiclass
    clus
vv   ITGA6 MUTATED ITGA6 WILD-TYPE
  T1             0              11
  T2             3              69
  T3             2             120
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ITGA6 MUTATED    4  2  0  0
  ITGA6 WILD-TYPE 89 79 50 53
D174V5, multiclass
    clus
vv   ITGA6 MUTATED ITGA6 WILD-TYPE
  N0             4              89
  N1             2              79
  N2             0              50
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V6, binary
                 cls
clus                0   1
  ITGA6 MUTATED     6   0
  ITGA6 WILD-TYPE 251  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      6    0
  ITGA6 WILD-TYPE  251   18
   clus
vv  ITGA6 MUTATED ITGA6 WILD-TYPE
  0             6             251
  1             0              18
[1] 2 2
[1] FALSE
D174V7, binary
                 cls
clus                0   1
  ITGA6 MUTATED     2   4
  ITGA6 WILD-TYPE 108 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      2    4
  ITGA6 WILD-TYPE  108  175
        clus
vv       ITGA6 MUTATED ITGA6 WILD-TYPE
  FEMALE             2             108
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ITGA6 MUTATED                                       2
  ITGA6 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ITGA6 MUTATED                                                        2
  ITGA6 WILD-TYPE                                                    133
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ITGA6 MUTATED                                                                   1
  ITGA6 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ITGA6 MUTATED                                                  1
  ITGA6 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ITGA6 MUTATED                                                          0
  ITGA6 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ITGA6 MUTATED                                                           0
  ITGA6 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ITGA6 MUTATED                                          0
  ITGA6 WILD-TYPE                                        3
D174V8, multiclass
                                                                   clus
vv                                                                  ITGA6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ITGA6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V9, binary
                 cls
clus                0   1
  ITGA6 MUTATED     0   6
  ITGA6 WILD-TYPE   5 278
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      0    6
  ITGA6 WILD-TYPE    5  278
     clus
vv    ITGA6 MUTATED ITGA6 WILD-TYPE
  NO              0               5
  YES             6             278
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ITGA6 MUTATED     4   0   0   1
  ITGA6 WILD-TYPE 223  10  10  23
D174V10, multiclass
    clus
vv   ITGA6 MUTATED ITGA6 WILD-TYPE
  R0             4             223
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ITGA6 MUTATED       2                         0     2
  ITGA6 WILD-TYPE    74                         4   166
D174V12, multiclass
                           clus
vv                          ITGA6 MUTATED ITGA6 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 2             166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(175) Variable = SDAD1 MUTATION ANALYSIS
D175V1, survival
                 sevent
clus2               0   1
  SDAD1 MUTATED     3   2
  SDAD1 WILD-TYPE 178  78
  SDAD1 MUTATED SDAD1 WILD-TYPE 
              5             256 
  SDAD1 MUTATED SDAD1 WILD-TYPE 
              2              78 
$`SDAD1 MUTATED`
TCGA-BR-7851 TCGA-BR-8372 TCGA-CD-A4MJ TCGA-CG-5733 TCGA-FP-7916 
       12.43        19.17        12.62        21.07        14.07 

$`SDAD1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 
       12.43        11.61         6.58        12.20         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  SDAD1 MUTATED SDAD1 WILD-TYPE 
          12.43            0.00 
  SDAD1 MUTATED SDAD1 WILD-TYPE 
          21.07          105.07 
  SDAD1 MUTATED SDAD1 WILD-TYPE 
         14.070          12.575 
[1] "12.4 - 21.1 (14.1)" "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D175V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SDAD1 MUTATED         0        0        1        0         0         1
  SDAD1 WILD-TYPE       1        9       26       26        31        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SDAD1 MUTATED           0          1          0          2        0
  SDAD1 WILD-TYPE         3         48         36         22       24
D175V3, multiclass
            clus
vv           SDAD1 MUTATED SDAD1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              0              31
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             2              22
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SDAD1 MUTATED     1   2   0   3
  SDAD1 WILD-TYPE  10  70 122  72
D175V4, multiclass
    clus
vv   SDAD1 MUTATED SDAD1 WILD-TYPE
  T1             1              10
  T2             2              70
  T3             0             122
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  SDAD1 MUTATED    2  1  1  2
  SDAD1 WILD-TYPE 91 80 49 51
D175V5, multiclass
    clus
vv   SDAD1 MUTATED SDAD1 WILD-TYPE
  N0             2              91
  N1             1              80
  N2             1              49
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V6, binary
                 cls
clus                0   1
  SDAD1 MUTATED     6   0
  SDAD1 WILD-TYPE 251  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDAD1 MUTATED      6    0
  SDAD1 WILD-TYPE  251   18
   clus
vv  SDAD1 MUTATED SDAD1 WILD-TYPE
  0             6             251
  1             0              18
[1] 2 2
[1] FALSE
D175V7, binary
                 cls
clus                0   1
  SDAD1 MUTATED     3   4
  SDAD1 WILD-TYPE 107 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDAD1 MUTATED      3    4
  SDAD1 WILD-TYPE  107  175
        clus
vv       SDAD1 MUTATED SDAD1 WILD-TYPE
  FEMALE             3             107
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SDAD1 MUTATED                                       1
  SDAD1 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SDAD1 MUTATED                                                        4
  SDAD1 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SDAD1 MUTATED                                                                   2
  SDAD1 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SDAD1 MUTATED                                                  0
  SDAD1 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SDAD1 MUTATED                                                          0
  SDAD1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SDAD1 MUTATED                                                           0
  SDAD1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SDAD1 MUTATED                                          0
  SDAD1 WILD-TYPE                                        3
D175V8, multiclass
                                                                   clus
vv                                                                  SDAD1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  SDAD1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V9, binary
                 cls
clus                0   1
  SDAD1 MUTATED     0   7
  SDAD1 WILD-TYPE   5 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDAD1 MUTATED      0    7
  SDAD1 WILD-TYPE    5  277
     clus
vv    SDAD1 MUTATED SDAD1 WILD-TYPE
  NO              0               5
  YES             7             277
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SDAD1 MUTATED     3   0   0   2
  SDAD1 WILD-TYPE 224  10  10  22
D175V10, multiclass
    clus
vv   SDAD1 MUTATED SDAD1 WILD-TYPE
  R0             3             224
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SDAD1 MUTATED       2                         0     4
  SDAD1 WILD-TYPE    74                         4   164
D175V12, multiclass
                           clus
vv                          SDAD1 MUTATED SDAD1 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(176) Variable = CDKN2A MUTATION ANALYSIS
D176V1, survival
                  sevent
clus2                0   1
  CDKN2A MUTATED     6   3
  CDKN2A WILD-TYPE 175  77
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               9              252 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               3               77 
$`CDKN2A MUTATED`
TCGA-BR-8487 TCGA-CD-5799 TCGA-CD-A489 TCGA-FP-8099 TCGA-HJ-7597 TCGA-HU-A4G8 
        1.12         3.25        11.31        17.06        26.47        11.84 
TCGA-HU-A4GX TCGA-HU-A4H8 TCGA-IN-8663 
       10.19         8.88         3.39 

$`CDKN2A WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
        1.15        13.64        11.57         5.13         2.83        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A 
        0.10         0.13         0.10         3.42         9.34        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        3.48        19.53        14.07        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56        11.08         5.52         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IP-7968 
        9.67        27.42        21.21         3.45        18.81         2.53 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            1.12             0.00 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           26.47           105.07 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
          10.190           12.775 
[1] "1.1 - 26.5 (10.2)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.5"
D176V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDKN2A MUTATED         0        0        2        1         3         2
  CDKN2A WILD-TYPE       1        9       25       25        28        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDKN2A MUTATED           0          1          0          1        0
  CDKN2A WILD-TYPE         3         48         36         23       24
D176V3, multiclass
            clus
vv           CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                2               25
  STAGE II                1               25
  STAGE IIA               3               28
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CDKN2A MUTATED     1   3   5   1
  CDKN2A WILD-TYPE  10  69 117  74
D176V4, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  T1              1               10
  T2              3               69
  T3              5              117
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CDKN2A MUTATED    4  5  2  0
  CDKN2A WILD-TYPE 89 76 48 53
D176V5, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  N0              4               89
  N1              5               76
  N2              2               48
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V6, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    10   0
  CDKN2A WILD-TYPE 247  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     10    0
  CDKN2A WILD-TYPE  247   18
   clus
vv  CDKN2A MUTATED CDKN2A WILD-TYPE
  0             10              247
  1              0               18
[1] 2 2
[1] FALSE
D176V7, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     5   7
  CDKN2A WILD-TYPE 105 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      5    7
  CDKN2A WILD-TYPE  105  172
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE              5              105
  MALE                7              172
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CDKN2A MUTATED                                       3
  CDKN2A WILD-TYPE                                    47
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CDKN2A MUTATED                                                        6
  CDKN2A WILD-TYPE                                                    129
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CDKN2A MUTATED                                                                   1
  CDKN2A WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CDKN2A MUTATED                                                  1
  CDKN2A WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CDKN2A MUTATED                                                          0
  CDKN2A WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CDKN2A MUTATED                                                           0
  CDKN2A WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CDKN2A MUTATED                                          1
  CDKN2A WILD-TYPE                                        2
D176V8, multiclass
                                                                   clus
vv                                                                  CDKN2A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       1
                                                                   clus
vv                                                                  CDKN2A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V9, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     1  11
  CDKN2A WILD-TYPE   4 273
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      1   11
  CDKN2A WILD-TYPE    4  273
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO               1                4
  YES             11              273
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CDKN2A MUTATED     6   1   0   2
  CDKN2A WILD-TYPE 221   9  10  22
D176V10, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  R0              6              221
  R1              1                9
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDKN2A MUTATED       5                         0     6
  CDKN2A WILD-TYPE    71                         4   162
D176V12, multiclass
                           clus
vv                          CDKN2A MUTATED CDKN2A WILD-TYPE
  ASIAN                                  5               71
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(177) Variable = RTN2 MUTATION ANALYSIS
D177V1, survival
                sevent
clus2              0   1
  RTN2 MUTATED     6   2
  RTN2 WILD-TYPE 175  78
  RTN2 MUTATED RTN2 WILD-TYPE 
             8            253 
  RTN2 MUTATED RTN2 WILD-TYPE 
             2             78 
$`RTN2 MUTATED`
TCGA-BR-6452 TCGA-BR-7851 TCGA-BR-8081 TCGA-BR-8360 TCGA-CD-A4MG TCGA-CG-4305 
       34.68        12.43        20.55         6.18         6.58        15.95 
TCGA-CG-5721 TCGA-D7-A4YV 
        6.02         5.92 

$`RTN2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69        12.26         9.60         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        2.66        16.31         2.20        15.58         7.40        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  RTN2 MUTATED RTN2 WILD-TYPE 
          5.92           0.00 
  RTN2 MUTATED RTN2 WILD-TYPE 
         34.68         105.07 
  RTN2 MUTATED RTN2 WILD-TYPE 
         9.505         12.660 
[1] "5.9 - 34.7 (9.5)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.2"
D177V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RTN2 MUTATED         1        0        0        1         3         3
  RTN2 WILD-TYPE       0        9       27       25        28        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RTN2 MUTATED           0          1          0          0        1
  RTN2 WILD-TYPE         3         48         36         24       23
D177V3, multiclass
            clus
vv           RTN2 MUTATED RTN2 WILD-TYPE
  STAGE I               1              0
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              1             25
  STAGE IIA             3             28
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RTN2 MUTATED     1   1   4   4
  RTN2 WILD-TYPE  10  71 118  71
D177V4, multiclass
    clus
vv   RTN2 MUTATED RTN2 WILD-TYPE
  T1            1             10
  T2            1             71
  T3            4            118
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  RTN2 MUTATED    6  4  0  0
  RTN2 WILD-TYPE 87 77 50 53
D177V5, multiclass
    clus
vv   RTN2 MUTATED RTN2 WILD-TYPE
  N0            6             87
  N1            4             77
  N2            0             50
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D177V6, binary
                cls
clus               0   1
  RTN2 MUTATED    10   0
  RTN2 WILD-TYPE 247  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTN2 MUTATED     10    0
  RTN2 WILD-TYPE  247   18
   clus
vv  RTN2 MUTATED RTN2 WILD-TYPE
  0           10            247
  1            0             18
[1] 2 2
[1] FALSE
D177V7, binary
                cls
clus               0   1
  RTN2 MUTATED     5   6
  RTN2 WILD-TYPE 105 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTN2 MUTATED      5    6
  RTN2 WILD-TYPE  105  173
        clus
vv       RTN2 MUTATED RTN2 WILD-TYPE
  FEMALE            5            105
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RTN2 MUTATED                                       1
  RTN2 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RTN2 MUTATED                                                        6
  RTN2 WILD-TYPE                                                    129
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RTN2 MUTATED                                                                   3
  RTN2 WILD-TYPE                                                                37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RTN2 MUTATED                                                  1
  RTN2 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RTN2 MUTATED                                                          0
  RTN2 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RTN2 MUTATED                                                           0
  RTN2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RTN2 MUTATED                                          0
  RTN2 WILD-TYPE                                        3
D177V8, multiclass
                                                                   clus
vv                                                                  RTN2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  RTN2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D177V9, binary
                cls
clus               0   1
  RTN2 MUTATED     0  11
  RTN2 WILD-TYPE   5 273
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTN2 MUTATED      0   11
  RTN2 WILD-TYPE    5  273
     clus
vv    RTN2 MUTATED RTN2 WILD-TYPE
  NO             0              5
  YES           11            273
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RTN2 MUTATED     8   0   0   2
  RTN2 WILD-TYPE 219  10  10  22
D177V10, multiclass
    clus
vv   RTN2 MUTATED RTN2 WILD-TYPE
  R0            8            219
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D177V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RTN2 MUTATED       1                         1     7
  RTN2 WILD-TYPE    75                         3   161
D177V12, multiclass
                           clus
vv                          RTN2 MUTATED RTN2 WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                                7            161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(178) Variable = DNAJC1 MUTATION ANALYSIS
D178V1, survival
                  sevent
clus2                0   1
  DNAJC1 MUTATED     9   1
  DNAJC1 WILD-TYPE 172  79
  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
              10              251 
  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
               1               79 
$`DNAJC1 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A4MI 
       34.68        32.94         1.12        13.45        15.81         0.10 
TCGA-CG-5721 TCGA-F1-6874 TCGA-HU-A4G8 TCGA-HU-A4GQ 
        6.02        14.47        11.84         0.10 

$`DNAJC1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
        9.21        20.22        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
       13.78        14.76         0.62         7.99        16.24        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
             0.1              0.0 
  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
           34.68           105.07 
  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
          12.645           12.620 
[1] "0.1 - 34.7 (12.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "3.1"
D178V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DNAJC1 MUTATED         0        0        1        0         3         1
  DNAJC1 WILD-TYPE       1        9       26       26        28        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJC1 MUTATED           0          1          1          2        2
  DNAJC1 WILD-TYPE         3         48         35         22       22
D178V3, multiclass
            clus
vv           DNAJC1 MUTATED DNAJC1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               3               28
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              2               22
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DNAJC1 MUTATED     0   1   5   5
  DNAJC1 WILD-TYPE  11  71 117  70
D178V4, multiclass
    clus
vv   DNAJC1 MUTATED DNAJC1 WILD-TYPE
  T1              0               11
  T2              1               71
  T3              5              117
  T4              5               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  DNAJC1 MUTATED    5  3  2  1
  DNAJC1 WILD-TYPE 88 78 48 52
D178V5, multiclass
    clus
vv   DNAJC1 MUTATED DNAJC1 WILD-TYPE
  N0              5               88
  N1              3               78
  N2              2               48
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V6, binary
                  cls
clus                 0   1
  DNAJC1 MUTATED    10   1
  DNAJC1 WILD-TYPE 247  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC1 MUTATED     10    1
  DNAJC1 WILD-TYPE  247   17
   clus
vv  DNAJC1 MUTATED DNAJC1 WILD-TYPE
  0             10              247
  1              1               17
[1] 2 2
[1] FALSE
D178V7, binary
                  cls
clus                 0   1
  DNAJC1 MUTATED     5   6
  DNAJC1 WILD-TYPE 105 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC1 MUTATED      5    6
  DNAJC1 WILD-TYPE  105  173
        clus
vv       DNAJC1 MUTATED DNAJC1 WILD-TYPE
  FEMALE              5              105
  MALE                6              173
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DNAJC1 MUTATED                                       1
  DNAJC1 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DNAJC1 MUTATED                                                        6
  DNAJC1 WILD-TYPE                                                    129
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DNAJC1 MUTATED                                                                   2
  DNAJC1 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DNAJC1 MUTATED                                                  2
  DNAJC1 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DNAJC1 MUTATED                                                          0
  DNAJC1 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DNAJC1 MUTATED                                                           0
  DNAJC1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DNAJC1 MUTATED                                          0
  DNAJC1 WILD-TYPE                                        3
D178V8, multiclass
                                                                   clus
vv                                                                  DNAJC1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  DNAJC1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V9, binary
                  cls
clus                 0   1
  DNAJC1 MUTATED     0  11
  DNAJC1 WILD-TYPE   5 273
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC1 MUTATED      0   11
  DNAJC1 WILD-TYPE    5  273
     clus
vv    DNAJC1 MUTATED DNAJC1 WILD-TYPE
  NO               0                5
  YES             11              273
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DNAJC1 MUTATED     8   0   0   1
  DNAJC1 WILD-TYPE 219  10  10  23
D178V10, multiclass
    clus
vv   DNAJC1 MUTATED DNAJC1 WILD-TYPE
  R0              8              219
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DNAJC1 MUTATED       4                         0     6
  DNAJC1 WILD-TYPE    72                         4   162
D178V12, multiclass
                           clus
vv                          DNAJC1 MUTATED DNAJC1 WILD-TYPE
  ASIAN                                  4               72
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(179) Variable = TP53RK MUTATION ANALYSIS
D179V1, survival
                  sevent
clus2                0   1
  TP53RK MUTATED     4   2
  TP53RK WILD-TYPE 177  78
  TP53RK MUTATED TP53RK WILD-TYPE 
               6              255 
  TP53RK MUTATED TP53RK WILD-TYPE 
               2               78 
$`TP53RK MUTATED`
TCGA-BR-6802 TCGA-BR-8487 TCGA-CG-4306 TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       30.90         1.12         1.02         0.10         6.25        10.19 

$`TP53RK WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  TP53RK MUTATED TP53RK WILD-TYPE 
             0.1              0.0 
  TP53RK MUTATED TP53RK WILD-TYPE 
           30.90           105.07 
  TP53RK MUTATED TP53RK WILD-TYPE 
           3.685           12.760 
[1] "0.1 - 30.9 (3.7)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.7"
D179V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TP53RK MUTATED         0        0        0        0         1         1
  TP53RK WILD-TYPE       1        9       27       26        30        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TP53RK MUTATED           0          1          0          2        1
  TP53RK WILD-TYPE         3         48         36         22       23
D179V3, multiclass
            clus
vv           TP53RK MUTATED TP53RK WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              2               22
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TP53RK MUTATED     0   0   4   2
  TP53RK WILD-TYPE  11  72 118  73
D179V4, multiclass
    clus
vv   TP53RK MUTATED TP53RK WILD-TYPE
  T1              0               11
  T2              0               72
  T3              4              118
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  TP53RK MUTATED    1  1  4  0
  TP53RK WILD-TYPE 92 80 46 53
D179V5, multiclass
    clus
vv   TP53RK MUTATED TP53RK WILD-TYPE
  N0              1               92
  N1              1               80
  N2              4               46
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D179V6, binary
                  cls
clus                 0   1
  TP53RK MUTATED     5   1
  TP53RK WILD-TYPE 252  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TP53RK MUTATED      5    1
  TP53RK WILD-TYPE  252   17
   clus
vv  TP53RK MUTATED TP53RK WILD-TYPE
  0              5              252
  1              1               17
[1] 2 2
[1] FALSE
D179V7, binary
                  cls
clus                 0   1
  TP53RK MUTATED     2   4
  TP53RK WILD-TYPE 108 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TP53RK MUTATED      2    4
  TP53RK WILD-TYPE  108  175
        clus
vv       TP53RK MUTATED TP53RK WILD-TYPE
  FEMALE              2              108
  MALE                4              175
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TP53RK MUTATED                                       2
  TP53RK WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TP53RK MUTATED                                                        3
  TP53RK WILD-TYPE                                                    132
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TP53RK MUTATED                                                                   0
  TP53RK WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TP53RK MUTATED                                                  1
  TP53RK WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TP53RK MUTATED                                                          0
  TP53RK WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TP53RK MUTATED                                                           0
  TP53RK WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TP53RK MUTATED                                          0
  TP53RK WILD-TYPE                                        3
D179V8, multiclass
                                                                   clus
vv                                                                  TP53RK MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  TP53RK WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D179V9, binary
                  cls
clus                 0   1
  TP53RK MUTATED     0   6
  TP53RK WILD-TYPE   5 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TP53RK MUTATED      0    6
  TP53RK WILD-TYPE    5  278
     clus
vv    TP53RK MUTATED TP53RK WILD-TYPE
  NO               0                5
  YES              6              278
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TP53RK MUTATED     5   0   1   0
  TP53RK WILD-TYPE 222  10   9  24
D179V10, multiclass
    clus
vv   TP53RK MUTATED TP53RK WILD-TYPE
  R0              5              222
  R1              0               10
  R2              1                9
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D179V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53RK MUTATED       3                         0     2
  TP53RK WILD-TYPE    73                         4   166
D179V12, multiclass
                           clus
vv                          TP53RK MUTATED TP53RK WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  2              166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(180) Variable = CCDC108 MUTATION ANALYSIS
D180V1, survival
                   sevent
clus2                 0   1
  CCDC108 MUTATED    18   3
  CCDC108 WILD-TYPE 163  77
  CCDC108 MUTATED CCDC108 WILD-TYPE 
               21               240 
  CCDC108 MUTATED CCDC108 WILD-TYPE 
                3                77 
$`CCDC108 MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8361 
       11.70         6.97        30.90        34.68        12.26        19.50 
TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4PE TCGA-CD-8527 
        4.31        15.85         1.12        15.81        20.42         0.07 
TCGA-CD-8529 TCGA-CD-8536 TCGA-CG-4465 TCGA-CG-5721 TCGA-FP-A4BE TCGA-HU-8602 
        0.13         0.10         9.01         6.02        11.08        11.41 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4H8 
       29.98         6.51         8.88 

$`CCDC108 WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 
       26.70         6.61         4.64         7.43        18.35         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        20.55         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
        2.20        15.58         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       19.17        14.79         0.26         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51        20.65         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8530 
        0.39         0.07         0.07         0.07         0.10         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.13         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       19.07        12.03         0.00        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       11.77         8.98         0.10         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  CCDC108 MUTATED CCDC108 WILD-TYPE 
             0.07              0.00 
  CCDC108 MUTATED CCDC108 WILD-TYPE 
            34.68            105.07 
  CCDC108 MUTATED CCDC108 WILD-TYPE 
            11.08             12.79 
[1] "0.1 - 34.7 (11.1)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "2"  
D180V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC108 MUTATED         0        0        5        3         5         2
  CCDC108 WILD-TYPE       1        9       22       23        26        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC108 MUTATED           0          2          0          2        4
  CCDC108 WILD-TYPE         3         47         36         22       20
D180V3, multiclass
            clus
vv           CCDC108 MUTATED CCDC108 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 5                22
  STAGE II                 3                23
  STAGE IIA                5                26
  STAGE IIB                2                42
  STAGE III                0                 3
  STAGE IIIA               2                47
  STAGE IIIB               0                36
  STAGE IIIC               2                22
  STAGE IV                 4                20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC108 MUTATED     2   8   6   9
  CCDC108 WILD-TYPE   9  64 116  66
D180V4, multiclass
    clus
vv   CCDC108 MUTATED CCDC108 WILD-TYPE
  T1               2                 9
  T2               8                64
  T3               6               116
  T4               9                66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  CCDC108 MUTATED   13  6  2  2
  CCDC108 WILD-TYPE 80 75 48 51
D180V5, multiclass
    clus
vv   CCDC108 MUTATED CCDC108 WILD-TYPE
  N0              13                80
  N1               6                75
  N2               2                48
  N3               2                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V6, binary
                   cls
clus                  0   1
  CCDC108 MUTATED    21   3
  CCDC108 WILD-TYPE 236  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC108 MUTATED     21    3
  CCDC108 WILD-TYPE  236   15
   clus
vv  CCDC108 MUTATED CCDC108 WILD-TYPE
  0              21               236
  1               3                15
[1] 2 2
[1] FALSE
D180V7, binary
                   cls
clus                  0   1
  CCDC108 MUTATED    14  11
  CCDC108 WILD-TYPE  96 168
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC108 MUTATED     14   11
  CCDC108 WILD-TYPE   96  168
        clus
vv       CCDC108 MUTATED CCDC108 WILD-TYPE
  FEMALE              14                96
  MALE                11               168
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CCDC108 MUTATED                                       3
  CCDC108 WILD-TYPE                                    47
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CCDC108 MUTATED                                                       13
  CCDC108 WILD-TYPE                                                    122
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CCDC108 MUTATED                                                                   3
  CCDC108 WILD-TYPE                                                                37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CCDC108 MUTATED                                                  4
  CCDC108 WILD-TYPE                                               34
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CCDC108 MUTATED                                                          2
  CCDC108 WILD-TYPE                                                       14
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CCDC108 MUTATED                                                           0
  CCDC108 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CCDC108 MUTATED                                          0
  CCDC108 WILD-TYPE                                        3
D180V8, multiclass
                                                                   clus
vv                                                                  CCDC108 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         13
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  CCDC108 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          122
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V9, binary
                   cls
clus                  0   1
  CCDC108 MUTATED     1  24
  CCDC108 WILD-TYPE   4 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC108 MUTATED      1   24
  CCDC108 WILD-TYPE    4  260
     clus
vv    CCDC108 MUTATED CCDC108 WILD-TYPE
  NO                1                 4
  YES              24               260
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CCDC108 MUTATED    20   0   1   4
  CCDC108 WILD-TYPE 207  10   9  20
D180V10, multiclass
    clus
vv   CCDC108 MUTATED CCDC108 WILD-TYPE
  R0              20               207
  R1               0                10
  R2               1                 9
  RX               4                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC108 MUTATED       8                         1    12
  CCDC108 WILD-TYPE    68                         3   156
D180V12, multiclass
                           clus
vv                          CCDC108 MUTATED CCDC108 WILD-TYPE
  ASIAN                                   8                68
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                  12               156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(181) Variable = PYGO2 MUTATION ANALYSIS
D181V1, survival
                 sevent
clus2               0   1
  PYGO2 MUTATED     7   0
  PYGO2 WILD-TYPE 174  80
  PYGO2 MUTATED PYGO2 WILD-TYPE 
              7             254 
  PYGO2 MUTATED PYGO2 WILD-TYPE 
              0              80 
$`PYGO2 MUTATED`
TCGA-BR-6566 TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8487 TCGA-HU-A4G8 TCGA-HU-A4GN 
       32.78        20.55        19.50         1.12        11.84        29.98 
TCGA-HU-A4H8 
        8.88 

$`PYGO2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       17.49        14.43         0.69        12.26         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       12.30         9.67        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  PYGO2 MUTATED PYGO2 WILD-TYPE 
           1.12            0.00 
  PYGO2 MUTATED PYGO2 WILD-TYPE 
          32.78          105.07 
  PYGO2 MUTATED PYGO2 WILD-TYPE 
         19.500          12.605 
[1] "1.1 - 32.8 (19.5)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "2.6e+07"
D181V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PYGO2 MUTATED         0        0        1        0         3         2
  PYGO2 WILD-TYPE       1        9       26       26        28        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PYGO2 MUTATED           0          0          0          1        0
  PYGO2 WILD-TYPE         3         49         36         23       24
D181V3, multiclass
            clus
vv           PYGO2 MUTATED PYGO2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              3              28
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PYGO2 MUTATED     1   1   3   2
  PYGO2 WILD-TYPE  10  71 119  73
D181V4, multiclass
    clus
vv   PYGO2 MUTATED PYGO2 WILD-TYPE
  T1             1              10
  T2             1              71
  T3             3             119
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PYGO2 MUTATED    3  3  1  0
  PYGO2 WILD-TYPE 90 78 49 53
D181V5, multiclass
    clus
vv   PYGO2 MUTATED PYGO2 WILD-TYPE
  N0             3              90
  N1             3              78
  N2             1              49
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V6, binary
                 cls
clus                0   1
  PYGO2 MUTATED     7   0
  PYGO2 WILD-TYPE 250  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PYGO2 MUTATED      7    0
  PYGO2 WILD-TYPE  250   18
   clus
vv  PYGO2 MUTATED PYGO2 WILD-TYPE
  0             7             250
  1             0              18
[1] 2 2
[1] FALSE
D181V7, binary
                 cls
clus                0   1
  PYGO2 MUTATED     5   2
  PYGO2 WILD-TYPE 105 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PYGO2 MUTATED      5    2
  PYGO2 WILD-TYPE  105  177
        clus
vv       PYGO2 MUTATED PYGO2 WILD-TYPE
  FEMALE             5             105
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PYGO2 MUTATED                                       1
  PYGO2 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PYGO2 MUTATED                                                        4
  PYGO2 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PYGO2 MUTATED                                                                   0
  PYGO2 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PYGO2 MUTATED                                                  2
  PYGO2 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PYGO2 MUTATED                                                          0
  PYGO2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PYGO2 MUTATED                                                           0
  PYGO2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PYGO2 MUTATED                                          0
  PYGO2 WILD-TYPE                                        3
D181V8, multiclass
                                                                   clus
vv                                                                  PYGO2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  PYGO2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V9, binary
                 cls
clus                0   1
  PYGO2 MUTATED     0   7
  PYGO2 WILD-TYPE   5 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PYGO2 MUTATED      0    7
  PYGO2 WILD-TYPE    5  277
     clus
vv    PYGO2 MUTATED PYGO2 WILD-TYPE
  NO              0               5
  YES             7             277
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PYGO2 MUTATED     6   0   0   0
  PYGO2 WILD-TYPE 221  10  10  24
D181V10, multiclass
    clus
vv   PYGO2 MUTATED PYGO2 WILD-TYPE
  R0             6             221
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PYGO2 MUTATED       3                         0     4
  PYGO2 WILD-TYPE    73                         4   164
D181V12, multiclass
                           clus
vv                          PYGO2 MUTATED PYGO2 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(182) Variable = C1R MUTATION ANALYSIS
D182V1, survival
               sevent
clus2             0   1
  C1R MUTATED     3   1
  C1R WILD-TYPE 178  79
  C1R MUTATED C1R WILD-TYPE 
            4           257 
  C1R MUTATED C1R WILD-TYPE 
            1            79 
$`C1R MUTATED`
TCGA-BR-8081 TCGA-BR-A4QL TCGA-CG-5723 TCGA-HU-A4GQ 
       20.55        11.57       105.07         0.10 

$`C1R WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  C1R MUTATED C1R WILD-TYPE 
          0.1           0.0 
  C1R MUTATED C1R WILD-TYPE 
       105.07         79.07 
  C1R MUTATED C1R WILD-TYPE 
        16.06         12.62 
[1] "0.1 - 105.1 (16.1)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "2.6"
D182V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C1R MUTATED         0        0        1        1         0         1
  C1R WILD-TYPE       1        9       26       25        31        43
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1R MUTATED           0          0          1          1        0
  C1R WILD-TYPE         3         49         35         23       24
D182V3, multiclass
            clus
vv           C1R MUTATED C1R WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             9
  STAGE IB             1            26
  STAGE II             1            25
  STAGE IIA            0            31
  STAGE IIB            1            43
  STAGE III            0             3
  STAGE IIIA           0            49
  STAGE IIIB           1            35
  STAGE IIIC           1            23
  STAGE IV             0            24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  C1R MUTATED     0   2   1   2
  C1R WILD-TYPE  11  70 121  73
D182V4, multiclass
    clus
vv   C1R MUTATED C1R WILD-TYPE
  T1           0            11
  T2           2            70
  T3           1           121
  T4           2            73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  C1R MUTATED    2  1  1  1
  C1R WILD-TYPE 91 80 49 52
D182V5, multiclass
    clus
vv   C1R MUTATED C1R WILD-TYPE
  N0           2            91
  N1           1            80
  N2           1            49
  N3           1            52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D182V6, binary
               cls
clus              0   1
  C1R MUTATED     5   0
  C1R WILD-TYPE 252  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  C1R MUTATED      5    0
  C1R WILD-TYPE  252   18
   clus
vv  C1R MUTATED C1R WILD-TYPE
  0           5           252
  1           0            18
[1] 2 2
[1] FALSE
D182V7, binary
               cls
clus              0   1
  C1R MUTATED     2   3
  C1R WILD-TYPE 108 176
[1] "tbl2"
               cls
clus            [,1] [,2]
  C1R MUTATED      2    3
  C1R WILD-TYPE  108  176
        clus
vv       C1R MUTATED C1R WILD-TYPE
  FEMALE           2           108
  MALE             3           176
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C1R MUTATED                                       0
  C1R WILD-TYPE                                    50
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C1R MUTATED                                                        3
  C1R WILD-TYPE                                                    132
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C1R MUTATED                                                                   1
  C1R WILD-TYPE                                                                39
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C1R MUTATED                                                  1
  C1R WILD-TYPE                                               37
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C1R MUTATED                                                          0
  C1R WILD-TYPE                                                       16
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C1R MUTATED                                                           0
  C1R WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C1R MUTATED                                          0
  C1R WILD-TYPE                                        3
D182V8, multiclass
                                                                   clus
vv                                                                  C1R MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  C1R WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D182V9, binary
               cls
clus              0   1
  C1R MUTATED     0   5
  C1R WILD-TYPE   5 279
[1] "tbl2"
               cls
clus            [,1] [,2]
  C1R MUTATED      0    5
  C1R WILD-TYPE    5  279
     clus
vv    C1R MUTATED C1R WILD-TYPE
  NO            0             5
  YES           5           279
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  C1R MUTATED     5   0   0   0
  C1R WILD-TYPE 222  10  10  24
D182V10, multiclass
    clus
vv   C1R MUTATED C1R WILD-TYPE
  R0           5           222
  R1           0            10
  R2           0            10
  RX           0            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D182V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C1R MUTATED       1                         0     2
  C1R WILD-TYPE    75                         4   166
D182V12, multiclass
                           clus
vv                          C1R MUTATED C1R WILD-TYPE
  ASIAN                               1            75
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                               2           166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(183) Variable = FGGY MUTATION ANALYSIS
D183V1, survival
                sevent
clus2              0   1
  FGGY MUTATED     6   2
  FGGY WILD-TYPE 175  78
  FGGY MUTATED FGGY WILD-TYPE 
             8            253 
  FGGY MUTATED FGGY WILD-TYPE 
             2             78 
$`FGGY MUTATED`
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8363 TCGA-CD-8536 TCGA-CG-4444 
        6.61        34.68        23.93         0.26         0.10        47.05 
TCGA-CG-4449 TCGA-HU-A4H2 
       19.07        12.95 

$`FGGY WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
       18.35        30.90         6.18         9.57        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       19.50        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       14.01        29.98        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  FGGY MUTATED FGGY WILD-TYPE 
           0.1            0.0 
  FGGY MUTATED FGGY WILD-TYPE 
         47.05         105.07 
  FGGY MUTATED FGGY WILD-TYPE 
         16.01          12.59 
[1] "0.1 - 47.0 (16.0)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.6"
D183V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FGGY MUTATED         0        0        2        2         1         0
  FGGY WILD-TYPE       1        9       25       24        30        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FGGY MUTATED           1          1          1          0        0
  FGGY WILD-TYPE         2         48         35         24       24
D183V3, multiclass
            clus
vv           FGGY MUTATED FGGY WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              2             24
  STAGE IIA             1             30
  STAGE IIB             0             44
  STAGE III             1              2
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FGGY MUTATED     1   5   3   0
  FGGY WILD-TYPE  10  67 119  75
D183V4, multiclass
    clus
vv   FGGY MUTATED FGGY WILD-TYPE
  T1            1             10
  T2            5             67
  T3            3            119
  T4            0             75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  FGGY MUTATED    4  2  1  1
  FGGY WILD-TYPE 89 79 49 52
D183V5, multiclass
    clus
vv   FGGY MUTATED FGGY WILD-TYPE
  N0            4             89
  N1            2             79
  N2            1             49
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D183V6, binary
                cls
clus               0   1
  FGGY MUTATED     9   0
  FGGY WILD-TYPE 248  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGGY MUTATED      9    0
  FGGY WILD-TYPE  248   18
   clus
vv  FGGY MUTATED FGGY WILD-TYPE
  0            9            248
  1            0             18
[1] 2 2
[1] FALSE
D183V7, binary
                cls
clus               0   1
  FGGY MUTATED     6   3
  FGGY WILD-TYPE 104 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGGY MUTATED      6    3
  FGGY WILD-TYPE  104  176
        clus
vv       FGGY MUTATED FGGY WILD-TYPE
  FEMALE            6            104
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FGGY MUTATED                                       1
  FGGY WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FGGY MUTATED                                                        6
  FGGY WILD-TYPE                                                    129
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FGGY MUTATED                                                                   0
  FGGY WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FGGY MUTATED                                                  1
  FGGY WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FGGY MUTATED                                                          1
  FGGY WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FGGY MUTATED                                                           0
  FGGY WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FGGY MUTATED                                          0
  FGGY WILD-TYPE                                        3
D183V8, multiclass
                                                                   clus
vv                                                                  FGGY MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  FGGY WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D183V9, binary
                cls
clus               0   1
  FGGY MUTATED     0   9
  FGGY WILD-TYPE   5 275
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGGY MUTATED      0    9
  FGGY WILD-TYPE    5  275
     clus
vv    FGGY MUTATED FGGY WILD-TYPE
  NO             0              5
  YES            9            275
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FGGY MUTATED     7   0   0   2
  FGGY WILD-TYPE 220  10  10  22
D183V10, multiclass
    clus
vv   FGGY MUTATED FGGY WILD-TYPE
  R0            7            220
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D183V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FGGY MUTATED       2                         0     5
  FGGY WILD-TYPE    74                         4   163
D183V12, multiclass
                           clus
vv                          FGGY MUTATED FGGY WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                5            163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(184) Variable = MSH6 MUTATION ANALYSIS
D184V1, survival
                sevent
clus2              0   1
  MSH6 MUTATED    12   3
  MSH6 WILD-TYPE 169  77
  MSH6 MUTATED MSH6 WILD-TYPE 
            15            246 
  MSH6 MUTATED MSH6 WILD-TYPE 
             3             77 
$`MSH6 MUTATED`
TCGA-BR-6852 TCGA-BR-7959 TCGA-BR-8372 TCGA-BR-8591 TCGA-CD-A4MG TCGA-CG-5721 
       32.94        18.71        19.17        13.45         6.58         6.02 
TCGA-CG-5733 TCGA-F1-A448 TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.07        21.27        11.41         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-IN-7806 
       10.19        19.36        21.21 

$`MSH6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        30.90        31.20        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       28.73        12.43         3.45         9.07        12.76        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       28.96        79.07        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       26.47         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        8.88        27.42         3.45        18.81         3.39         2.53 

  MSH6 MUTATED MSH6 WILD-TYPE 
           0.1            0.0 
  MSH6 MUTATED MSH6 WILD-TYPE 
         32.94         105.07 
  MSH6 MUTATED MSH6 WILD-TYPE 
        13.450         12.605 
[1] "0.1 - 32.9 (13.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.6"
D184V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MSH6 MUTATED         0        0        0        0         3         3
  MSH6 WILD-TYPE       1        9       27       26        28        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MSH6 MUTATED           0          3          1          6        2
  MSH6 WILD-TYPE         3         46         35         18       22
D184V3, multiclass
            clus
vv           MSH6 MUTATED MSH6 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              0             26
  STAGE IIA             3             28
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            3             46
  STAGE IIIB            1             35
  STAGE IIIC            6             18
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MSH6 MUTATED     0   1   6  11
  MSH6 WILD-TYPE  11  71 116  64
D184V4, multiclass
    clus
vv   MSH6 MUTATED MSH6 WILD-TYPE
  T1            0             11
  T2            1             71
  T3            6            116
  T4           11             64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  MSH6 MUTATED    5  4  4  5
  MSH6 WILD-TYPE 88 77 46 48
D184V5, multiclass
    clus
vv   MSH6 MUTATED MSH6 WILD-TYPE
  N0            5             88
  N1            4             77
  N2            4             46
  N3            5             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V6, binary
                cls
clus               0   1
  MSH6 MUTATED    19   0
  MSH6 WILD-TYPE 238  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH6 MUTATED     19    0
  MSH6 WILD-TYPE  238   18
   clus
vv  MSH6 MUTATED MSH6 WILD-TYPE
  0           19            238
  1            0             18
[1] 2 2
[1] FALSE
D184V7, binary
                cls
clus               0   1
  MSH6 MUTATED     9  10
  MSH6 WILD-TYPE 101 169
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH6 MUTATED      9   10
  MSH6 WILD-TYPE  101  169
        clus
vv       MSH6 MUTATED MSH6 WILD-TYPE
  FEMALE            9            101
  MALE             10            169
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MSH6 MUTATED                                       7
  MSH6 WILD-TYPE                                    43
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MSH6 MUTATED                                                        6
  MSH6 WILD-TYPE                                                    129
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MSH6 MUTATED                                                                   2
  MSH6 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MSH6 MUTATED                                                  2
  MSH6 WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MSH6 MUTATED                                                          2
  MSH6 WILD-TYPE                                                       14
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MSH6 MUTATED                                                           0
  MSH6 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MSH6 MUTATED                                          0
  MSH6 WILD-TYPE                                        3
D184V8, multiclass
                                                                   clus
vv                                                                  MSH6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  MSH6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         43
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V9, binary
                cls
clus               0   1
  MSH6 MUTATED     0  19
  MSH6 WILD-TYPE   5 265
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH6 MUTATED      0   19
  MSH6 WILD-TYPE    5  265
     clus
vv    MSH6 MUTATED MSH6 WILD-TYPE
  NO             0              5
  YES           19            265
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MSH6 MUTATED    15   0   0   3
  MSH6 WILD-TYPE 212  10  10  21
D184V10, multiclass
    clus
vv   MSH6 MUTATED MSH6 WILD-TYPE
  R0           15            212
  R1            0             10
  R2            0             10
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MSH6 MUTATED       7                         0     9
  MSH6 WILD-TYPE    69                         4   159
D184V12, multiclass
                           clus
vv                          MSH6 MUTATED MSH6 WILD-TYPE
  ASIAN                                7             69
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                9            159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(185) Variable = RNF111 MUTATION ANALYSIS
D185V1, survival
                  sevent
clus2                0   1
  RNF111 MUTATED     4   4
  RNF111 WILD-TYPE 177  76
  RNF111 MUTATED RNF111 WILD-TYPE 
               8              253 
  RNF111 MUTATED RNF111 WILD-TYPE 
               4               76 
$`RNF111 MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6566 TCGA-BR-8680 TCGA-CG-4465 TCGA-CG-5721 
        6.97         6.61        32.78        15.81         9.01         6.02 
TCGA-D7-A4YU TCGA-D7-A4YV 
       16.44         5.92 

$`RNF111 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YX TCGA-D7-A4YY 
       14.66        21.14        20.91        14.27        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  RNF111 MUTATED RNF111 WILD-TYPE 
            5.92             0.00 
  RNF111 MUTATED RNF111 WILD-TYPE 
           32.78           105.07 
  RNF111 MUTATED RNF111 WILD-TYPE 
            7.99            12.66 
[1] "5.9 - 32.8 (8.0)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.9"
D185V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RNF111 MUTATED         0        0        0        0         1         1
  RNF111 WILD-TYPE       1        9       27       26        30        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF111 MUTATED           1          1          1          0        3
  RNF111 WILD-TYPE         2         48         35         24       21
D185V3, multiclass
            clus
vv           RNF111 MUTATED RNF111 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               1               43
  STAGE III               1                2
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              0               24
  STAGE IV                3               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNF111 MUTATED     0   1   5   3
  RNF111 WILD-TYPE  11  71 117  72
D185V4, multiclass
    clus
vv   RNF111 MUTATED RNF111 WILD-TYPE
  T1              0               11
  T2              1               71
  T3              5              117
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  RNF111 MUTATED    1  5  1  2
  RNF111 WILD-TYPE 92 76 49 51
D185V5, multiclass
    clus
vv   RNF111 MUTATED RNF111 WILD-TYPE
  N0              1               92
  N1              5               76
  N2              1               49
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V6, binary
                  cls
clus                 0   1
  RNF111 MUTATED     6   2
  RNF111 WILD-TYPE 251  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF111 MUTATED      6    2
  RNF111 WILD-TYPE  251   16
   clus
vv  RNF111 MUTATED RNF111 WILD-TYPE
  0              6              251
  1              2               16
[1] 2 2
[1] FALSE
D185V7, binary
                  cls
clus                 0   1
  RNF111 MUTATED     6   4
  RNF111 WILD-TYPE 104 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF111 MUTATED      6    4
  RNF111 WILD-TYPE  104  175
        clus
vv       RNF111 MUTATED RNF111 WILD-TYPE
  FEMALE              6              104
  MALE                4              175
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RNF111 MUTATED                                       1
  RNF111 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RNF111 MUTATED                                                        5
  RNF111 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RNF111 MUTATED                                                                   1
  RNF111 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RNF111 MUTATED                                                  3
  RNF111 WILD-TYPE                                               35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RNF111 MUTATED                                                          0
  RNF111 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RNF111 MUTATED                                                           0
  RNF111 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RNF111 MUTATED                                          0
  RNF111 WILD-TYPE                                        3
D185V8, multiclass
                                                                   clus
vv                                                                  RNF111 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  RNF111 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V9, binary
                  cls
clus                 0   1
  RNF111 MUTATED     0  10
  RNF111 WILD-TYPE   5 274
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF111 MUTATED      0   10
  RNF111 WILD-TYPE    5  274
     clus
vv    RNF111 MUTATED RNF111 WILD-TYPE
  NO               0                5
  YES             10              274
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RNF111 MUTATED     5   0   1   4
  RNF111 WILD-TYPE 222  10   9  20
D185V10, multiclass
    clus
vv   RNF111 MUTATED RNF111 WILD-TYPE
  R0              5              222
  R1              0               10
  R2              1                9
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RNF111 MUTATED       1                         0     7
  RNF111 WILD-TYPE    75                         4   161
D185V12, multiclass
                           clus
vv                          RNF111 MUTATED RNF111 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  7              161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(186) Variable = ABCA6 MUTATION ANALYSIS
D186V1, survival
                 sevent
clus2               0   1
  ABCA6 MUTATED     6   4
  ABCA6 WILD-TYPE 175  76
  ABCA6 MUTATED ABCA6 WILD-TYPE 
             10             251 
  ABCA6 MUTATED ABCA6 WILD-TYPE 
              4              76 
$`ABCA6 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6706 TCGA-BR-7851 TCGA-BR-8297 TCGA-BR-8487 
        6.97        34.68        18.05        12.43         7.40         1.12 
TCGA-BR-8680 TCGA-CG-4465 TCGA-D7-A4YV TCGA-FP-A4BE 
       15.81         9.01         5.92        11.08 

$`ABCA6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       32.78        25.61        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       15.42        28.01        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       16.31         2.20        15.58         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       47.05        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
        5.03        13.58         0.56         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  ABCA6 MUTATED ABCA6 WILD-TYPE 
           1.12            0.00 
  ABCA6 MUTATED ABCA6 WILD-TYPE 
          34.68          105.07 
  ABCA6 MUTATED ABCA6 WILD-TYPE 
         10.045          12.760 
[1] "1.1 - 34.7 (10.0)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.6"
D186V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCA6 MUTATED         0        0        0        1         3         2
  ABCA6 WILD-TYPE       1        9       27       25        28        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ABCA6 MUTATED           0          3          0          1        2
  ABCA6 WILD-TYPE         3         46         36         23       22
D186V3, multiclass
            clus
vv           ABCA6 MUTATED ABCA6 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              3              28
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             3              46
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCA6 MUTATED     0   1   6   5
  ABCA6 WILD-TYPE  11  71 116  70
D186V4, multiclass
    clus
vv   ABCA6 MUTATED ABCA6 WILD-TYPE
  T1             0              11
  T2             1              71
  T3             6             116
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ABCA6 MUTATED    5  5  1  2
  ABCA6 WILD-TYPE 88 76 49 51
D186V5, multiclass
    clus
vv   ABCA6 MUTATED ABCA6 WILD-TYPE
  N0             5              88
  N1             5              76
  N2             1              49
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D186V6, binary
                 cls
clus                0   1
  ABCA6 MUTATED    10   2
  ABCA6 WILD-TYPE 247  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA6 MUTATED     10    2
  ABCA6 WILD-TYPE  247   16
   clus
vv  ABCA6 MUTATED ABCA6 WILD-TYPE
  0            10             247
  1             2              16
[1] 2 2
[1] FALSE
D186V7, binary
                 cls
clus                0   1
  ABCA6 MUTATED     6   7
  ABCA6 WILD-TYPE 104 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA6 MUTATED      6    7
  ABCA6 WILD-TYPE  104  172
        clus
vv       ABCA6 MUTATED ABCA6 WILD-TYPE
  FEMALE             6             104
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ABCA6 MUTATED                                       2
  ABCA6 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ABCA6 MUTATED                                                        7
  ABCA6 WILD-TYPE                                                    128
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ABCA6 MUTATED                                                                   1
  ABCA6 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ABCA6 MUTATED                                                  2
  ABCA6 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ABCA6 MUTATED                                                          1
  ABCA6 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ABCA6 MUTATED                                                           0
  ABCA6 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ABCA6 MUTATED                                          0
  ABCA6 WILD-TYPE                                        3
D186V8, multiclass
                                                                   clus
vv                                                                  ABCA6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ABCA6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D186V9, binary
                 cls
clus                0   1
  ABCA6 MUTATED     1  12
  ABCA6 WILD-TYPE   4 272
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA6 MUTATED      1   12
  ABCA6 WILD-TYPE    4  272
     clus
vv    ABCA6 MUTATED ABCA6 WILD-TYPE
  NO              1               4
  YES            12             272
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ABCA6 MUTATED     9   0   1   3
  ABCA6 WILD-TYPE 218  10   9  21
D186V10, multiclass
    clus
vv   ABCA6 MUTATED ABCA6 WILD-TYPE
  R0             9             218
  R1             0              10
  R2             1               9
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D186V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ABCA6 MUTATED       1                         1     9
  ABCA6 WILD-TYPE    75                         3   159
D186V12, multiclass
                           clus
vv                          ABCA6 MUTATED ABCA6 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 9             159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(187) Variable = WDR7 MUTATION ANALYSIS
D187V1, survival
                sevent
clus2              0   1
  WDR7 MUTATED    12   1
  WDR7 WILD-TYPE 169  79
  WDR7 MUTATED WDR7 WILD-TYPE 
            13            248 
  WDR7 MUTATED WDR7 WILD-TYPE 
             1             79 
$`WDR7 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7851 TCGA-CD-A4MI TCGA-CG-5721 
       34.68        32.94        24.76        12.43         0.10         6.02 
TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 TCGA-F1-A448 TCGA-FP-A4BE TCGA-HU-A4GT 
      105.07        65.10        21.07        21.27        11.08         6.51 
TCGA-HU-A4GX 
       10.19 

$`WDR7 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 
       21.11        30.90        31.20        12.82         9.21        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       15.42        28.01        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
       36.00         1.02         0.99         0.99        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       79.07         4.01        69.04         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        0.62         7.99        16.24        14.47        72.23         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         0.10         6.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  WDR7 MUTATED WDR7 WILD-TYPE 
           0.1            0.0 
  WDR7 MUTATED WDR7 WILD-TYPE 
        105.07          79.07 
  WDR7 MUTATED WDR7 WILD-TYPE 
        21.070         12.605 
[1] "0.1 - 105.1 (21.1)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "7.8"
D187V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WDR7 MUTATED         1        1        2        1         4         1
  WDR7 WILD-TYPE       0        8       25       25        27        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WDR7 MUTATED           0          1          2          1        1
  WDR7 WILD-TYPE         3         48         34         23       23
D187V3, multiclass
            clus
vv           WDR7 MUTATED WDR7 WILD-TYPE
  STAGE I               1              0
  STAGE IA              1              8
  STAGE IB              2             25
  STAGE II              1             25
  STAGE IIA             4             27
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            2             34
  STAGE IIIC            1             23
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WDR7 MUTATED     3   4   6   3
  WDR7 WILD-TYPE   8  68 116  72
D187V4, multiclass
    clus
vv   WDR7 MUTATED WDR7 WILD-TYPE
  T1            3              8
  T2            4             68
  T3            6            116
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  WDR7 MUTATED    8  5  2  1
  WDR7 WILD-TYPE 85 76 48 52
D187V5, multiclass
    clus
vv   WDR7 MUTATED WDR7 WILD-TYPE
  N0            8             85
  N1            5             76
  N2            2             48
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D187V6, binary
                cls
clus               0   1
  WDR7 MUTATED    16   0
  WDR7 WILD-TYPE 241  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR7 MUTATED     16    0
  WDR7 WILD-TYPE  241   18
   clus
vv  WDR7 MUTATED WDR7 WILD-TYPE
  0           16            241
  1            0             18
[1] 2 2
[1] FALSE
D187V7, binary
                cls
clus               0   1
  WDR7 MUTATED     7  10
  WDR7 WILD-TYPE 103 169
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR7 MUTATED      7   10
  WDR7 WILD-TYPE  103  169
        clus
vv       WDR7 MUTATED WDR7 WILD-TYPE
  FEMALE            7            103
  MALE             10            169
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  WDR7 MUTATED                                       1
  WDR7 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WDR7 MUTATED                                                        8
  WDR7 WILD-TYPE                                                    127
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WDR7 MUTATED                                                                   5
  WDR7 WILD-TYPE                                                                35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  WDR7 MUTATED                                                  1
  WDR7 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  WDR7 MUTATED                                                          1
  WDR7 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  WDR7 MUTATED                                                           1
  WDR7 WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  WDR7 MUTATED                                          0
  WDR7 WILD-TYPE                                        3
D187V8, multiclass
                                                                   clus
vv                                                                  WDR7 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  WDR7 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D187V9, binary
                cls
clus               0   1
  WDR7 MUTATED     0  17
  WDR7 WILD-TYPE   5 267
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR7 MUTATED      0   17
  WDR7 WILD-TYPE    5  267
     clus
vv    WDR7 MUTATED WDR7 WILD-TYPE
  NO             0              5
  YES           17            267
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  WDR7 MUTATED    14   0   0   2
  WDR7 WILD-TYPE 213  10  10  22
D187V10, multiclass
    clus
vv   WDR7 MUTATED WDR7 WILD-TYPE
  R0           14            213
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D187V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WDR7 MUTATED       3                         2     7
  WDR7 WILD-TYPE    73                         2   161
D187V12, multiclass
                           clus
vv                          WDR7 MUTATED WDR7 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            2              2
  WHITE                                7            161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(188) Variable = ZC3H13 MUTATION ANALYSIS
D188V1, survival
                  sevent
clus2                0   1
  ZC3H13 MUTATED    17   7
  ZC3H13 WILD-TYPE 164  73
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
              24              237 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
               7               73 
$`ZC3H13 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-6852 
       30.90        34.68        15.95        32.78        30.90        32.94 
TCGA-BR-7851 TCGA-BR-8360 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-A4MG 
       12.43         6.18        15.85         1.12        15.81         6.58 
TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-5723 TCGA-CG-5726 TCGA-D7-A4YV 
       12.62         1.02         4.01       105.07        28.96         5.92 
TCGA-FP-A4BE TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.08        24.20        29.98         0.10         6.51         6.25 

$`ZC3H13 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6455 TCGA-BR-6456 
       18.35         6.18         9.57         6.61        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       13.68        19.33        39.12        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 
       18.05        19.89         8.98        21.11        31.20        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
        0.10        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        8.05        54.08        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
        0.99        12.03        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       11.84         3.25        22.75        25.81        11.77         8.98 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
             0.1              0.0 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
          105.07            79.07 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
          14.215           12.590 
[1] "0.1 - 105.1 (14.2)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.6"
D188V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZC3H13 MUTATED         0        2        2        1        10         3
  ZC3H13 WILD-TYPE       1        7       25       25        21        41
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZC3H13 MUTATED           0          2          0          2        3
  ZC3H13 WILD-TYPE         3         47         36         22       21
D188V3, multiclass
            clus
vv           ZC3H13 MUTATED ZC3H13 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                2                7
  STAGE IB                2               25
  STAGE II                1               25
  STAGE IIA              10               21
  STAGE IIB               3               41
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              0               36
  STAGE IIIC              2               22
  STAGE IV                3               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZC3H13 MUTATED     3   6  14   5
  ZC3H13 WILD-TYPE   8  66 108  70
D188V4, multiclass
    clus
vv   ZC3H13 MUTATED ZC3H13 WILD-TYPE
  T1              3                8
  T2              6               66
  T3             14              108
  T4              5               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZC3H13 MUTATED   14  6  4  2
  ZC3H13 WILD-TYPE 79 75 46 51
D188V5, multiclass
    clus
vv   ZC3H13 MUTATED ZC3H13 WILD-TYPE
  N0             14               79
  N1              6               75
  N2              4               46
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D188V6, binary
                  cls
clus                 0   1
  ZC3H13 MUTATED    25   3
  ZC3H13 WILD-TYPE 232  15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED     25    3
  ZC3H13 WILD-TYPE  232   15
   clus
vv  ZC3H13 MUTATED ZC3H13 WILD-TYPE
  0             25              232
  1              3               15
[1] 2 2
[1] FALSE
D188V7, binary
                  cls
clus                 0   1
  ZC3H13 MUTATED    13  16
  ZC3H13 WILD-TYPE  97 163
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED     13   16
  ZC3H13 WILD-TYPE   97  163
        clus
vv       ZC3H13 MUTATED ZC3H13 WILD-TYPE
  FEMALE             13               97
  MALE               16              163
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZC3H13 MUTATED                                       2
  ZC3H13 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZC3H13 MUTATED                                                       16
  ZC3H13 WILD-TYPE                                                    119
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZC3H13 MUTATED                                                                   5
  ZC3H13 WILD-TYPE                                                                35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZC3H13 MUTATED                                                  6
  ZC3H13 WILD-TYPE                                               32
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZC3H13 MUTATED                                                          0
  ZC3H13 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZC3H13 MUTATED                                                           0
  ZC3H13 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZC3H13 MUTATED                                          0
  ZC3H13 WILD-TYPE                                        3
D188V8, multiclass
                                                                   clus
vv                                                                  ZC3H13 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ZC3H13 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         119
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D188V9, binary
                  cls
clus                 0   1
  ZC3H13 MUTATED     0  29
  ZC3H13 WILD-TYPE   5 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED      0   29
  ZC3H13 WILD-TYPE    5  255
     clus
vv    ZC3H13 MUTATED ZC3H13 WILD-TYPE
  NO               0                5
  YES             29              255
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZC3H13 MUTATED    20   0   2   5
  ZC3H13 WILD-TYPE 207  10   8  19
D188V10, multiclass
    clus
vv   ZC3H13 MUTATED ZC3H13 WILD-TYPE
  R0             20              207
  R1              0               10
  R2              2                8
  RX              5               19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D188V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZC3H13 MUTATED       8                         1    15
  ZC3H13 WILD-TYPE    68                         3   153
D188V12, multiclass
                           clus
vv                          ZC3H13 MUTATED ZC3H13 WILD-TYPE
  ASIAN                                  8               68
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                 15              153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(189) Variable = IGFBP7 MUTATION ANALYSIS
D189V1, survival
                  sevent
clus2                0   1
  IGFBP7 MUTATED     2   1
  IGFBP7 WILD-TYPE 179  79
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               3              258 
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               1               79 
$`IGFBP7 MUTATED`
TCGA-BR-8487 TCGA-CG-5733 TCGA-FP-A4BE 
        1.12        21.07        11.08 

$`IGFBP7 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10         4.01        69.04         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 
       59.54         5.03        13.58         0.56         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
            1.12             0.00 
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
           21.07           105.07 
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
           11.08            12.64 
[1] "1.1 - 21.1 (11.1)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D189V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IGFBP7 MUTATED         0        0        1        0         2         0
  IGFBP7 WILD-TYPE       1        9       26       26        29        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IGFBP7 MUTATED           0          1          0          0        0
  IGFBP7 WILD-TYPE         3         48         36         24       24
D189V3, multiclass
            clus
vv           IGFBP7 MUTATED IGFBP7 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               2               29
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IGFBP7 MUTATED     0   2   2   0
  IGFBP7 WILD-TYPE  11  70 120  75
D189V4, multiclass
    clus
vv   IGFBP7 MUTATED IGFBP7 WILD-TYPE
  T1              0               11
  T2              2               70
  T3              2              120
  T4              0               75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  IGFBP7 MUTATED    3  0  1  0
  IGFBP7 WILD-TYPE 90 81 49 53
D189V5, multiclass
    clus
vv   IGFBP7 MUTATED IGFBP7 WILD-TYPE
  N0              3               90
  N1              0               81
  N2              1               49
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D189V6, binary
                  cls
clus                 0   1
  IGFBP7 MUTATED     4   0
  IGFBP7 WILD-TYPE 253  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP7 MUTATED      4    0
  IGFBP7 WILD-TYPE  253   18
   clus
vv  IGFBP7 MUTATED IGFBP7 WILD-TYPE
  0              4              253
  1              0               18
[1] 2 2
[1] FALSE
D189V7, binary
                  cls
clus                 0   1
  IGFBP7 MUTATED     2   2
  IGFBP7 WILD-TYPE 108 177
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP7 MUTATED      2    2
  IGFBP7 WILD-TYPE  108  177
        clus
vv       IGFBP7 MUTATED IGFBP7 WILD-TYPE
  FEMALE              2              108
  MALE                2              177
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  IGFBP7 MUTATED                                       0
  IGFBP7 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IGFBP7 MUTATED                                                        2
  IGFBP7 WILD-TYPE                                                    133
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IGFBP7 MUTATED                                                                   2
  IGFBP7 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  IGFBP7 MUTATED                                                  0
  IGFBP7 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  IGFBP7 MUTATED                                                          0
  IGFBP7 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  IGFBP7 MUTATED                                                           0
  IGFBP7 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  IGFBP7 MUTATED                                          0
  IGFBP7 WILD-TYPE                                        3
D189V8, multiclass
                                                                   clus
vv                                                                  IGFBP7 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  IGFBP7 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D189V9, binary
                  cls
clus                 0   1
  IGFBP7 MUTATED     0   4
  IGFBP7 WILD-TYPE   5 280
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP7 MUTATED      0    4
  IGFBP7 WILD-TYPE    5  280
     clus
vv    IGFBP7 MUTATED IGFBP7 WILD-TYPE
  NO               0                5
  YES              4              280
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  IGFBP7 MUTATED     4   0   0   0
  IGFBP7 WILD-TYPE 223  10  10  24
D189V10, multiclass
    clus
vv   IGFBP7 MUTATED IGFBP7 WILD-TYPE
  R0              4              223
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D189V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IGFBP7 MUTATED       0                         1     1
  IGFBP7 WILD-TYPE    76                         3   167
D189V12, multiclass
[1] "Remove cluster labels:" "IGFBP7 MUTATED"        
clus
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               2              246 
      TCGA-B7-5816       TCGA-B7-5818       TCGA-BR-4183       TCGA-BR-4184 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-4187       TCGA-BR-4188       TCGA-BR-4191       TCGA-BR-4201 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-4253       TCGA-BR-4255       TCGA-BR-4256       TCGA-BR-4257 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-4267       TCGA-BR-4279       TCGA-BR-4280       TCGA-BR-4292 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-4294       TCGA-BR-4357       TCGA-BR-4361       TCGA-BR-4362 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-4363       TCGA-BR-4366       TCGA-BR-4368       TCGA-BR-4369 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-4370       TCGA-BR-4371       TCGA-BR-6452       TCGA-BR-6453 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-6454       TCGA-BR-6455       TCGA-BR-6456       TCGA-BR-6457 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-6458       TCGA-BR-6563       TCGA-BR-6564       TCGA-BR-6565 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-6566       TCGA-BR-6705       TCGA-BR-6706       TCGA-BR-6707 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-6710       TCGA-BR-6801       TCGA-BR-6802       TCGA-BR-6803 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-6852       TCGA-BR-7196       TCGA-BR-7197       TCGA-BR-7703 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-7707       TCGA-BR-7715       TCGA-BR-7716       TCGA-BR-7717 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-7722       TCGA-BR-7723       TCGA-BR-7851       TCGA-BR-7901 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-7957       TCGA-BR-7958       TCGA-BR-7959       TCGA-BR-8058 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8059       TCGA-BR-8077       TCGA-BR-8078       TCGA-BR-8080 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8081       TCGA-BR-8284       TCGA-BR-8286       TCGA-BR-8289 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8291       TCGA-BR-8295       TCGA-BR-8296       TCGA-BR-8297 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8360       TCGA-BR-8361       TCGA-BR-8363       TCGA-BR-8364 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8365       TCGA-BR-8366       TCGA-BR-8367       TCGA-BR-8368 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8369       TCGA-BR-8370       TCGA-BR-8371       TCGA-BR-8372 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8373       TCGA-BR-8380       TCGA-BR-8381       TCGA-BR-8382 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8384       TCGA-BR-8483       TCGA-BR-8484       TCGA-BR-8485 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8486       TCGA-BR-8588       TCGA-BR-8589       TCGA-BR-8590 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8591       TCGA-BR-8592       TCGA-BR-8676       TCGA-BR-8677 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8678       TCGA-BR-8679       TCGA-BR-8680       TCGA-BR-8682 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8683       TCGA-BR-8686       TCGA-BR-8687       TCGA-BR-8690 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-A44T       TCGA-BR-A44U       TCGA-BR-A452       TCGA-BR-A453 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-A4CQ       TCGA-BR-A4CR       TCGA-BR-A4CS       TCGA-BR-A4IU 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-A4IV       TCGA-BR-A4IY       TCGA-BR-A4IZ       TCGA-BR-A4J1 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-A4J2       TCGA-BR-A4J4       TCGA-BR-A4J6       TCGA-BR-A4J7 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-A4J8       TCGA-BR-A4PD       TCGA-BR-A4PE       TCGA-BR-A4PF 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-A4QI       TCGA-BR-A4QL       TCGA-BR-A4QM       TCGA-CD-5798 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-CD-5799       TCGA-CD-5800       TCGA-CD-5801       TCGA-CD-5802 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-CD-5803       TCGA-CD-5804       TCGA-CD-5813       TCGA-CD-8524 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-CD-8525       TCGA-CD-8526       TCGA-CD-8527       TCGA-CD-8528 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-CD-8529       TCGA-CD-8530       TCGA-CD-8531       TCGA-CD-8532 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-CD-8534       TCGA-CD-8535       TCGA-CD-8536       TCGA-CD-A486 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-CD-A487       TCGA-CD-A489       TCGA-CD-A48A       TCGA-CD-A48C 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-CD-A4MG       TCGA-CD-A4MH       TCGA-CD-A4MI       TCGA-CD-A4MJ 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-D7-5577       TCGA-D7-5578       TCGA-D7-5579       TCGA-D7-6518 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-D7-6519       TCGA-D7-6520       TCGA-D7-6521       TCGA-D7-6522 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-D7-6524       TCGA-D7-6525       TCGA-D7-6526       TCGA-D7-6527 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-D7-6528       TCGA-D7-6815       TCGA-D7-6817       TCGA-D7-6818 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-D7-6820       TCGA-D7-6822       TCGA-D7-8570       TCGA-D7-8572 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-D7-8573       TCGA-D7-8574       TCGA-D7-8575       TCGA-D7-8576 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-D7-8578       TCGA-D7-8579       TCGA-D7-A4YT       TCGA-D7-A4YU 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-D7-A4YV       TCGA-D7-A4YX       TCGA-D7-A4YY       TCGA-D7-A4Z0 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-EQ-5647       TCGA-EQ-8122       TCGA-EQ-A4SO       TCGA-F1-6177 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-F1-6874       TCGA-F1-6875       TCGA-F1-A448       TCGA-FP-7735 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-FP-7829       TCGA-FP-7916       TCGA-FP-7998       TCGA-FP-8099 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-FP-8209       TCGA-FP-8210       TCGA-FP-8211       TCGA-FP-8631 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-FP-A4BF       TCGA-HJ-7597       TCGA-HU-8243       TCGA-HU-8245 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-HU-8249       TCGA-HU-8602       TCGA-HU-8604       TCGA-HU-8608 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-HU-8610       TCGA-HU-A4G2       TCGA-HU-A4G3       TCGA-HU-A4G6 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-HU-A4G8       TCGA-HU-A4G9       TCGA-HU-A4GC       TCGA-HU-A4GD 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-HU-A4GF       TCGA-HU-A4GH       TCGA-HU-A4GN       TCGA-HU-A4GP 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-HU-A4GQ       TCGA-HU-A4GT       TCGA-HU-A4GU       TCGA-HU-A4GX 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-HU-A4GY       TCGA-HU-A4H0       TCGA-HU-A4H2       TCGA-HU-A4H3 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-HU-A4H4       TCGA-HU-A4H5       TCGA-HU-A4H6       TCGA-HU-A4H8 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-HU-A4HD       TCGA-IN-7806       TCGA-IN-7808       TCGA-IN-8462 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-IN-8663       TCGA-IP-7968 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 

Clustering(190) Variable = HNF1B MUTATION ANALYSIS
D190V1, survival
                 sevent
clus2               0   1
  HNF1B MUTATED     4   1
  HNF1B WILD-TYPE 177  79
  HNF1B MUTATED HNF1B WILD-TYPE 
              5             256 
  HNF1B MUTATED HNF1B WILD-TYPE 
              1              79 
$`HNF1B MUTATED`
TCGA-B7-5816 TCGA-BR-8078 TCGA-BR-A4IY TCGA-BR-A4QL TCGA-CD-A4MG 
       26.70        12.26        12.89        11.57         6.58 

$`HNF1B WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       13.51         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  HNF1B MUTATED HNF1B WILD-TYPE 
           6.58            0.00 
  HNF1B MUTATED HNF1B WILD-TYPE 
          26.70          105.07 
  HNF1B MUTATED HNF1B WILD-TYPE 
          12.26           12.64 
[1] "6.6 - 26.7 (12.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.5"
D190V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HNF1B MUTATED         0        0        0        0         1         3
  HNF1B WILD-TYPE       1        9       27       26        30        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HNF1B MUTATED           0          0          1          0        0
  HNF1B WILD-TYPE         3         49         35         24       24
D190V3, multiclass
            clus
vv           HNF1B MUTATED HNF1B WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              3              41
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HNF1B MUTATED     0   0   2   3
  HNF1B WILD-TYPE  11  72 120  72
D190V4, multiclass
    clus
vv   HNF1B MUTATED HNF1B WILD-TYPE
  T1             0              11
  T2             0              72
  T3             2             120
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  HNF1B MUTATED    4  1  0  1
  HNF1B WILD-TYPE 89 80 50 52
D190V5, multiclass
    clus
vv   HNF1B MUTATED HNF1B WILD-TYPE
  N0             4              89
  N1             1              80
  N2             0              50
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D190V6, binary
                 cls
clus                0   1
  HNF1B MUTATED     6   0
  HNF1B WILD-TYPE 251  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      6    0
  HNF1B WILD-TYPE  251   18
   clus
vv  HNF1B MUTATED HNF1B WILD-TYPE
  0             6             251
  1             0              18
[1] 2 2
[1] FALSE
D190V7, binary
                 cls
clus                0   1
  HNF1B MUTATED     4   2
  HNF1B WILD-TYPE 106 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      4    2
  HNF1B WILD-TYPE  106  177
        clus
vv       HNF1B MUTATED HNF1B WILD-TYPE
  FEMALE             4             106
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  HNF1B MUTATED                                       2
  HNF1B WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HNF1B MUTATED                                                        4
  HNF1B WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HNF1B MUTATED                                                                   0
  HNF1B WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  HNF1B MUTATED                                                  0
  HNF1B WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  HNF1B MUTATED                                                          0
  HNF1B WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  HNF1B MUTATED                                                           0
  HNF1B WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  HNF1B MUTATED                                          0
  HNF1B WILD-TYPE                                        3
D190V8, multiclass
                                                                   clus
vv                                                                  HNF1B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  HNF1B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D190V9, binary
                 cls
clus                0   1
  HNF1B MUTATED     0   6
  HNF1B WILD-TYPE   5 278
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      0    6
  HNF1B WILD-TYPE    5  278
     clus
vv    HNF1B MUTATED HNF1B WILD-TYPE
  NO              0               5
  YES             6             278
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HNF1B MUTATED     4   0   0   1
  HNF1B WILD-TYPE 223  10  10  23
D190V10, multiclass
    clus
vv   HNF1B MUTATED HNF1B WILD-TYPE
  R0             4             223
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D190V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HNF1B MUTATED       2                         0     4
  HNF1B WILD-TYPE    74                         4   164
D190V12, multiclass
                           clus
vv                          HNF1B MUTATED HNF1B WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(191) Variable = FAM113B MUTATION ANALYSIS
D191V1, survival
                   sevent
clus2                 0   1
  FAM113B MUTATED     9   3
  FAM113B WILD-TYPE 172  77
  FAM113B MUTATED FAM113B WILD-TYPE 
               12               249 
  FAM113B MUTATED FAM113B WILD-TYPE 
                3                77 
$`FAM113B MUTATED`
TCGA-BR-4201 TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-8059 TCGA-BR-8361 TCGA-BR-8372 
       30.90        23.93        12.43        14.43        19.50        19.17 
TCGA-BR-8680 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5733 TCGA-F1-6874 TCGA-FP-A4BE 
       15.81         6.02       105.07        21.07        14.47        11.08 

$`FAM113B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 
        3.45         9.07        12.76        18.71        17.49         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
       16.31         2.20        15.58         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99         0.99        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.99        16.24        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  FAM113B MUTATED FAM113B WILD-TYPE 
             6.02              0.00 
  FAM113B MUTATED FAM113B WILD-TYPE 
           105.07             79.07 
  FAM113B MUTATED FAM113B WILD-TYPE 
            17.49             12.43 
[1] "6.0 - 105.1 (17.5)" "0.0 - 79.1 (12.4)" 
[1] "hr=" "2.1"
D191V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM113B MUTATED         0        0        2        1         1         1
  FAM113B WILD-TYPE       1        9       25       25        30        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM113B MUTATED           1          2          0          2        2
  FAM113B WILD-TYPE         2         47         36         22       22
D191V3, multiclass
            clus
vv           FAM113B MUTATED FAM113B WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 2                25
  STAGE II                 1                25
  STAGE IIA                1                30
  STAGE IIB                1                43
  STAGE III                1                 2
  STAGE IIIA               2                47
  STAGE IIIB               0                36
  STAGE IIIC               2                22
  STAGE IV                 2                22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM113B MUTATED     0   5   1   7
  FAM113B WILD-TYPE  11  67 121  68
D191V4, multiclass
    clus
vv   FAM113B MUTATED FAM113B WILD-TYPE
  T1               0                11
  T2               5                67
  T3               1               121
  T4               7                68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  FAM113B MUTATED    5  3  3  1
  FAM113B WILD-TYPE 88 78 47 52
D191V5, multiclass
    clus
vv   FAM113B MUTATED FAM113B WILD-TYPE
  N0               5                88
  N1               3                78
  N2               3                47
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D191V6, binary
                   cls
clus                  0   1
  FAM113B MUTATED    12   1
  FAM113B WILD-TYPE 245  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM113B MUTATED     12    1
  FAM113B WILD-TYPE  245   17
   clus
vv  FAM113B MUTATED FAM113B WILD-TYPE
  0              12               245
  1               1                17
[1] 2 2
[1] FALSE
D191V7, binary
                   cls
clus                  0   1
  FAM113B MUTATED     5   8
  FAM113B WILD-TYPE 105 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM113B MUTATED      5    8
  FAM113B WILD-TYPE  105  171
        clus
vv       FAM113B MUTATED FAM113B WILD-TYPE
  FEMALE               5               105
  MALE                 8               171
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FAM113B MUTATED                                       0
  FAM113B WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAM113B MUTATED                                                        7
  FAM113B WILD-TYPE                                                    128
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAM113B MUTATED                                                                   5
  FAM113B WILD-TYPE                                                                35
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FAM113B MUTATED                                                  1
  FAM113B WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FAM113B MUTATED                                                          0
  FAM113B WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FAM113B MUTATED                                                           0
  FAM113B WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FAM113B MUTATED                                          0
  FAM113B WILD-TYPE                                        3
D191V8, multiclass
                                                                   clus
vv                                                                  FAM113B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  FAM113B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D191V9, binary
                   cls
clus                  0   1
  FAM113B MUTATED     0  13
  FAM113B WILD-TYPE   5 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM113B MUTATED      0   13
  FAM113B WILD-TYPE    5  271
     clus
vv    FAM113B MUTATED FAM113B WILD-TYPE
  NO                0                 5
  YES              13               271
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM113B MUTATED    11   0   0   2
  FAM113B WILD-TYPE 216  10  10  22
D191V10, multiclass
    clus
vv   FAM113B MUTATED FAM113B WILD-TYPE
  R0              11               216
  R1               0                10
  R2               0                10
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D191V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM113B MUTATED       1                         1     8
  FAM113B WILD-TYPE    75                         3   160
D191V12, multiclass
                           clus
vv                          FAM113B MUTATED FAM113B WILD-TYPE
  ASIAN                                   1                75
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   8               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(192) Variable = RRS1 MUTATION ANALYSIS
D192V1, survival
                sevent
clus2              0   1
  RRS1 MUTATED     5   0
  RRS1 WILD-TYPE 176  80
  RRS1 MUTATED RRS1 WILD-TYPE 
             5            256 
  RRS1 MUTATED RRS1 WILD-TYPE 
             0             80 
$`RRS1 MUTATED`
TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-8487 TCGA-D7-5578 TCGA-D7-A4YT 
       23.93        12.43         1.12        12.66        14.27 

$`RRS1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 
        4.01        69.04        21.07         7.99        12.36        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       17.19        18.21        14.66        21.14        20.91        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  RRS1 MUTATED RRS1 WILD-TYPE 
          1.12           0.00 
  RRS1 MUTATED RRS1 WILD-TYPE 
         23.93         105.07 
  RRS1 MUTATED RRS1 WILD-TYPE 
        12.660         12.605 
[1] "1.1 - 23.9 (12.7)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "9200000"
D192V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RRS1 MUTATED         0        0        2        0         1         1
  RRS1 WILD-TYPE       1        9       25       26        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RRS1 MUTATED           0          3          0          0        0
  RRS1 WILD-TYPE         3         46         36         24       24
D192V3, multiclass
            clus
vv           RRS1 MUTATED RRS1 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              0             26
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            3             46
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RRS1 MUTATED     0   3   2   2
  RRS1 WILD-TYPE  11  69 120  73
D192V4, multiclass
    clus
vv   RRS1 MUTATED RRS1 WILD-TYPE
  T1            0             11
  T2            3             69
  T3            2            120
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  RRS1 MUTATED    5  0  1  1
  RRS1 WILD-TYPE 88 81 49 52
D192V5, multiclass
    clus
vv   RRS1 MUTATED RRS1 WILD-TYPE
  N0            5             88
  N1            0             81
  N2            1             49
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D192V6, binary
                cls
clus               0   1
  RRS1 MUTATED     7   0
  RRS1 WILD-TYPE 250  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRS1 MUTATED      7    0
  RRS1 WILD-TYPE  250   18
   clus
vv  RRS1 MUTATED RRS1 WILD-TYPE
  0            7            250
  1            0             18
[1] 2 2
[1] FALSE
D192V7, binary
                cls
clus               0   1
  RRS1 MUTATED     3   4
  RRS1 WILD-TYPE 107 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRS1 MUTATED      3    4
  RRS1 WILD-TYPE  107  175
        clus
vv       RRS1 MUTATED RRS1 WILD-TYPE
  FEMALE            3            107
  MALE              4            175
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RRS1 MUTATED                                       0
  RRS1 WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RRS1 MUTATED                                                        3
  RRS1 WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RRS1 MUTATED                                                                   2
  RRS1 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RRS1 MUTATED                                                  2
  RRS1 WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RRS1 MUTATED                                                          0
  RRS1 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RRS1 MUTATED                                                           0
  RRS1 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RRS1 MUTATED                                          0
  RRS1 WILD-TYPE                                        3
D192V8, multiclass
                                                                   clus
vv                                                                  RRS1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  RRS1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D192V9, binary
                cls
clus               0   1
  RRS1 MUTATED     0   7
  RRS1 WILD-TYPE   5 277
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRS1 MUTATED      0    7
  RRS1 WILD-TYPE    5  277
     clus
vv    RRS1 MUTATED RRS1 WILD-TYPE
  NO             0              5
  YES            7            277
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RRS1 MUTATED     6   0   0   1
  RRS1 WILD-TYPE 221  10  10  23
D192V10, multiclass
    clus
vv   RRS1 MUTATED RRS1 WILD-TYPE
  R0            6            221
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D192V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RRS1 MUTATED       0                         0     6
  RRS1 WILD-TYPE    76                         4   162
D192V12, multiclass
                           clus
vv                          RRS1 MUTATED RRS1 WILD-TYPE
  ASIAN                                0             76
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                6            162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(193) Variable = WNK4 MUTATION ANALYSIS
D193V1, survival
                sevent
clus2              0   1
  WNK4 MUTATED    11   5
  WNK4 WILD-TYPE 170  75
  WNK4 MUTATED WNK4 WILD-TYPE 
            16            245 
  WNK4 MUTATED WNK4 WILD-TYPE 
             5             75 
$`WNK4 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-8487 
        6.97        34.68        23.93        28.73        12.43         1.12 
TCGA-BR-A4QL TCGA-CD-8527 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-D7-A4YV 
       11.57         0.07         6.02       105.07        28.96         5.92 
TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4H3 
       11.41        11.84         0.10        19.36 

$`WNK4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 
       15.42        28.01        18.15        15.32         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        20.55         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
        0.99        12.03        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       12.95        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  WNK4 MUTATED WNK4 WILD-TYPE 
          0.07           0.00 
  WNK4 MUTATED WNK4 WILD-TYPE 
        105.07          79.07 
  WNK4 MUTATED WNK4 WILD-TYPE 
        11.705         12.760 
[1] "0.1 - 105.1 (11.7)" "0.0 - 79.1 (12.8)" 
[1] "hr=" "1.3"
D193V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WNK4 MUTATED         0        1        2        3         2         4
  WNK4 WILD-TYPE       1        8       25       23        29        40
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WNK4 MUTATED           0          2          2          2        1
  WNK4 WILD-TYPE         3         47         34         22       23
D193V3, multiclass
            clus
vv           WNK4 MUTATED WNK4 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              2             25
  STAGE II              3             23
  STAGE IIA             2             29
  STAGE IIB             4             40
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            2             34
  STAGE IIIC            2             22
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WNK4 MUTATED     1   5   8   6
  WNK4 WILD-TYPE  10  67 114  69
D193V4, multiclass
    clus
vv   WNK4 MUTATED WNK4 WILD-TYPE
  T1            1             10
  T2            5             67
  T3            8            114
  T4            6             69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  WNK4 MUTATED    8  7  1  3
  WNK4 WILD-TYPE 85 74 49 50
D193V5, multiclass
    clus
vv   WNK4 MUTATED WNK4 WILD-TYPE
  N0            8             85
  N1            7             74
  N2            1             49
  N3            3             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D193V6, binary
                cls
clus               0   1
  WNK4 MUTATED    19   0
  WNK4 WILD-TYPE 238  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK4 MUTATED     19    0
  WNK4 WILD-TYPE  238   18
   clus
vv  WNK4 MUTATED WNK4 WILD-TYPE
  0           19            238
  1            0             18
[1] 2 2
[1] FALSE
D193V7, binary
                cls
clus               0   1
  WNK4 MUTATED    12   9
  WNK4 WILD-TYPE  98 170
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK4 MUTATED     12    9
  WNK4 WILD-TYPE   98  170
        clus
vv       WNK4 MUTATED WNK4 WILD-TYPE
  FEMALE           12             98
  MALE              9            170
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  WNK4 MUTATED                                       3
  WNK4 WILD-TYPE                                    47
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WNK4 MUTATED                                                       10
  WNK4 WILD-TYPE                                                    125
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WNK4 MUTATED                                                                   5
  WNK4 WILD-TYPE                                                                35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  WNK4 MUTATED                                                  2
  WNK4 WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  WNK4 MUTATED                                                          1
  WNK4 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  WNK4 MUTATED                                                           0
  WNK4 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  WNK4 MUTATED                                          0
  WNK4 WILD-TYPE                                        3
D193V8, multiclass
                                                                   clus
vv                                                                  WNK4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  WNK4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D193V9, binary
                cls
clus               0   1
  WNK4 MUTATED     1  20
  WNK4 WILD-TYPE   4 264
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK4 MUTATED      1   20
  WNK4 WILD-TYPE    4  264
     clus
vv    WNK4 MUTATED WNK4 WILD-TYPE
  NO             1              4
  YES           20            264
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  WNK4 MUTATED    16   0   0   4
  WNK4 WILD-TYPE 211  10  10  20
D193V10, multiclass
    clus
vv   WNK4 MUTATED WNK4 WILD-TYPE
  R0           16            211
  R1            0             10
  R2            0             10
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D193V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WNK4 MUTATED       5                         0    11
  WNK4 WILD-TYPE    71                         4   157
D193V12, multiclass
                           clus
vv                          WNK4 MUTATED WNK4 WILD-TYPE
  ASIAN                                5             71
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               11            157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(194) Variable = RAD51AP2 MUTATION ANALYSIS
D194V1, survival
                    sevent
clus2                  0   1
  RAD51AP2 MUTATED     8   3
  RAD51AP2 WILD-TYPE 173  77
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                11                250 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                 3                 77 
$`RAD51AP2 MUTATED`
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8295 TCGA-BR-8361 TCGA-CG-4306 
       24.76        23.93        12.26         2.20        19.50         1.02 
TCGA-CG-5721 TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4GT TCGA-HU-A4HD 
        6.02        26.47        11.41         6.51        27.42 

$`RAD51AP2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
        9.21        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
        2.66        16.31        15.58         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        5.52         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-IN-7806 
       19.36        23.84        12.30         9.67         8.88        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
              1.02               0.00 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
             27.42             105.07 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
             12.26              12.64 
[1] "1.0 - 27.4 (12.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D194V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RAD51AP2 MUTATED         0        1        2        0         1         3
  RAD51AP2 WILD-TYPE       1        8       25       26        30        41
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAD51AP2 MUTATED           0          1          0          1        2
  RAD51AP2 WILD-TYPE         3         48         36         23       22
D194V3, multiclass
            clus
vv           RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  1                  8
  STAGE IB                  2                 25
  STAGE II                  0                 26
  STAGE IIA                 1                 30
  STAGE IIB                 3                 41
  STAGE III                 0                  3
  STAGE IIIA                1                 48
  STAGE IIIB                0                 36
  STAGE IIIC                1                 23
  STAGE IV                  2                 22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  RAD51AP2 MUTATED     1   2   3   5
  RAD51AP2 WILD-TYPE  10  70 119  70
D194V4, multiclass
    clus
vv   RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  T1                1                 10
  T2                2                 70
  T3                3                119
  T4                5                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  RAD51AP2 MUTATED    7  1  3  0
  RAD51AP2 WILD-TYPE 86 80 47 53
D194V5, multiclass
    clus
vv   RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  N0                7                 86
  N1                1                 80
  N2                3                 47
  N3                0                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D194V6, binary
                    cls
clus                   0   1
  RAD51AP2 MUTATED    10   1
  RAD51AP2 WILD-TYPE 247  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAD51AP2 MUTATED     10    1
  RAD51AP2 WILD-TYPE  247   17
   clus
vv  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  0               10                247
  1                1                 17
[1] 2 2
[1] FALSE
D194V7, binary
                    cls
clus                   0   1
  RAD51AP2 MUTATED     8   4
  RAD51AP2 WILD-TYPE 102 175
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAD51AP2 MUTATED      8    4
  RAD51AP2 WILD-TYPE  102  175
        clus
vv       RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  FEMALE                8                102
  MALE                  4                175
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RAD51AP2 MUTATED                                       1
  RAD51AP2 WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RAD51AP2 MUTATED                                                        6
  RAD51AP2 WILD-TYPE                                                    129
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RAD51AP2 MUTATED                                                                   1
  RAD51AP2 WILD-TYPE                                                                39
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RAD51AP2 MUTATED                                                  2
  RAD51AP2 WILD-TYPE                                               36
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RAD51AP2 MUTATED                                                          0
  RAD51AP2 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RAD51AP2 MUTATED                                                           1
  RAD51AP2 WILD-TYPE                                                         5
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RAD51AP2 MUTATED                                          1
  RAD51AP2 WILD-TYPE                                        2
D194V8, multiclass
                                                                   clus
vv                                                                  RAD51AP2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  RAD51AP2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D194V9, binary
                    cls
clus                   0   1
  RAD51AP2 MUTATED     0  12
  RAD51AP2 WILD-TYPE   5 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAD51AP2 MUTATED      0   12
  RAD51AP2 WILD-TYPE    5  272
     clus
vv    RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  NO                 0                  5
  YES               12                272
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  RAD51AP2 MUTATED    10   0   1   1
  RAD51AP2 WILD-TYPE 217  10   9  23
D194V10, multiclass
    clus
vv   RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  R0               10                217
  R1                0                 10
  R2                1                  9
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D194V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RAD51AP2 MUTATED       3                         0     7
  RAD51AP2 WILD-TYPE    73                         4   161
D194V12, multiclass
                           clus
vv                          RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  ASIAN                                    3                 73
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    7                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(195) Variable = PIGB MUTATION ANALYSIS
D195V1, survival
                sevent
clus2              0   1
  PIGB MUTATED     5   1
  PIGB WILD-TYPE 176  79
  PIGB MUTATED PIGB WILD-TYPE 
             6            255 
  PIGB MUTATED PIGB WILD-TYPE 
             1             79 
$`PIGB MUTATED`
TCGA-B7-5816 TCGA-BR-7707 TCGA-BR-8487 TCGA-BR-8589 TCGA-CG-5721 TCGA-HU-A4GQ 
       26.70        23.93         1.12        15.81         6.02         0.10 

$`PIGB WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        9.21        20.22        12.79         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  PIGB MUTATED PIGB WILD-TYPE 
           0.1            0.0 
  PIGB MUTATED PIGB WILD-TYPE 
         26.70         105.07 
  PIGB MUTATED PIGB WILD-TYPE 
        10.915         12.620 
[1] "0.1 - 26.7 (10.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.7"
D195V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIGB MUTATED         0        0        2        1         1         1
  PIGB WILD-TYPE       1        9       25       25        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIGB MUTATED           0          0          1          1        1
  PIGB WILD-TYPE         3         49         35         23       23
D195V3, multiclass
            clus
vv           PIGB MUTATED PIGB WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              1             25
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            1             35
  STAGE IIIC            1             23
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PIGB MUTATED     1   3   1   4
  PIGB WILD-TYPE  10  69 121  71
D195V4, multiclass
    clus
vv   PIGB MUTATED PIGB WILD-TYPE
  T1            1             10
  T2            3             69
  T3            1            121
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  PIGB MUTATED    4  3  1  0
  PIGB WILD-TYPE 89 78 49 53
D195V5, multiclass
    clus
vv   PIGB MUTATED PIGB WILD-TYPE
  N0            4             89
  N1            3             78
  N2            1             49
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D195V6, binary
                cls
clus               0   1
  PIGB MUTATED    10   0
  PIGB WILD-TYPE 247  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGB MUTATED     10    0
  PIGB WILD-TYPE  247   18
   clus
vv  PIGB MUTATED PIGB WILD-TYPE
  0           10            247
  1            0             18
[1] 2 2
[1] FALSE
D195V7, binary
                cls
clus               0   1
  PIGB MUTATED     5   5
  PIGB WILD-TYPE 105 174
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGB MUTATED      5    5
  PIGB WILD-TYPE  105  174
        clus
vv       PIGB MUTATED PIGB WILD-TYPE
  FEMALE            5            105
  MALE              5            174
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PIGB MUTATED                                       1
  PIGB WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIGB MUTATED                                                        5
  PIGB WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIGB MUTATED                                                                   2
  PIGB WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PIGB MUTATED                                                  1
  PIGB WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PIGB MUTATED                                                          1
  PIGB WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PIGB MUTATED                                                           0
  PIGB WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PIGB MUTATED                                          0
  PIGB WILD-TYPE                                        3
D195V8, multiclass
                                                                   clus
vv                                                                  PIGB MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  PIGB WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D195V9, binary
                cls
clus               0   1
  PIGB MUTATED     1   9
  PIGB WILD-TYPE   4 275
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGB MUTATED      1    9
  PIGB WILD-TYPE    4  275
     clus
vv    PIGB MUTATED PIGB WILD-TYPE
  NO             1              4
  YES            9            275
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PIGB MUTATED     8   0   0   2
  PIGB WILD-TYPE 219  10  10  22
D195V10, multiclass
    clus
vv   PIGB MUTATED PIGB WILD-TYPE
  R0            8            219
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D195V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIGB MUTATED       1                         0     6
  PIGB WILD-TYPE    75                         4   162
D195V12, multiclass
                           clus
vv                          PIGB MUTATED PIGB WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                6            162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(196) Variable = OGDH MUTATION ANALYSIS
D196V1, survival
                sevent
clus2              0   1
  OGDH MUTATED     4   2
  OGDH WILD-TYPE 177  78
  OGDH MUTATED OGDH WILD-TYPE 
             6            255 
  OGDH MUTATED OGDH WILD-TYPE 
             2             78 
$`OGDH MUTATED`
TCGA-BR-4201 TCGA-BR-8059 TCGA-CG-4449 TCGA-F1-6874 TCGA-HU-A4G8 TCGA-HU-A4GT 
       30.90        14.43        19.07        14.47        11.84         6.51 

$`OGDH WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        0.62         7.99        16.24        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         0.10         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  OGDH MUTATED OGDH WILD-TYPE 
          6.51           0.00 
  OGDH MUTATED OGDH WILD-TYPE 
         30.90         105.07 
  OGDH MUTATED OGDH WILD-TYPE 
         14.45          12.59 
[1] "6.5 - 30.9 (14.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D196V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OGDH MUTATED         0        0        2        1         1         1
  OGDH WILD-TYPE       1        9       25       25        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OGDH MUTATED           1          0          0          0        0
  OGDH WILD-TYPE         2         49         36         24       24
D196V3, multiclass
            clus
vv           OGDH MUTATED OGDH WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              1             25
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             1              2
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  OGDH MUTATED     1   4   2   1
  OGDH WILD-TYPE  10  68 120  74
D196V4, multiclass
    clus
vv   OGDH MUTATED OGDH WILD-TYPE
  T1            1             10
  T2            4             68
  T3            2            120
  T4            1             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  OGDH MUTATED    3  4  0  0
  OGDH WILD-TYPE 90 77 50 53
D196V5, multiclass
    clus
vv   OGDH MUTATED OGDH WILD-TYPE
  N0            3             90
  N1            4             77
  N2            0             50
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D196V6, binary
                cls
clus               0   1
  OGDH MUTATED     9   0
  OGDH WILD-TYPE 248  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  OGDH MUTATED      9    0
  OGDH WILD-TYPE  248   18
   clus
vv  OGDH MUTATED OGDH WILD-TYPE
  0            9            248
  1            0             18
[1] 2 2
[1] FALSE
D196V7, binary
                cls
clus               0   1
  OGDH MUTATED     5   4
  OGDH WILD-TYPE 105 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  OGDH MUTATED      5    4
  OGDH WILD-TYPE  105  175
        clus
vv       OGDH MUTATED OGDH WILD-TYPE
  FEMALE            5            105
  MALE              4            175
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  OGDH MUTATED                                       1
  OGDH WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OGDH MUTATED                                                        3
  OGDH WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OGDH MUTATED                                                                   3
  OGDH WILD-TYPE                                                                37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  OGDH MUTATED                                                  1
  OGDH WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  OGDH MUTATED                                                          1
  OGDH WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  OGDH MUTATED                                                           0
  OGDH WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  OGDH MUTATED                                          0
  OGDH WILD-TYPE                                        3
D196V8, multiclass
                                                                   clus
vv                                                                  OGDH MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  OGDH WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D196V9, binary
                cls
clus               0   1
  OGDH MUTATED     0   9
  OGDH WILD-TYPE   5 275
[1] "tbl2"
                cls
clus             [,1] [,2]
  OGDH MUTATED      0    9
  OGDH WILD-TYPE    5  275
     clus
vv    OGDH MUTATED OGDH WILD-TYPE
  NO             0              5
  YES            9            275
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  OGDH MUTATED     5   0   0   3
  OGDH WILD-TYPE 222  10  10  21
D196V10, multiclass
    clus
vv   OGDH MUTATED OGDH WILD-TYPE
  R0            5            222
  R1            0             10
  R2            0             10
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D196V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OGDH MUTATED       2                         0     5
  OGDH WILD-TYPE    74                         4   163
D196V12, multiclass
                           clus
vv                          OGDH MUTATED OGDH WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                5            163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(197) Variable = SERPINB12 MUTATION ANALYSIS
D197V1, survival
                     sevent
clus2                   0   1
  SERPINB12 MUTATED     5   1
  SERPINB12 WILD-TYPE 176  79
  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
                  6                 255 
  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
                  1                  79 
$`SERPINB12 MUTATED`
TCGA-BR-4184 TCGA-BR-8286 TCGA-BR-8487 TCGA-CG-5721 TCGA-HU-A4GH TCGA-HU-A4GN 
        6.97        12.95         1.12         6.02        11.77        29.98 

$`SERPINB12 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        8.05         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       22.75        25.81         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
               1.12                0.00 
  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
              29.98              105.07 
  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
               9.37               12.66 
[1] "1.1 - 30.0 (9.4)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.5"
D197V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SERPINB12 MUTATED         0        1        0        1         2         0
  SERPINB12 WILD-TYPE       1        8       27       25        29        44
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINB12 MUTATED           0          2          0          0        1
  SERPINB12 WILD-TYPE         3         47         36         24       23
D197V3, multiclass
            clus
vv           SERPINB12 MUTATED SERPINB12 WILD-TYPE
  STAGE I                    0                   1
  STAGE IA                   1                   8
  STAGE IB                   0                  27
  STAGE II                   1                  25
  STAGE IIA                  2                  29
  STAGE IIB                  0                  44
  STAGE III                  0                   3
  STAGE IIIA                 2                  47
  STAGE IIIB                 0                  36
  STAGE IIIC                 0                  24
  STAGE IV                   1                  23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  SERPINB12 MUTATED     1   2   3   2
  SERPINB12 WILD-TYPE  10  70 119  73
D197V4, multiclass
    clus
vv   SERPINB12 MUTATED SERPINB12 WILD-TYPE
  T1                 1                  10
  T2                 2                  70
  T3                 3                 119
  T4                 2                  73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  N0 N1 N2 N3
  SERPINB12 MUTATED    4  3  0  0
  SERPINB12 WILD-TYPE 89 78 50 53
D197V5, multiclass
    clus
vv   SERPINB12 MUTATED SERPINB12 WILD-TYPE
  N0                 4                  89
  N1                 3                  78
  N2                 0                  50
  N3                 0                  53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D197V6, binary
                     cls
clus                    0   1
  SERPINB12 MUTATED     7   0
  SERPINB12 WILD-TYPE 250  18
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB12 MUTATED      7    0
  SERPINB12 WILD-TYPE  250   18
   clus
vv  SERPINB12 MUTATED SERPINB12 WILD-TYPE
  0                 7                 250
  1                 0                  18
[1] 2 2
[1] FALSE
D197V7, binary
                     cls
clus                    0   1
  SERPINB12 MUTATED     3   5
  SERPINB12 WILD-TYPE 107 174
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB12 MUTATED      3    5
  SERPINB12 WILD-TYPE  107  174
        clus
vv       SERPINB12 MUTATED SERPINB12 WILD-TYPE
  FEMALE                 3                 107
  MALE                   5                 174
[1] 2 2
[1] FALSE
                     vv
clus                  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SERPINB12 MUTATED                                       0
  SERPINB12 WILD-TYPE                                    50
                     vv
clus                  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SERPINB12 MUTATED                                                        5
  SERPINB12 WILD-TYPE                                                    130
                     vv
clus                  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SERPINB12 MUTATED                                                                   1
  SERPINB12 WILD-TYPE                                                                39
                     vv
clus                  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SERPINB12 MUTATED                                                  2
  SERPINB12 WILD-TYPE                                               36
                     vv
clus                  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SERPINB12 MUTATED                                                          0
  SERPINB12 WILD-TYPE                                                       16
                     vv
clus                  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SERPINB12 MUTATED                                                           0
  SERPINB12 WILD-TYPE                                                         6
                     vv
clus                  STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SERPINB12 MUTATED                                          0
  SERPINB12 WILD-TYPE                                        3
D197V8, multiclass
                                                                   clus
vv                                                                  SERPINB12 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          0
                                                                   clus
vv                                                                  SERPINB12 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                              50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                   36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                           16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                           6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                            3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D197V9, binary
                     cls
clus                    0   1
  SERPINB12 MUTATED     0   8
  SERPINB12 WILD-TYPE   5 276
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB12 MUTATED      0    8
  SERPINB12 WILD-TYPE    5  276
     clus
vv    SERPINB12 MUTATED SERPINB12 WILD-TYPE
  NO                  0                   5
  YES                 8                 276
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  SERPINB12 MUTATED     5   0   0   3
  SERPINB12 WILD-TYPE 222  10  10  21
D197V10, multiclass
    clus
vv   SERPINB12 MUTATED SERPINB12 WILD-TYPE
  R0                 5                 222
  R1                 0                  10
  R2                 0                  10
  RX                 3                  21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D197V11, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SERPINB12 MUTATED       2                         0     5
  SERPINB12 WILD-TYPE    74                         4   163
D197V12, multiclass
                           clus
vv                          SERPINB12 MUTATED SERPINB12 WILD-TYPE
  ASIAN                                     2                  74
  BLACK OR AFRICAN AMERICAN                 0                   4
  WHITE                                     5                 163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(198) Variable = HEXDC MUTATION ANALYSIS
D198V1, survival
                 sevent
clus2               0   1
  HEXDC MUTATED     2   1
  HEXDC WILD-TYPE 179  79
  HEXDC MUTATED HEXDC WILD-TYPE 
              3             258 
  HEXDC MUTATED HEXDC WILD-TYPE 
              1              79 
$`HEXDC MUTATED`
TCGA-BR-8372 TCGA-CD-A4MI TCGA-HJ-7597 
       19.17         0.10        26.47 

$`HEXDC WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  HEXDC MUTATED HEXDC WILD-TYPE 
            0.1             0.0 
  HEXDC MUTATED HEXDC WILD-TYPE 
          26.47          105.07 
  HEXDC MUTATED HEXDC WILD-TYPE 
         19.170          12.605 
[1] "0.1 - 26.5 (19.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D198V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HEXDC MUTATED         0        0        1        1         0         0
  HEXDC WILD-TYPE       1        9       26       25        31        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HEXDC MUTATED           0          0          1          1        0
  HEXDC WILD-TYPE         3         49         35         23       24
D198V3, multiclass
            clus
vv           HEXDC MUTATED HEXDC WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              0              31
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HEXDC MUTATED     1   2   1   1
  HEXDC WILD-TYPE  10  70 121  74
D198V4, multiclass
    clus
vv   HEXDC MUTATED HEXDC WILD-TYPE
  T1             1              10
  T2             2              70
  T3             1             121
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  HEXDC MUTATED    1  2  0  1
  HEXDC WILD-TYPE 92 79 50 52
D198V5, multiclass
    clus
vv   HEXDC MUTATED HEXDC WILD-TYPE
  N0             1              92
  N1             2              79
  N2             0              50
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D198V6, binary
                 cls
clus                0   1
  HEXDC MUTATED     4   0
  HEXDC WILD-TYPE 253  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HEXDC MUTATED      4    0
  HEXDC WILD-TYPE  253   18
   clus
vv  HEXDC MUTATED HEXDC WILD-TYPE
  0             4             253
  1             0              18
[1] 2 2
[1] FALSE
D198V7, binary
                 cls
clus                0   1
  HEXDC MUTATED     2   3
  HEXDC WILD-TYPE 108 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HEXDC MUTATED      2    3
  HEXDC WILD-TYPE  108  176
        clus
vv       HEXDC MUTATED HEXDC WILD-TYPE
  FEMALE             2             108
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  HEXDC MUTATED                                       0
  HEXDC WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HEXDC MUTATED                                                        3
  HEXDC WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HEXDC MUTATED                                                                   0
  HEXDC WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  HEXDC MUTATED                                                  0
  HEXDC WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  HEXDC MUTATED                                                          1
  HEXDC WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  HEXDC MUTATED                                                           0
  HEXDC WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  HEXDC MUTATED                                          1
  HEXDC WILD-TYPE                                        2
D198V8, multiclass
                                                                   clus
vv                                                                  HEXDC MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  HEXDC WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D198V9, binary
                 cls
clus                0   1
  HEXDC MUTATED     1   4
  HEXDC WILD-TYPE   4 280
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HEXDC MUTATED      1    4
  HEXDC WILD-TYPE    4  280
     clus
vv    HEXDC MUTATED HEXDC WILD-TYPE
  NO              1               4
  YES             4             280
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HEXDC MUTATED     3   0   0   1
  HEXDC WILD-TYPE 224  10  10  23
D198V10, multiclass
    clus
vv   HEXDC MUTATED HEXDC WILD-TYPE
  R0             3             224
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D198V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HEXDC MUTATED       1                         0     3
  HEXDC WILD-TYPE    75                         4   165
D198V12, multiclass
                           clus
vv                          HEXDC MUTATED HEXDC WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(199) Variable = GATA3 MUTATION ANALYSIS
D199V1, survival
                 sevent
clus2               0   1
  GATA3 MUTATED     8   5
  GATA3 WILD-TYPE 173  75
  GATA3 MUTATED GATA3 WILD-TYPE 
             13             248 
  GATA3 MUTATED GATA3 WILD-TYPE 
              5              75 
$`GATA3 MUTATED`
TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-7958 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8382 
       34.68        24.76        12.76         0.26         4.31        15.85 
TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-8687 TCGA-CG-4469 TCGA-EQ-5647 
        1.12        13.45        15.81         8.22         7.07         0.62 
TCGA-HU-A4GQ 
        0.10 

$`GATA3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         3.45         9.07        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
       19.50        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
        3.32        11.80        19.17        14.79         0.26         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        9.34         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        9.86        15.68        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-8122 TCGA-EQ-A4SO 
        5.92        15.16        13.78        14.76         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  GATA3 MUTATED GATA3 WILD-TYPE 
            0.1             0.0 
  GATA3 MUTATED GATA3 WILD-TYPE 
          34.68          105.07 
  GATA3 MUTATED GATA3 WILD-TYPE 
           8.22           12.64 
[1] "0.1 - 34.7 (8.2)"   "0.0 - 105.1 (12.6)"
[1] "hr=" "1.7"
D199V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GATA3 MUTATED         0        1        2        0         2         0
  GATA3 WILD-TYPE       1        8       25       26        29        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GATA3 MUTATED           0          0          1          5        3
  GATA3 WILD-TYPE         3         49         35         19       21
D199V3, multiclass
            clus
vv           GATA3 MUTATED GATA3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             5              19
  STAGE IV               3              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GATA3 MUTATED     2   2   3   8
  GATA3 WILD-TYPE   9  70 119  67
D199V4, multiclass
    clus
vv   GATA3 MUTATED GATA3 WILD-TYPE
  T1             2               9
  T2             2              70
  T3             3             119
  T4             8              67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  GATA3 MUTATED    6  0  3  5
  GATA3 WILD-TYPE 87 81 47 48
D199V5, multiclass
    clus
vv   GATA3 MUTATED GATA3 WILD-TYPE
  N0             6              87
  N1             0              81
  N2             3              47
  N3             5              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D199V6, binary
                 cls
clus                0   1
  GATA3 MUTATED    14   2
  GATA3 WILD-TYPE 243  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA3 MUTATED     14    2
  GATA3 WILD-TYPE  243   16
   clus
vv  GATA3 MUTATED GATA3 WILD-TYPE
  0            14             243
  1             2              16
[1] 2 2
[1] FALSE
D199V7, binary
                 cls
clus                0   1
  GATA3 MUTATED     9   7
  GATA3 WILD-TYPE 101 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA3 MUTATED      9    7
  GATA3 WILD-TYPE  101  172
        clus
vv       GATA3 MUTATED GATA3 WILD-TYPE
  FEMALE             9             101
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GATA3 MUTATED                                       0
  GATA3 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GATA3 MUTATED                                                       12
  GATA3 WILD-TYPE                                                    123
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GATA3 MUTATED                                                                   1
  GATA3 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GATA3 MUTATED                                                  2
  GATA3 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GATA3 MUTATED                                                          0
  GATA3 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GATA3 MUTATED                                                           1
  GATA3 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GATA3 MUTATED                                          0
  GATA3 WILD-TYPE                                        3
D199V8, multiclass
                                                                   clus
vv                                                                  GATA3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       12
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  GATA3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        123
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D199V9, binary
                 cls
clus                0   1
  GATA3 MUTATED     0  16
  GATA3 WILD-TYPE   5 268
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA3 MUTATED      0   16
  GATA3 WILD-TYPE    5  268
     clus
vv    GATA3 MUTATED GATA3 WILD-TYPE
  NO              0               5
  YES            16             268
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GATA3 MUTATED    10   3   1   2
  GATA3 WILD-TYPE 217   7   9  22
D199V10, multiclass
    clus
vv   GATA3 MUTATED GATA3 WILD-TYPE
  R0            10             217
  R1             3               7
  R2             1               9
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D199V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GATA3 MUTATED       2                         0    13
  GATA3 WILD-TYPE    74                         4   155
D199V12, multiclass
                           clus
vv                          GATA3 MUTATED GATA3 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                13             155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(200) Variable = GPR82 MUTATION ANALYSIS
D200V1, survival
                 sevent
clus2               0   1
  GPR82 MUTATED     7   1
  GPR82 WILD-TYPE 174  79
  GPR82 MUTATED GPR82 WILD-TYPE 
              8             253 
  GPR82 MUTATED GPR82 WILD-TYPE 
              1              79 
$`GPR82 MUTATED`
TCGA-BR-6452 TCGA-BR-8382 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-5728 
       34.68        15.85        15.81         6.58        12.62        65.10 
TCGA-HU-A4GH TCGA-HU-A4GU 
       11.77         6.25 

$`GPR82 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       19.17        14.79         0.26         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       11.61        12.20         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        79.07         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  GPR82 MUTATED GPR82 WILD-TYPE 
           6.25            0.00 
  GPR82 MUTATED GPR82 WILD-TYPE 
          65.10          105.07 
  GPR82 MUTATED GPR82 WILD-TYPE 
         14.215          12.590 
[1] "6.2 - 65.1 (14.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "3.5"
D200V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPR82 MUTATED         0        1        2        1         2         1
  GPR82 WILD-TYPE       1        8       25       25        29        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR82 MUTATED           0          0          0          1        1
  GPR82 WILD-TYPE         3         49         36         23       23
D200V3, multiclass
            clus
vv           GPR82 MUTATED GPR82 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               2              25
  STAGE II               1              25
  STAGE IIA              2              29
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GPR82 MUTATED     1   3   3   2
  GPR82 WILD-TYPE  10  69 119  73
D200V4, multiclass
    clus
vv   GPR82 MUTATED GPR82 WILD-TYPE
  T1             1              10
  T2             3              69
  T3             3             119
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  GPR82 MUTATED    5  2  1  1
  GPR82 WILD-TYPE 88 79 49 52
D200V5, multiclass
    clus
vv   GPR82 MUTATED GPR82 WILD-TYPE
  N0             5              88
  N1             2              79
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D200V6, binary
                 cls
clus                0   1
  GPR82 MUTATED     8   1
  GPR82 WILD-TYPE 249  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR82 MUTATED      8    1
  GPR82 WILD-TYPE  249   17
   clus
vv  GPR82 MUTATED GPR82 WILD-TYPE
  0             8             249
  1             1              17
[1] 2 2
[1] FALSE
D200V7, binary
                 cls
clus                0   1
  GPR82 MUTATED     3   6
  GPR82 WILD-TYPE 107 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR82 MUTATED      3    6
  GPR82 WILD-TYPE  107  173
        clus
vv       GPR82 MUTATED GPR82 WILD-TYPE
  FEMALE             3             107
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GPR82 MUTATED                                       2
  GPR82 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPR82 MUTATED                                                        3
  GPR82 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPR82 MUTATED                                                                   1
  GPR82 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GPR82 MUTATED                                                  2
  GPR82 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GPR82 MUTATED                                                          1
  GPR82 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GPR82 MUTATED                                                           0
  GPR82 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GPR82 MUTATED                                          0
  GPR82 WILD-TYPE                                        3
D200V8, multiclass
                                                                   clus
vv                                                                  GPR82 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  GPR82 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D200V9, binary
                 cls
clus                0   1
  GPR82 MUTATED     1   8
  GPR82 WILD-TYPE   4 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR82 MUTATED      1    8
  GPR82 WILD-TYPE    4  276
     clus
vv    GPR82 MUTATED GPR82 WILD-TYPE
  NO              1               4
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GPR82 MUTATED     7   0   0   0
  GPR82 WILD-TYPE 220  10  10  24
D200V10, multiclass
    clus
vv   GPR82 MUTATED GPR82 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D200V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPR82 MUTATED       5                         0     2
  GPR82 WILD-TYPE    71                         4   166
D200V12, multiclass
                           clus
vv                          GPR82 MUTATED GPR82 WILD-TYPE
  ASIAN                                 5              71
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 2             166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(201) Variable = ELF3 MUTATION ANALYSIS
D201V1, survival
                sevent
clus2              0   1
  ELF3 MUTATED     8   2
  ELF3 WILD-TYPE 173  78
  ELF3 MUTATED ELF3 WILD-TYPE 
            10            251 
  ELF3 MUTATED ELF3 WILD-TYPE 
             2             78 
$`ELF3 MUTATED`
TCGA-B7-5816 TCGA-BR-6852 TCGA-CD-5813 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5721 
       26.70        32.94         0.39         7.07        30.97         6.02 
TCGA-CG-5733 TCGA-D7-A4YY TCGA-F1-6874 TCGA-HU-A4GT 
       21.07        13.78        14.47         6.51 

$`ELF3 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5717 
       12.03         0.00         9.01        18.97        22.98         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       28.96        79.07        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 
       14.76         0.62         7.99        16.24        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  ELF3 MUTATED ELF3 WILD-TYPE 
          0.39           0.00 
  ELF3 MUTATED ELF3 WILD-TYPE 
         32.94         105.07 
  ELF3 MUTATED ELF3 WILD-TYPE 
        14.125         12.590 
[1] "0.4 - 32.9 (14.1)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.9"
D201V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ELF3 MUTATED         0        0        2        1         2         1
  ELF3 WILD-TYPE       1        9       25       25        29        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ELF3 MUTATED           0          2          1          0        2
  ELF3 WILD-TYPE         3         47         35         24       22
D201V3, multiclass
            clus
vv           ELF3 MUTATED ELF3 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              1             25
  STAGE IIA             2             29
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            1             35
  STAGE IIIC            0             24
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ELF3 MUTATED     0   3   5   3
  ELF3 WILD-TYPE  11  69 117  72
D201V4, multiclass
    clus
vv   ELF3 MUTATED ELF3 WILD-TYPE
  T1            0             11
  T2            3             69
  T3            5            117
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  ELF3 MUTATED    7  1  1  2
  ELF3 WILD-TYPE 86 80 49 51
D201V5, multiclass
    clus
vv   ELF3 MUTATED ELF3 WILD-TYPE
  N0            7             86
  N1            1             80
  N2            1             49
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D201V6, binary
                cls
clus               0   1
  ELF3 MUTATED    11   0
  ELF3 WILD-TYPE 246  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED     11    0
  ELF3 WILD-TYPE  246   18
   clus
vv  ELF3 MUTATED ELF3 WILD-TYPE
  0           11            246
  1            0             18
[1] 2 2
[1] FALSE
D201V7, binary
                cls
clus               0   1
  ELF3 MUTATED     6   5
  ELF3 WILD-TYPE 104 174
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      6    5
  ELF3 WILD-TYPE  104  174
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  FEMALE            6            104
  MALE              5            174
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ELF3 MUTATED                                       1
  ELF3 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ELF3 MUTATED                                                        3
  ELF3 WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ELF3 MUTATED                                                                   5
  ELF3 WILD-TYPE                                                                35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ELF3 MUTATED                                                  1
  ELF3 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ELF3 MUTATED                                                          1
  ELF3 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ELF3 MUTATED                                                           0
  ELF3 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ELF3 MUTATED                                          0
  ELF3 WILD-TYPE                                        3
D201V8, multiclass
                                                                   clus
vv                                                                  ELF3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  ELF3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D201V9, binary
                cls
clus               0   1
  ELF3 MUTATED     0  11
  ELF3 WILD-TYPE   5 273
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      0   11
  ELF3 WILD-TYPE    5  273
     clus
vv    ELF3 MUTATED ELF3 WILD-TYPE
  NO             0              5
  YES           11            273
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ELF3 MUTATED     8   1   0   1
  ELF3 WILD-TYPE 219   9  10  23
D201V10, multiclass
    clus
vv   ELF3 MUTATED ELF3 WILD-TYPE
  R0            8            219
  R1            1              9
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D201V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ELF3 MUTATED       2                         0     5
  ELF3 WILD-TYPE    74                         4   163
D201V12, multiclass
                           clus
vv                          ELF3 MUTATED ELF3 WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                5            163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(202) Variable = EPHX1 MUTATION ANALYSIS
D202V1, survival
                 sevent
clus2               0   1
  EPHX1 MUTATED     5   3
  EPHX1 WILD-TYPE 176  77
  EPHX1 MUTATED EPHX1 WILD-TYPE 
              8             253 
  EPHX1 MUTATED EPHX1 WILD-TYPE 
              3              77 
$`EPHX1 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8360 TCGA-CD-A4MG TCGA-CG-4465 TCGA-CG-5723 
        6.97        34.68         6.18         6.58         9.01       105.07 
TCGA-F1-6874 TCGA-HU-A4G8 
       14.47        11.84 

$`EPHX1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  EPHX1 MUTATED EPHX1 WILD-TYPE 
           6.18            0.00 
  EPHX1 MUTATED EPHX1 WILD-TYPE 
         105.07           79.07 
  EPHX1 MUTATED EPHX1 WILD-TYPE 
         10.425          12.660 
[1] "6.2 - 105.1 (10.4)" "0.0 - 79.1 (12.7)" 
[1] "hr=" "1.2"
D202V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPHX1 MUTATED         0        0        1        1         3         1
  EPHX1 WILD-TYPE       1        9       26       25        28        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EPHX1 MUTATED           0          1          0          0        1
  EPHX1 WILD-TYPE         3         48         36         24       23
D202V3, multiclass
            clus
vv           EPHX1 MUTATED EPHX1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              3              28
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EPHX1 MUTATED     0   2   5   1
  EPHX1 WILD-TYPE  11  70 117  74
D202V4, multiclass
    clus
vv   EPHX1 MUTATED EPHX1 WILD-TYPE
  T1             0              11
  T2             2              70
  T3             5             117
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  EPHX1 MUTATED    4  3  0  1
  EPHX1 WILD-TYPE 89 78 50 52
D202V5, multiclass
    clus
vv   EPHX1 MUTATED EPHX1 WILD-TYPE
  N0             4              89
  N1             3              78
  N2             0              50
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D202V6, binary
                 cls
clus                0   1
  EPHX1 MUTATED     7   1
  EPHX1 WILD-TYPE 250  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHX1 MUTATED      7    1
  EPHX1 WILD-TYPE  250   17
   clus
vv  EPHX1 MUTATED EPHX1 WILD-TYPE
  0             7             250
  1             1              17
[1] 2 2
[1] FALSE
D202V7, binary
                 cls
clus                0   1
  EPHX1 MUTATED     4   5
  EPHX1 WILD-TYPE 106 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHX1 MUTATED      4    5
  EPHX1 WILD-TYPE  106  174
        clus
vv       EPHX1 MUTATED EPHX1 WILD-TYPE
  FEMALE             4             106
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  EPHX1 MUTATED                                       3
  EPHX1 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EPHX1 MUTATED                                                        4
  EPHX1 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EPHX1 MUTATED                                                                   2
  EPHX1 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  EPHX1 MUTATED                                                  0
  EPHX1 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  EPHX1 MUTATED                                                          0
  EPHX1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  EPHX1 MUTATED                                                           0
  EPHX1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  EPHX1 MUTATED                                          0
  EPHX1 WILD-TYPE                                        3
D202V8, multiclass
                                                                   clus
vv                                                                  EPHX1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  EPHX1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D202V9, binary
                 cls
clus                0   1
  EPHX1 MUTATED     0   9
  EPHX1 WILD-TYPE   5 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHX1 MUTATED      0    9
  EPHX1 WILD-TYPE    5  275
     clus
vv    EPHX1 MUTATED EPHX1 WILD-TYPE
  NO              0               5
  YES             9             275
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EPHX1 MUTATED     4   0   1   2
  EPHX1 WILD-TYPE 223  10   9  22
D202V10, multiclass
    clus
vv   EPHX1 MUTATED EPHX1 WILD-TYPE
  R0             4             223
  R1             0              10
  R2             1               9
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D202V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EPHX1 MUTATED       2                         0     5
  EPHX1 WILD-TYPE    74                         4   163
D202V12, multiclass
                           clus
vv                          EPHX1 MUTATED EPHX1 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(203) Variable = CNBD1 MUTATION ANALYSIS
D203V1, survival
                 sevent
clus2               0   1
  CNBD1 MUTATED     7   3
  CNBD1 WILD-TYPE 174  77
  CNBD1 MUTATED CNBD1 WILD-TYPE 
             10             251 
  CNBD1 MUTATED CNBD1 WILD-TYPE 
              3              77 
$`CNBD1 MUTATED`
TCGA-BR-7707 TCGA-BR-7901 TCGA-BR-A4QM TCGA-CD-A48C TCGA-D7-6519 TCGA-D7-6528 
       23.93         3.45         5.13        11.61        20.55        15.22 
TCGA-HU-8602 TCGA-HU-A4GH TCGA-HU-A4HD TCGA-IN-8663 
       11.41        11.77        27.42         3.39 

$`CNBD1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73        12.43         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64        11.57         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN 
       11.84        24.20         3.25        22.75        25.81        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IP-7968 
        8.88        21.21         3.45        18.81         2.53 

  CNBD1 MUTATED CNBD1 WILD-TYPE 
           3.39            0.00 
  CNBD1 MUTATED CNBD1 WILD-TYPE 
          27.42          105.07 
  CNBD1 MUTATED CNBD1 WILD-TYPE 
          11.69           12.66 
[1] "3.4 - 27.4 (11.7)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1"  
D203V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CNBD1 MUTATED         0        1        2        0         0         4
  CNBD1 WILD-TYPE       1        8       25       26        31        40
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNBD1 MUTATED           0          2          1          0        0
  CNBD1 WILD-TYPE         3         47         35         24       24
D203V3, multiclass
            clus
vv           CNBD1 MUTATED CNBD1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              0              31
  STAGE IIB              4              40
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CNBD1 MUTATED     1   4   4   1
  CNBD1 WILD-TYPE  10  68 118  74
D203V4, multiclass
    clus
vv   CNBD1 MUTATED CNBD1 WILD-TYPE
  T1             1              10
  T2             4              68
  T3             4             118
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CNBD1 MUTATED    4  4  3  0
  CNBD1 WILD-TYPE 89 77 47 53
D203V5, multiclass
    clus
vv   CNBD1 MUTATED CNBD1 WILD-TYPE
  N0             4              89
  N1             4              77
  N2             3              47
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D203V6, binary
                 cls
clus                0   1
  CNBD1 MUTATED    13   0
  CNBD1 WILD-TYPE 244  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNBD1 MUTATED     13    0
  CNBD1 WILD-TYPE  244   18
   clus
vv  CNBD1 MUTATED CNBD1 WILD-TYPE
  0            13             244
  1             0              18
[1] 2 2
[1] FALSE
D203V7, binary
                 cls
clus                0   1
  CNBD1 MUTATED     5   8
  CNBD1 WILD-TYPE 105 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNBD1 MUTATED      5    8
  CNBD1 WILD-TYPE  105  171
        clus
vv       CNBD1 MUTATED CNBD1 WILD-TYPE
  FEMALE             5             105
  MALE               8             171
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CNBD1 MUTATED                                       2
  CNBD1 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CNBD1 MUTATED                                                        8
  CNBD1 WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CNBD1 MUTATED                                                                   0
  CNBD1 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CNBD1 MUTATED                                                  3
  CNBD1 WILD-TYPE                                               35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CNBD1 MUTATED                                                          0
  CNBD1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CNBD1 MUTATED                                                           0
  CNBD1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CNBD1 MUTATED                                          0
  CNBD1 WILD-TYPE                                        3
D203V8, multiclass
                                                                   clus
vv                                                                  CNBD1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  CNBD1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D203V9, binary
                 cls
clus                0   1
  CNBD1 MUTATED     0  13
  CNBD1 WILD-TYPE   5 271
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNBD1 MUTATED      0   13
  CNBD1 WILD-TYPE    5  271
     clus
vv    CNBD1 MUTATED CNBD1 WILD-TYPE
  NO              0               5
  YES            13             271
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CNBD1 MUTATED     9   0   0   3
  CNBD1 WILD-TYPE 218  10  10  21
D203V10, multiclass
    clus
vv   CNBD1 MUTATED CNBD1 WILD-TYPE
  R0             9             218
  R1             0              10
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D203V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CNBD1 MUTATED       4                         0     9
  CNBD1 WILD-TYPE    72                         4   159
D203V12, multiclass
                           clus
vv                          CNBD1 MUTATED CNBD1 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 9             159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(204) Variable = SLC26A7 MUTATION ANALYSIS
D204V1, survival
                   sevent
clus2                 0   1
  SLC26A7 MUTATED    12   0
  SLC26A7 WILD-TYPE 169  80
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
               12               249 
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
                0                80 
$`SLC26A7 MUTATED`
TCGA-BR-6452 TCGA-BR-8381 TCGA-BR-8591 TCGA-BR-A4PD TCGA-BR-A4QL TCGA-CD-A48A 
       34.68         0.26        13.45        20.65        11.57        12.43 
TCGA-CG-5721 TCGA-D7-6817 TCGA-F1-A448 TCGA-FP-A4BE TCGA-HU-A4GX TCGA-HU-A4H8 
        6.02        12.79        21.27        11.08        10.19         8.88 

$`SLC26A7 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       19.17        14.79        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       19.36        13.51        20.42         1.15        13.64         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        3.42         9.34        11.31        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        15.98        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
        5.03        13.58         0.56         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.25         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
             0.26              0.00 
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
            34.68            105.07 
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
            12.00             12.66 
[1] "0.3 - 34.7 (12.0)"  "0.0 - 105.1 (12.7)"
[1] "hr="     "2.6e+07"
D204V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC26A7 MUTATED         0        0        1        0         3         2
  SLC26A7 WILD-TYPE       1        9       26       26        28        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC26A7 MUTATED           0          2          2          2        1
  SLC26A7 WILD-TYPE         3         47         34         22       23
D204V3, multiclass
            clus
vv           SLC26A7 MUTATED SLC26A7 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 0                26
  STAGE IIA                3                28
  STAGE IIB                2                42
  STAGE III                0                 3
  STAGE IIIA               2                47
  STAGE IIIB               2                34
  STAGE IIIC               2                22
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC26A7 MUTATED     2   1   6   5
  SLC26A7 WILD-TYPE   9  71 116  70
D204V4, multiclass
    clus
vv   SLC26A7 MUTATED SLC26A7 WILD-TYPE
  T1               2                 9
  T2               1                71
  T3               6               116
  T4               5                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  SLC26A7 MUTATED    5  3  1  4
  SLC26A7 WILD-TYPE 88 78 49 49
D204V5, multiclass
    clus
vv   SLC26A7 MUTATED SLC26A7 WILD-TYPE
  N0               5                88
  N1               3                78
  N2               1                49
  N3               4                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D204V6, binary
                   cls
clus                  0   1
  SLC26A7 MUTATED    14   0
  SLC26A7 WILD-TYPE 243  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A7 MUTATED     14    0
  SLC26A7 WILD-TYPE  243   18
   clus
vv  SLC26A7 MUTATED SLC26A7 WILD-TYPE
  0              14               243
  1               0                18
[1] 2 2
[1] FALSE
D204V7, binary
                   cls
clus                  0   1
  SLC26A7 MUTATED     6   8
  SLC26A7 WILD-TYPE 104 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A7 MUTATED      6    8
  SLC26A7 WILD-TYPE  104  171
        clus
vv       SLC26A7 MUTATED SLC26A7 WILD-TYPE
  FEMALE               6               104
  MALE                 8               171
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SLC26A7 MUTATED                                       1
  SLC26A7 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC26A7 MUTATED                                                        9
  SLC26A7 WILD-TYPE                                                    126
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC26A7 MUTATED                                                                   1
  SLC26A7 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SLC26A7 MUTATED                                                  2
  SLC26A7 WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SLC26A7 MUTATED                                                          1
  SLC26A7 WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SLC26A7 MUTATED                                                           0
  SLC26A7 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SLC26A7 MUTATED                                          0
  SLC26A7 WILD-TYPE                                        3
D204V8, multiclass
                                                                   clus
vv                                                                  SLC26A7 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  SLC26A7 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D204V9, binary
                   cls
clus                  0   1
  SLC26A7 MUTATED     1  13
  SLC26A7 WILD-TYPE   4 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A7 MUTATED      1   13
  SLC26A7 WILD-TYPE    4  271
     clus
vv    SLC26A7 MUTATED SLC26A7 WILD-TYPE
  NO                1                 4
  YES              13               271
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC26A7 MUTATED    11   0   0   2
  SLC26A7 WILD-TYPE 216  10  10  22
D204V10, multiclass
    clus
vv   SLC26A7 MUTATED SLC26A7 WILD-TYPE
  R0              11               216
  R1               0                10
  R2               0                10
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D204V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC26A7 MUTATED       3                         1     9
  SLC26A7 WILD-TYPE    73                         3   159
D204V12, multiclass
                           clus
vv                          SLC26A7 MUTATED SLC26A7 WILD-TYPE
  ASIAN                                   3                73
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   9               159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(205) Variable = RCOR3 MUTATION ANALYSIS
D205V1, survival
                 sevent
clus2               0   1
  RCOR3 MUTATED     7   4
  RCOR3 WILD-TYPE 174  76
  RCOR3 MUTATED RCOR3 WILD-TYPE 
             11             250 
  RCOR3 MUTATED RCOR3 WILD-TYPE 
              4              76 
$`RCOR3 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL 
        6.97        34.68         0.26        13.45        15.81        11.57 
TCGA-CG-5726 TCGA-CG-5728 TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-A4GQ 
       28.96        65.10        11.08        11.41         0.10 

$`RCOR3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        19.50        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 
       59.54         5.03        13.58         0.56         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        11.77        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  RCOR3 MUTATED RCOR3 WILD-TYPE 
            0.1             0.0 
  RCOR3 MUTATED RCOR3 WILD-TYPE 
          65.10          105.07 
  RCOR3 MUTATED RCOR3 WILD-TYPE 
          11.57           12.64 
[1] "0.1 - 65.1 (11.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1"  
D205V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RCOR3 MUTATED         0        1        2        0         2         1
  RCOR3 WILD-TYPE       1        8       25       26        29        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RCOR3 MUTATED           0          1          1          2        1
  RCOR3 WILD-TYPE         3         48         35         22       23
D205V3, multiclass
            clus
vv           RCOR3 MUTATED RCOR3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             2              22
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RCOR3 MUTATED     1   2   4   4
  RCOR3 WILD-TYPE  10  70 118  71
D205V4, multiclass
    clus
vv   RCOR3 MUTATED RCOR3 WILD-TYPE
  T1             1              10
  T2             2              70
  T3             4             118
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  RCOR3 MUTATED    6  2  2  2
  RCOR3 WILD-TYPE 87 79 48 51
D205V5, multiclass
    clus
vv   RCOR3 MUTATED RCOR3 WILD-TYPE
  N0             6              87
  N1             2              79
  N2             2              48
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D205V6, binary
                 cls
clus                0   1
  RCOR3 MUTATED    10   1
  RCOR3 WILD-TYPE 247  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR3 MUTATED     10    1
  RCOR3 WILD-TYPE  247   17
   clus
vv  RCOR3 MUTATED RCOR3 WILD-TYPE
  0            10             247
  1             1              17
[1] 2 2
[1] FALSE
D205V7, binary
                 cls
clus                0   1
  RCOR3 MUTATED     6   6
  RCOR3 WILD-TYPE 104 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR3 MUTATED      6    6
  RCOR3 WILD-TYPE  104  173
        clus
vv       RCOR3 MUTATED RCOR3 WILD-TYPE
  FEMALE             6             104
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RCOR3 MUTATED                                       1
  RCOR3 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RCOR3 MUTATED                                                        7
  RCOR3 WILD-TYPE                                                    128
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RCOR3 MUTATED                                                                   2
  RCOR3 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RCOR3 MUTATED                                                  2
  RCOR3 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RCOR3 MUTATED                                                          0
  RCOR3 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RCOR3 MUTATED                                                           0
  RCOR3 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RCOR3 MUTATED                                          0
  RCOR3 WILD-TYPE                                        3
D205V8, multiclass
                                                                   clus
vv                                                                  RCOR3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  RCOR3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D205V9, binary
                 cls
clus                0   1
  RCOR3 MUTATED     0  12
  RCOR3 WILD-TYPE   5 272
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR3 MUTATED      0   12
  RCOR3 WILD-TYPE    5  272
     clus
vv    RCOR3 MUTATED RCOR3 WILD-TYPE
  NO              0               5
  YES            12             272
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RCOR3 MUTATED    10   0   0   2
  RCOR3 WILD-TYPE 217  10  10  22
D205V10, multiclass
    clus
vv   RCOR3 MUTATED RCOR3 WILD-TYPE
  R0            10             217
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D205V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RCOR3 MUTATED       3                         1     6
  RCOR3 WILD-TYPE    73                         3   162
D205V12, multiclass
                           clus
vv                          RCOR3 MUTATED RCOR3 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(206) Variable = CASC3 MUTATION ANALYSIS
D206V1, survival
                 sevent
clus2               0   1
  CASC3 MUTATED     5   2
  CASC3 WILD-TYPE 176  78
  CASC3 MUTATED CASC3 WILD-TYPE 
              7             254 
  CASC3 MUTATED CASC3 WILD-TYPE 
              2              78 
$`CASC3 MUTATED`
TCGA-BR-8284 TCGA-BR-8372 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-A487 TCGA-D7-8579 
        8.05        19.17        13.45        11.57         9.34        20.91 
TCGA-EQ-8122 
        7.99 

$`CASC3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
       20.55        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         3.42        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        14.66        21.14        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 
       15.16        13.78        14.76         0.62        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  CASC3 MUTATED CASC3 WILD-TYPE 
           7.99            0.00 
  CASC3 MUTATED CASC3 WILD-TYPE 
          20.91          105.07 
  CASC3 MUTATED CASC3 WILD-TYPE 
          11.57           12.64 
[1] "8.0 - 20.9 (11.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1"  
D206V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CASC3 MUTATED         0        0        0        1         0         3
  CASC3 WILD-TYPE       1        9       27       25        31        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CASC3 MUTATED           0          0          1          3        0
  CASC3 WILD-TYPE         3         49         35         21       24
D206V3, multiclass
            clus
vv           CASC3 MUTATED CASC3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              0              31
  STAGE IIB              3              41
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             3              21
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CASC3 MUTATED     0   2   3   3
  CASC3 WILD-TYPE  11  70 119  72
D206V4, multiclass
    clus
vv   CASC3 MUTATED CASC3 WILD-TYPE
  T1             0              11
  T2             2              70
  T3             3             119
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CASC3 MUTATED    0  3  1  4
  CASC3 WILD-TYPE 93 78 49 49
D206V5, multiclass
    clus
vv   CASC3 MUTATED CASC3 WILD-TYPE
  N0             0              93
  N1             3              78
  N2             1              49
  N3             4              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D206V6, binary
                 cls
clus                0   1
  CASC3 MUTATED     7   0
  CASC3 WILD-TYPE 250  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC3 MUTATED      7    0
  CASC3 WILD-TYPE  250   18
   clus
vv  CASC3 MUTATED CASC3 WILD-TYPE
  0             7             250
  1             0              18
[1] 2 2
[1] FALSE
D206V7, binary
                 cls
clus                0   1
  CASC3 MUTATED     4   4
  CASC3 WILD-TYPE 106 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC3 MUTATED      4    4
  CASC3 WILD-TYPE  106  175
        clus
vv       CASC3 MUTATED CASC3 WILD-TYPE
  FEMALE             4             106
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CASC3 MUTATED                                       1
  CASC3 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CASC3 MUTATED                                                        3
  CASC3 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CASC3 MUTATED                                                                   3
  CASC3 WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CASC3 MUTATED                                                  0
  CASC3 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CASC3 MUTATED                                                          1
  CASC3 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CASC3 MUTATED                                                           0
  CASC3 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CASC3 MUTATED                                          0
  CASC3 WILD-TYPE                                        3
D206V8, multiclass
                                                                   clus
vv                                                                  CASC3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  CASC3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D206V9, binary
                 cls
clus                0   1
  CASC3 MUTATED     1   7
  CASC3 WILD-TYPE   4 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC3 MUTATED      1    7
  CASC3 WILD-TYPE    4  277
     clus
vv    CASC3 MUTATED CASC3 WILD-TYPE
  NO              1               4
  YES             7             277
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CASC3 MUTATED     7   0   0   0
  CASC3 WILD-TYPE 220  10  10  24
D206V10, multiclass
    clus
vv   CASC3 MUTATED CASC3 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D206V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CASC3 MUTATED       1                         0     6
  CASC3 WILD-TYPE    75                         4   162
D206V12, multiclass
                           clus
vv                          CASC3 MUTATED CASC3 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(207) Variable = ACVR1B MUTATION ANALYSIS
D207V1, survival
                  sevent
clus2                0   1
  ACVR1B MUTATED     7   3
  ACVR1B WILD-TYPE 174  77
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              10              251 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
               3               77 
$`ACVR1B MUTATED`
TCGA-BR-4184 TCGA-BR-6566 TCGA-BR-7703 TCGA-BR-8588 TCGA-BR-A4QL TCGA-CD-A4MG 
        6.97        32.78        24.76        12.79        11.57         6.58 
TCGA-CG-4305 TCGA-CG-4477 TCGA-CG-5733 TCGA-IN-7806 
       15.95        30.97        21.07        21.21 

$`ACVR1B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 
       30.90        31.20        32.94        12.82         9.21        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        13.64         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
        0.10        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        22.98         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42         3.45        18.81         3.39         2.53 

  ACVR1B MUTATED ACVR1B WILD-TYPE 
            6.58             0.00 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
           32.78           105.07 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
           18.51            12.56 
[1] "6.6 - 32.8 (18.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D207V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ACVR1B MUTATED         1        1        1        1         2         2
  ACVR1B WILD-TYPE       0        8       26       25        29        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACVR1B MUTATED           0          2          1          0        0
  ACVR1B WILD-TYPE         3         47         35         24       24
D207V3, multiclass
            clus
vv           ACVR1B MUTATED ACVR1B WILD-TYPE
  STAGE I                 1                0
  STAGE IA                1                8
  STAGE IB                1               26
  STAGE II                1               25
  STAGE IIA               2               29
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              1               35
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ACVR1B MUTATED     2   3   5   1
  ACVR1B WILD-TYPE   9  69 117  74
D207V4, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  T1              2                9
  T2              3               69
  T3              5              117
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ACVR1B MUTATED    5  4  1  1
  ACVR1B WILD-TYPE 88 77 49 52
D207V5, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  N0              5               88
  N1              4               77
  N2              1               49
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D207V6, binary
                  cls
clus                 0   1
  ACVR1B MUTATED     9   0
  ACVR1B WILD-TYPE 248  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED      9    0
  ACVR1B WILD-TYPE  248   18
   clus
vv  ACVR1B MUTATED ACVR1B WILD-TYPE
  0              9              248
  1              0               18
[1] 2 2
[1] FALSE
D207V7, binary
                  cls
clus                 0   1
  ACVR1B MUTATED     5   6
  ACVR1B WILD-TYPE 105 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED      5    6
  ACVR1B WILD-TYPE  105  173
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  FEMALE              5              105
  MALE                6              173
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ACVR1B MUTATED                                       2
  ACVR1B WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ACVR1B MUTATED                                                        6
  ACVR1B WILD-TYPE                                                    129
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ACVR1B MUTATED                                                                   2
  ACVR1B WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ACVR1B MUTATED                                                  0
  ACVR1B WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ACVR1B MUTATED                                                          0
  ACVR1B WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ACVR1B MUTATED                                                           1
  ACVR1B WILD-TYPE                                                         5
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ACVR1B MUTATED                                          0
  ACVR1B WILD-TYPE                                        3
D207V8, multiclass
                                                                   clus
vv                                                                  ACVR1B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ACVR1B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D207V9, binary
                  cls
clus                 0   1
  ACVR1B MUTATED     0  11
  ACVR1B WILD-TYPE   5 273
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED      0   11
  ACVR1B WILD-TYPE    5  273
     clus
vv    ACVR1B MUTATED ACVR1B WILD-TYPE
  NO               0                5
  YES             11              273
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ACVR1B MUTATED     9   0   0   1
  ACVR1B WILD-TYPE 218  10  10  23
D207V10, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  R0              9              218
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D207V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACVR1B MUTATED       1                         1     6
  ACVR1B WILD-TYPE    75                         3   162
D207V12, multiclass
                           clus
vv                          ACVR1B MUTATED ACVR1B WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(208) Variable = VPS13A MUTATION ANALYSIS
D208V1, survival
                  sevent
clus2                0   1
  VPS13A MUTATED    22   6
  VPS13A WILD-TYPE 159  74
  VPS13A MUTATED VPS13A WILD-TYPE 
              28              233 
  VPS13A MUTATED VPS13A WILD-TYPE 
               6               74 
$`VPS13A MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7716 TCGA-BR-8078 
        6.97         6.61        34.68        32.78        28.01        12.26 
TCGA-BR-8289 TCGA-BR-8361 TCGA-BR-8589 TCGA-BR-8680 TCGA-BR-A4IY TCGA-BR-A4QL 
        2.66        19.50        15.81        15.81        12.89        11.57 
TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-5719 
        9.34         6.58        12.62         1.02         8.05         1.02 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-A4YV 
        6.02       105.07        65.10        12.36        11.93         5.92 
TCGA-F1-6874 TCGA-HU-A4GN TCGA-HU-A4GX TCGA-HU-A4H3 
       14.47        29.98        10.19        19.36 

$`VPS13A WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       30.90         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       13.68        19.33        39.12        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 
       12.76        18.71        17.49        14.43         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
       20.55         8.05        12.95        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22         1.12        12.79         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        6.08        22.26         1.48        13.41        13.51         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 
       11.31        12.43        11.61        12.20         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
        3.02        27.02        15.95         7.99        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
       36.00         0.99         0.99        12.03        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-6518 
        4.01        69.04        21.07         7.99        12.66        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       12.95        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  VPS13A MUTATED VPS13A WILD-TYPE 
            1.02             0.00 
  VPS13A MUTATED VPS13A WILD-TYPE 
          105.07            79.07 
  VPS13A MUTATED VPS13A WILD-TYPE 
           12.31            12.76 
[1] "1.0 - 105.1 (12.3)" "0.0 - 79.1 (12.8)" 
[1] "hr=" "1.9"
D208V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  VPS13A MUTATED         0        0        4        2         4         5
  VPS13A WILD-TYPE       1        9       23       24        27        39
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VPS13A MUTATED           1          3          2          3        5
  VPS13A WILD-TYPE         2         46         34         21       19
D208V3, multiclass
            clus
vv           VPS13A MUTATED VPS13A WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                4               23
  STAGE II                2               24
  STAGE IIA               4               27
  STAGE IIB               5               39
  STAGE III               1                2
  STAGE IIIA              3               46
  STAGE IIIB              2               34
  STAGE IIIC              3               21
  STAGE IV                5               19
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  VPS13A MUTATED     0   9  10  10
  VPS13A WILD-TYPE  11  63 112  65
D208V4, multiclass
    clus
vv   VPS13A MUTATED VPS13A WILD-TYPE
  T1              0               11
  T2              9               63
  T3             10              112
  T4             10               65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  VPS13A MUTATED   10 12  5  4
  VPS13A WILD-TYPE 83 69 45 49
D208V5, multiclass
    clus
vv   VPS13A MUTATED VPS13A WILD-TYPE
  N0             10               83
  N1             12               69
  N2              5               45
  N3              4               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D208V6, binary
                  cls
clus                 0   1
  VPS13A MUTATED    27   4
  VPS13A WILD-TYPE 230  14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13A MUTATED     27    4
  VPS13A WILD-TYPE  230   14
   clus
vv  VPS13A MUTATED VPS13A WILD-TYPE
  0             27              230
  1              4               14
[1] 2 2
[1] FALSE
D208V7, binary
                  cls
clus                 0   1
  VPS13A MUTATED    15  17
  VPS13A WILD-TYPE  95 162
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13A MUTATED     15   17
  VPS13A WILD-TYPE   95  162
        clus
vv       VPS13A MUTATED VPS13A WILD-TYPE
  FEMALE             15               95
  MALE               17              162
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  VPS13A MUTATED                                       4
  VPS13A WILD-TYPE                                    46
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  VPS13A MUTATED                                                       16
  VPS13A WILD-TYPE                                                    119
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  VPS13A MUTATED                                                                   7
  VPS13A WILD-TYPE                                                                33
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  VPS13A MUTATED                                                  4
  VPS13A WILD-TYPE                                               34
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  VPS13A MUTATED                                                          1
  VPS13A WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  VPS13A MUTATED                                                           0
  VPS13A WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  VPS13A MUTATED                                          0
  VPS13A WILD-TYPE                                        3
D208V8, multiclass
                                                                   clus
vv                                                                  VPS13A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  VPS13A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         119
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D208V9, binary
                  cls
clus                 0   1
  VPS13A MUTATED     0  32
  VPS13A WILD-TYPE   5 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13A MUTATED      0   32
  VPS13A WILD-TYPE    5  252
     clus
vv    VPS13A MUTATED VPS13A WILD-TYPE
  NO               0                5
  YES             32              252
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  VPS13A MUTATED    23   1   1   5
  VPS13A WILD-TYPE 204   9   9  19
D208V10, multiclass
    clus
vv   VPS13A MUTATED VPS13A WILD-TYPE
  R0             23              204
  R1              1                9
  R2              1                9
  RX              5               19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D208V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  VPS13A MUTATED       8                         0    17
  VPS13A WILD-TYPE    68                         4   151
D208V12, multiclass
                           clus
vv                          VPS13A MUTATED VPS13A WILD-TYPE
  ASIAN                                  8               68
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                 17              151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(209) Variable = PLA2G1B MUTATION ANALYSIS
D209V1, survival
                   sevent
clus2                 0   1
  PLA2G1B MUTATED     4   0
  PLA2G1B WILD-TYPE 177  80
  PLA2G1B MUTATED PLA2G1B WILD-TYPE 
                4               257 
  PLA2G1B MUTATED PLA2G1B WILD-TYPE 
                0                80 
$`PLA2G1B MUTATED`
TCGA-BR-8372 TCGA-CD-8530 TCGA-D7-8574 TCGA-HU-8610 
       19.17         0.16        17.19         0.76 

$`PLA2G1B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
        0.07         0.07         0.07         0.10         0.13         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  PLA2G1B MUTATED PLA2G1B WILD-TYPE 
             0.16              0.00 
  PLA2G1B MUTATED PLA2G1B WILD-TYPE 
            19.17            105.07 
  PLA2G1B MUTATED PLA2G1B WILD-TYPE 
            8.975            12.620 
[1] "0.2 - 19.2 (9.0)"   "0.0 - 105.1 (12.6)"
[1] "hr="     "9100000"
D209V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLA2G1B MUTATED         0        1        0        1         0         0
  PLA2G1B WILD-TYPE       1        8       27       25        31        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLA2G1B MUTATED           0          1          0          1        0
  PLA2G1B WILD-TYPE         3         48         36         23       24
D209V3, multiclass
            clus
vv           PLA2G1B MUTATED PLA2G1B WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 1                 8
  STAGE IB                 0                27
  STAGE II                 1                25
  STAGE IIA                0                31
  STAGE IIB                0                44
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               0                36
  STAGE IIIC               1                23
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLA2G1B MUTATED     1   1   1   1
  PLA2G1B WILD-TYPE  10  71 121  74
D209V4, multiclass
    clus
vv   PLA2G1B MUTATED PLA2G1B WILD-TYPE
  T1               1                10
  T2               1                71
  T3               1               121
  T4               1                74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  PLA2G1B MUTATED    2  0  0  2
  PLA2G1B WILD-TYPE 91 81 50 51
D209V5, multiclass
    clus
vv   PLA2G1B MUTATED PLA2G1B WILD-TYPE
  N0               2                91
  N1               0                81
  N2               0                50
  N3               2                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D209V6, binary
                   cls
clus                  0   1
  PLA2G1B MUTATED     4   0
  PLA2G1B WILD-TYPE 253  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G1B MUTATED      4    0
  PLA2G1B WILD-TYPE  253   18
   clus
vv  PLA2G1B MUTATED PLA2G1B WILD-TYPE
  0               4               253
  1               0                18
[1] 2 2
[1] FALSE
D209V7, binary
                   cls
clus                  0   1
  PLA2G1B MUTATED     0   4
  PLA2G1B WILD-TYPE 110 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G1B MUTATED      0    4
  PLA2G1B WILD-TYPE  110  175
        clus
vv       PLA2G1B MUTATED PLA2G1B WILD-TYPE
  FEMALE               0               110
  MALE                 4               175
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PLA2G1B MUTATED                                       1
  PLA2G1B WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLA2G1B MUTATED                                                        2
  PLA2G1B WILD-TYPE                                                    133
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLA2G1B MUTATED                                                                   0
  PLA2G1B WILD-TYPE                                                                40
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PLA2G1B MUTATED                                                  1
  PLA2G1B WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PLA2G1B MUTATED                                                          0
  PLA2G1B WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PLA2G1B MUTATED                                                           0
  PLA2G1B WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PLA2G1B MUTATED                                          0
  PLA2G1B WILD-TYPE                                        3
D209V8, multiclass
                                                                   clus
vv                                                                  PLA2G1B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  PLA2G1B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D209V9, binary
                   cls
clus                  0   1
  PLA2G1B MUTATED     0   4
  PLA2G1B WILD-TYPE   5 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G1B MUTATED      0    4
  PLA2G1B WILD-TYPE    5  280
     clus
vv    PLA2G1B MUTATED PLA2G1B WILD-TYPE
  NO                0                 5
  YES               4               280
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PLA2G1B MUTATED     4   0   0   0
  PLA2G1B WILD-TYPE 223  10  10  24
D209V10, multiclass
    clus
vv   PLA2G1B MUTATED PLA2G1B WILD-TYPE
  R0               4               223
  R1               0                10
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D209V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLA2G1B MUTATED       2                         0     2
  PLA2G1B WILD-TYPE    74                         4   166
D209V12, multiclass
                           clus
vv                          PLA2G1B MUTATED PLA2G1B WILD-TYPE
  ASIAN                                   2                74
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   2               166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(210) Variable = ZCCHC6 MUTATION ANALYSIS
D210V1, survival
                  sevent
clus2                0   1
  ZCCHC6 MUTATED     8   1
  ZCCHC6 WILD-TYPE 173  79
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
               9              252 
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
               1               79 
$`ZCCHC6 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8360 TCGA-BR-8680 TCGA-CG-5721 
       26.70        34.68        32.78         6.18        15.81         6.02 
TCGA-HJ-7597 TCGA-HU-A4GN TCGA-HU-A4GX 
       26.47        29.98        10.19 

$`ZCCHC6 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        2.66        16.31         2.20        15.58         7.40        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       11.08         5.52         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
            6.02             0.00 
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
           34.68           105.07 
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
          26.470           12.575 
[1] "6.0 - 34.7 (26.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "4.9"
D210V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZCCHC6 MUTATED         0        0        1        1         4         1
  ZCCHC6 WILD-TYPE       1        9       26       25        27        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZCCHC6 MUTATED           0          1          0          1        3
  ZCCHC6 WILD-TYPE         3         48         36         23       21
D210V3, multiclass
            clus
vv           ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                1               25
  STAGE IIA               4               27
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                3               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZCCHC6 MUTATED     0   3   3   6
  ZCCHC6 WILD-TYPE  11  69 119  69
D210V4, multiclass
    clus
vv   ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  T1              0               11
  T2              3               69
  T3              3              119
  T4              6               69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZCCHC6 MUTATED    6  3  3  0
  ZCCHC6 WILD-TYPE 87 78 47 53
D210V5, multiclass
    clus
vv   ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  N0              6               87
  N1              3               78
  N2              3               47
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D210V6, binary
                  cls
clus                 0   1
  ZCCHC6 MUTATED    11   1
  ZCCHC6 WILD-TYPE 246  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC6 MUTATED     11    1
  ZCCHC6 WILD-TYPE  246   17
   clus
vv  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  0             11              246
  1              1               17
[1] 2 2
[1] FALSE
D210V7, binary
                  cls
clus                 0   1
  ZCCHC6 MUTATED     8   5
  ZCCHC6 WILD-TYPE 102 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC6 MUTATED      8    5
  ZCCHC6 WILD-TYPE  102  174
        clus
vv       ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  FEMALE              8              102
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZCCHC6 MUTATED                                       2
  ZCCHC6 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZCCHC6 MUTATED                                                        5
  ZCCHC6 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZCCHC6 MUTATED                                                                   2
  ZCCHC6 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZCCHC6 MUTATED                                                  2
  ZCCHC6 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZCCHC6 MUTATED                                                          1
  ZCCHC6 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZCCHC6 MUTATED                                                           0
  ZCCHC6 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZCCHC6 MUTATED                                          1
  ZCCHC6 WILD-TYPE                                        2
D210V8, multiclass
                                                                   clus
vv                                                                  ZCCHC6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       1
                                                                   clus
vv                                                                  ZCCHC6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D210V9, binary
                  cls
clus                 0   1
  ZCCHC6 MUTATED     1  12
  ZCCHC6 WILD-TYPE   4 272
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC6 MUTATED      1   12
  ZCCHC6 WILD-TYPE    4  272
     clus
vv    ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  NO               1                4
  YES             12              272
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZCCHC6 MUTATED    10   0   0   3
  ZCCHC6 WILD-TYPE 217  10  10  21
D210V10, multiclass
    clus
vv   ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  R0             10              217
  R1              0               10
  R2              0               10
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D210V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZCCHC6 MUTATED       3                         0     8
  ZCCHC6 WILD-TYPE    73                         4   160
D210V12, multiclass
                           clus
vv                          ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  8              160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(211) Variable = ITPR2 MUTATION ANALYSIS
D211V1, survival
                 sevent
clus2               0   1
  ITPR2 MUTATED    17   3
  ITPR2 WILD-TYPE 164  77
  ITPR2 MUTATED ITPR2 WILD-TYPE 
             20             241 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
              3              77 
$`ITPR2 MUTATED`
TCGA-BR-4191 TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8589 
       18.35        34.68         6.18        19.50         1.12        15.81 
TCGA-BR-8680 TCGA-CD-5801 TCGA-CD-8536 TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5723 
       15.81        13.18         0.10        15.95         6.02       105.07 
TCGA-D7-5577 TCGA-F1-6874 TCGA-FP-8631 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-A4GP 
       12.36        14.47         0.56        14.17        11.41         8.98 
TCGA-HU-A4GQ TCGA-HU-A4H8 
        0.10         8.88 

$`ITPR2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.15         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
        6.97        36.00         1.02         0.99         0.99        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        7.99        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
       13.78        14.76         0.62         7.99        16.24        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
       59.54         5.03        13.58        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
        5.92        12.59        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       25.81        11.77        29.98         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        9.67        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  ITPR2 MUTATED ITPR2 WILD-TYPE 
            0.1             0.0 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
         105.07           79.07 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
          12.77           12.62 
[1] "0.1 - 105.1 (12.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "2.3"
D211V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ITPR2 MUTATED         0        0        2        3         4         1
  ITPR2 WILD-TYPE       1        9       25       23        27        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ITPR2 MUTATED           0          5          1          2        2
  ITPR2 WILD-TYPE         3         44         35         22       22
D211V3, multiclass
            clus
vv           ITPR2 MUTATED ITPR2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               3              23
  STAGE IIA              4              27
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             5              44
  STAGE IIIB             1              35
  STAGE IIIC             2              22
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITPR2 MUTATED     2   5   7   7
  ITPR2 WILD-TYPE   9  67 115  68
D211V4, multiclass
    clus
vv   ITPR2 MUTATED ITPR2 WILD-TYPE
  T1             2               9
  T2             5              67
  T3             7             115
  T4             7              68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ITPR2 MUTATED    7 10  5  1
  ITPR2 WILD-TYPE 86 71 45 52
D211V5, multiclass
    clus
vv   ITPR2 MUTATED ITPR2 WILD-TYPE
  N0             7              86
  N1            10              71
  N2             5              45
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D211V6, binary
                 cls
clus                0   1
  ITPR2 MUTATED    23   1
  ITPR2 WILD-TYPE 234  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED     23    1
  ITPR2 WILD-TYPE  234   17
   clus
vv  ITPR2 MUTATED ITPR2 WILD-TYPE
  0            23             234
  1             1              17
[1] 2 2
[1] FALSE
D211V7, binary
                 cls
clus                0   1
  ITPR2 MUTATED    10  15
  ITPR2 WILD-TYPE 100 164
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED     10   15
  ITPR2 WILD-TYPE  100  164
        clus
vv       ITPR2 MUTATED ITPR2 WILD-TYPE
  FEMALE            10             100
  MALE              15             164
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ITPR2 MUTATED                                       2
  ITPR2 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ITPR2 MUTATED                                                       14
  ITPR2 WILD-TYPE                                                    121
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ITPR2 MUTATED                                                                   4
  ITPR2 WILD-TYPE                                                                36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ITPR2 MUTATED                                                  5
  ITPR2 WILD-TYPE                                               33
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ITPR2 MUTATED                                                          0
  ITPR2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ITPR2 MUTATED                                                           0
  ITPR2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ITPR2 MUTATED                                          0
  ITPR2 WILD-TYPE                                        3
D211V8, multiclass
                                                                   clus
vv                                                                  ITPR2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       14
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ITPR2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        121
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D211V9, binary
                 cls
clus                0   1
  ITPR2 MUTATED     0  25
  ITPR2 WILD-TYPE   5 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED      0   25
  ITPR2 WILD-TYPE    5  259
     clus
vv    ITPR2 MUTATED ITPR2 WILD-TYPE
  NO              0               5
  YES            25             259
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ITPR2 MUTATED    19   0   0   6
  ITPR2 WILD-TYPE 208  10  10  18
D211V10, multiclass
    clus
vv   ITPR2 MUTATED ITPR2 WILD-TYPE
  R0            19             208
  R1             0              10
  R2             0              10
  RX             6              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D211V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ITPR2 MUTATED       8                         0    14
  ITPR2 WILD-TYPE    68                         4   154
D211V12, multiclass
                           clus
vv                          ITPR2 MUTATED ITPR2 WILD-TYPE
  ASIAN                                 8              68
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                14             154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(212) Variable = MLL3 MUTATION ANALYSIS
D212V1, survival
                sevent
clus2              0   1
  MLL3 MUTATED    27   8
  MLL3 WILD-TYPE 154  72
  MLL3 MUTATED MLL3 WILD-TYPE 
            35            226 
  MLL3 MUTATED MLL3 WILD-TYPE 
             8             72 
$`MLL3 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-8361 TCGA-BR-8363 
        6.97        34.68        23.93        12.43        19.50         0.26 
TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-A4QL 
       19.17        15.85        13.45         7.53        15.81        11.57 
TCGA-CD-5801 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI 
       13.18         0.13         0.10         0.10         6.58         0.10 
TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4465 TCGA-CG-5721 
       12.62        15.95         1.02         7.99         9.01         6.02 
TCGA-CG-5726 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-EQ-A4SO TCGA-FP-7916 TCGA-HU-A4G9 
       28.96        14.27        16.44        16.24        14.07        24.20 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H8 
        8.98         6.51        10.19        19.36         8.88 

$`MLL3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       15.42        28.01        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 
       16.31         2.20        15.58         7.40         6.18        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       11.80        14.79         0.26         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        6.28         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
        3.25        13.15         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8532 
        0.07         0.07         0.07         0.10         0.16         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4437 TCGA-CG-4438 
       12.20        20.02         3.02        27.02         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       21.14        20.91         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        0.62         7.99        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        11.84         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
       11.77        29.98         0.10         6.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
       12.95        23.84        12.30         9.67        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  MLL3 MUTATED MLL3 WILD-TYPE 
           0.1            0.0 
  MLL3 MUTATED MLL3 WILD-TYPE 
         34.68         105.07 
  MLL3 MUTATED MLL3 WILD-TYPE 
         12.43          12.71 
[1] "0.1 - 34.7 (12.4)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.2"
D212V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MLL3 MUTATED         1        2        6        3         4         1
  MLL3 WILD-TYPE       0        7       21       23        27        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MLL3 MUTATED           0          5          5          7        6
  MLL3 WILD-TYPE         3         44         31         17       18
D212V3, multiclass
            clus
vv           MLL3 MUTATED MLL3 WILD-TYPE
  STAGE I               1              0
  STAGE IA              2              7
  STAGE IB              6             21
  STAGE II              3             23
  STAGE IIA             4             27
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            5             44
  STAGE IIIB            5             31
  STAGE IIIC            7             17
  STAGE IV              6             18
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MLL3 MUTATED     5   9  13  15
  MLL3 WILD-TYPE   6  63 109  60
D212V4, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  T1            5              6
  T2            9             63
  T3           13            109
  T4           15             60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  MLL3 MUTATED   14 12  5 10
  MLL3 WILD-TYPE 79 69 45 43
D212V5, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  N0           14             79
  N1           12             69
  N2            5             45
  N3           10             43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D212V6, binary
                cls
clus               0   1
  MLL3 MUTATED    36   4
  MLL3 WILD-TYPE 221  14
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     36    4
  MLL3 WILD-TYPE  221   14
   clus
vv  MLL3 MUTATED MLL3 WILD-TYPE
  0           36            221
  1            4             14
[1] 2 2
[1] FALSE
D212V7, binary
                cls
clus               0   1
  MLL3 MUTATED    18  27
  MLL3 WILD-TYPE  92 152
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     18   27
  MLL3 WILD-TYPE   92  152
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  FEMALE           18             92
  MALE             27            152
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MLL3 MUTATED                                       7
  MLL3 WILD-TYPE                                    43
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MLL3 MUTATED                                                       24
  MLL3 WILD-TYPE                                                    111
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MLL3 MUTATED                                                                   6
  MLL3 WILD-TYPE                                                                34
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MLL3 MUTATED                                                  6
  MLL3 WILD-TYPE                                               32
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MLL3 MUTATED                                                          2
  MLL3 WILD-TYPE                                                       14
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MLL3 MUTATED                                                           0
  MLL3 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MLL3 MUTATED                                          0
  MLL3 WILD-TYPE                                        3
D212V8, multiclass
                                                                   clus
vv                                                                  MLL3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  MLL3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         43
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       111
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D212V9, binary
                cls
clus               0   1
  MLL3 MUTATED     1  44
  MLL3 WILD-TYPE   4 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED      1   44
  MLL3 WILD-TYPE    4  240
     clus
vv    MLL3 MUTATED MLL3 WILD-TYPE
  NO             1              4
  YES           44            240
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MLL3 MUTATED    31   0   2   8
  MLL3 WILD-TYPE 196  10   8  16
D212V10, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  R0           31            196
  R1            0             10
  R2            2              8
  RX            8             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D212V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL3 MUTATED      15                         1    21
  MLL3 WILD-TYPE    61                         3   147
D212V12, multiclass
                           clus
vv                          MLL3 MUTATED MLL3 WILD-TYPE
  ASIAN                               15             61
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                               21            147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(213) Variable = CDK12 MUTATION ANALYSIS
D213V1, survival
                 sevent
clus2               0   1
  CDK12 MUTATED    11   7
  CDK12 WILD-TYPE 170  73
  CDK12 MUTATED CDK12 WILD-TYPE 
             18             243 
  CDK12 MUTATED CDK12 WILD-TYPE 
              7              73 
$`CDK12 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6706 TCGA-BR-7851 TCGA-BR-8081 
       26.70         6.97        30.90        18.05        12.43        20.55 
TCGA-BR-8680 TCGA-CD-5801 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5728 
       15.81        13.18         6.02       105.07        12.03        65.10 
TCGA-CG-5733 TCGA-D7-6822 TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-A4GH TCGA-HU-A4H4 
       21.07        12.33        11.08        26.47        11.77        23.84 

$`CDK12 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 
       11.70         6.61         4.64         7.43        18.35         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       25.61        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       28.01        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        9.60         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.15         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
        0.99        28.96        79.07         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       15.22        15.98        12.79        10.55        11.31        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8243 
       59.54         5.03        13.58         0.56         5.52         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       22.75        25.81        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  CDK12 MUTATED CDK12 WILD-TYPE 
           6.02            0.00 
  CDK12 MUTATED CDK12 WILD-TYPE 
         105.07           79.07 
  CDK12 MUTATED CDK12 WILD-TYPE 
          16.93           12.56 
[1] "6.0 - 105.1 (16.9)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.3"
D213V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDK12 MUTATED         0        1        4        1         1         4
  CDK12 WILD-TYPE       1        8       23       25        30        40
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDK12 MUTATED           0          4          0          0        3
  CDK12 WILD-TYPE         3         45         36         24       21
D213V3, multiclass
            clus
vv           CDK12 MUTATED CDK12 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               4              23
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              4              40
  STAGE III              0               3
  STAGE IIIA             4              45
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               3              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDK12 MUTATED     1   8   5   5
  CDK12 WILD-TYPE  10  64 117  70
D213V4, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  T1             1              10
  T2             8              64
  T3             5             117
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CDK12 MUTATED    9  5  3  1
  CDK12 WILD-TYPE 84 76 47 52
D213V5, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  N0             9              84
  N1             5              76
  N2             3              47
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D213V6, binary
                 cls
clus                0   1
  CDK12 MUTATED    15   2
  CDK12 WILD-TYPE 242  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED     15    2
  CDK12 WILD-TYPE  242   16
   clus
vv  CDK12 MUTATED CDK12 WILD-TYPE
  0            15             242
  1             2              16
[1] 2 2
[1] FALSE
D213V7, binary
                 cls
clus                0   1
  CDK12 MUTATED     7  12
  CDK12 WILD-TYPE 103 167
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED      7   12
  CDK12 WILD-TYPE  103  167
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  FEMALE             7             103
  MALE              12             167
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CDK12 MUTATED                                       2
  CDK12 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CDK12 MUTATED                                                        7
  CDK12 WILD-TYPE                                                    128
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CDK12 MUTATED                                                                   5
  CDK12 WILD-TYPE                                                                35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CDK12 MUTATED                                                  4
  CDK12 WILD-TYPE                                               34
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CDK12 MUTATED                                                          0
  CDK12 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CDK12 MUTATED                                                           0
  CDK12 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CDK12 MUTATED                                          1
  CDK12 WILD-TYPE                                        2
D213V8, multiclass
                                                                   clus
vv                                                                  CDK12 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  CDK12 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D213V9, binary
                 cls
clus                0   1
  CDK12 MUTATED     0  19
  CDK12 WILD-TYPE   5 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED      0   19
  CDK12 WILD-TYPE    5  265
     clus
vv    CDK12 MUTATED CDK12 WILD-TYPE
  NO              0               5
  YES            19             265
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDK12 MUTATED    16   0   1   2
  CDK12 WILD-TYPE 211  10   9  22
D213V10, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  R0            16             211
  R1             0              10
  R2             1               9
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D213V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDK12 MUTATED       4                         1     8
  CDK12 WILD-TYPE    72                         3   160
D213V12, multiclass
                           clus
vv                          CDK12 MUTATED CDK12 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 8             160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(214) Variable = PODN MUTATION ANALYSIS
D214V1, survival
                sevent
clus2              0   1
  PODN MUTATED     8   2
  PODN WILD-TYPE 173  78
  PODN MUTATED PODN WILD-TYPE 
            10            251 
  PODN MUTATED PODN WILD-TYPE 
             2             78 
$`PODN MUTATED`
TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-8363 TCGA-BR-8591 TCGA-CD-8529 
       34.68        24.76        15.42         0.26        13.45         0.13 
TCGA-CG-5726 TCGA-CG-5728 TCGA-FP-A4BE TCGA-HU-A4GX 
       28.96        65.10        11.08        10.19 

$`PODN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       23.93        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       19.50        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        15.81         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 
       59.54         5.03        13.58         0.56         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  PODN MUTATED PODN WILD-TYPE 
          0.13           0.00 
  PODN MUTATED PODN WILD-TYPE 
         65.10         105.07 
  PODN MUTATED PODN WILD-TYPE 
        14.435         12.590 
[1] "0.1 - 65.1 (14.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.2"
D214V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PODN MUTATED         0        2        2        0         3         0
  PODN WILD-TYPE       1        7       25       26        28        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PODN MUTATED           0          1          0          2        2
  PODN WILD-TYPE         3         48         36         22       22
D214V3, multiclass
            clus
vv           PODN MUTATED PODN WILD-TYPE
  STAGE I               0              1
  STAGE IA              2              7
  STAGE IB              2             25
  STAGE II              0             26
  STAGE IIA             3             28
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            2             22
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PODN MUTATED     2   2   4   4
  PODN WILD-TYPE   9  70 118  71
D214V4, multiclass
    clus
vv   PODN MUTATED PODN WILD-TYPE
  T1            2              9
  T2            2             70
  T3            4            118
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  PODN MUTATED    8  2  2  1
  PODN WILD-TYPE 85 79 48 52
D214V5, multiclass
    clus
vv   PODN MUTATED PODN WILD-TYPE
  N0            8             85
  N1            2             79
  N2            2             48
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D214V6, binary
                cls
clus               0   1
  PODN MUTATED    12   1
  PODN WILD-TYPE 245  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  PODN MUTATED     12    1
  PODN WILD-TYPE  245   17
   clus
vv  PODN MUTATED PODN WILD-TYPE
  0           12            245
  1            1             17
[1] 2 2
[1] FALSE
D214V7, binary
                cls
clus               0   1
  PODN MUTATED     7   6
  PODN WILD-TYPE 103 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  PODN MUTATED      7    6
  PODN WILD-TYPE  103  173
        clus
vv       PODN MUTATED PODN WILD-TYPE
  FEMALE            7            103
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PODN MUTATED                                       1
  PODN WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PODN MUTATED                                                        8
  PODN WILD-TYPE                                                    127
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PODN MUTATED                                                                   2
  PODN WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PODN MUTATED                                                  0
  PODN WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PODN MUTATED                                                          1
  PODN WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PODN MUTATED                                                           1
  PODN WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PODN MUTATED                                          0
  PODN WILD-TYPE                                        3
D214V8, multiclass
                                                                   clus
vv                                                                  PODN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  PODN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D214V9, binary
                cls
clus               0   1
  PODN MUTATED     0  13
  PODN WILD-TYPE   5 271
[1] "tbl2"
                cls
clus             [,1] [,2]
  PODN MUTATED      0   13
  PODN WILD-TYPE    5  271
     clus
vv    PODN MUTATED PODN WILD-TYPE
  NO             0              5
  YES           13            271
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PODN MUTATED    10   0   0   3
  PODN WILD-TYPE 217  10  10  21
D214V10, multiclass
    clus
vv   PODN MUTATED PODN WILD-TYPE
  R0           10            217
  R1            0             10
  R2            0             10
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D214V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PODN MUTATED       2                         1     8
  PODN WILD-TYPE    74                         3   160
D214V12, multiclass
                           clus
vv                          PODN MUTATED PODN WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                                8            160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(215) Variable = AKNAD1 MUTATION ANALYSIS
D215V1, survival
                  sevent
clus2                0   1
  AKNAD1 MUTATED    14   2
  AKNAD1 WILD-TYPE 167  78
  AKNAD1 MUTATED AKNAD1 WILD-TYPE 
              16              245 
  AKNAD1 MUTATED AKNAD1 WILD-TYPE 
               2               78 
$`AKNAD1 MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8081 TCGA-BR-8382 
       11.70         6.97        34.68        23.93        20.55        15.85 
TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-5801 TCGA-CG-4438 TCGA-CG-5723 TCGA-D7-A4YT 
       13.45        15.81        13.18        54.08       105.07        14.27 
TCGA-F1-6874 TCGA-FP-A4BE TCGA-HU-A4G9 TCGA-HU-A4GH 
       14.47        11.08        24.20        11.77 

$`AKNAD1 WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       26.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 
       31.20        32.94        12.82         9.21        24.76        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       12.26         9.60         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
        3.32        11.80        19.17        14.79         0.26         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       15.81         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        14.66        21.14        20.91        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  AKNAD1 MUTATED AKNAD1 WILD-TYPE 
            6.97             0.00 
  AKNAD1 MUTATED AKNAD1 WILD-TYPE 
          105.07            79.07 
  AKNAD1 MUTATED AKNAD1 WILD-TYPE 
           15.14            12.43 
[1] "7.0 - 105.1 (15.1)" "0.0 - 79.1 (12.4)" 
[1] "hr=" "4.2"
D215V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AKNAD1 MUTATED         0        2        3        1         2         1
  AKNAD1 WILD-TYPE       1        7       24       25        29        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AKNAD1 MUTATED           0          3          0          2        2
  AKNAD1 WILD-TYPE         3         46         36         22       22
D215V3, multiclass
            clus
vv           AKNAD1 MUTATED AKNAD1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                2                7
  STAGE IB                3               24
  STAGE II                1               25
  STAGE IIA               2               29
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              3               46
  STAGE IIIB              0               36
  STAGE IIIC              2               22
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  AKNAD1 MUTATED     2   5   4   5
  AKNAD1 WILD-TYPE   9  67 118  70
D215V4, multiclass
    clus
vv   AKNAD1 MUTATED AKNAD1 WILD-TYPE
  T1              2                9
  T2              5               67
  T3              4              118
  T4              5               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  AKNAD1 MUTATED    8  5  2  3
  AKNAD1 WILD-TYPE 85 76 48 50
D215V5, multiclass
    clus
vv   AKNAD1 MUTATED AKNAD1 WILD-TYPE
  N0              8               85
  N1              5               76
  N2              2               48
  N3              3               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D215V6, binary
                  cls
clus                 0   1
  AKNAD1 MUTATED    16   1
  AKNAD1 WILD-TYPE 241  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKNAD1 MUTATED     16    1
  AKNAD1 WILD-TYPE  241   17
   clus
vv  AKNAD1 MUTATED AKNAD1 WILD-TYPE
  0             16              241
  1              1               17
[1] 2 2
[1] FALSE
D215V7, binary
                  cls
clus                 0   1
  AKNAD1 MUTATED     6  12
  AKNAD1 WILD-TYPE 104 167
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKNAD1 MUTATED      6   12
  AKNAD1 WILD-TYPE  104  167
        clus
vv       AKNAD1 MUTATED AKNAD1 WILD-TYPE
  FEMALE              6              104
  MALE               12              167
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AKNAD1 MUTATED                                       1
  AKNAD1 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AKNAD1 MUTATED                                                       11
  AKNAD1 WILD-TYPE                                                    124
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AKNAD1 MUTATED                                                                   2
  AKNAD1 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AKNAD1 MUTATED                                                  4
  AKNAD1 WILD-TYPE                                               34
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AKNAD1 MUTATED                                                          0
  AKNAD1 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AKNAD1 MUTATED                                                           0
  AKNAD1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AKNAD1 MUTATED                                          0
  AKNAD1 WILD-TYPE                                        3
D215V8, multiclass
                                                                   clus
vv                                                                  AKNAD1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  AKNAD1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D215V9, binary
                  cls
clus                 0   1
  AKNAD1 MUTATED     0  18
  AKNAD1 WILD-TYPE   5 266
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKNAD1 MUTATED      0   18
  AKNAD1 WILD-TYPE    5  266
     clus
vv    AKNAD1 MUTATED AKNAD1 WILD-TYPE
  NO               0                5
  YES             18              266
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  AKNAD1 MUTATED    15   0   0   3
  AKNAD1 WILD-TYPE 212  10  10  21
D215V10, multiclass
    clus
vv   AKNAD1 MUTATED AKNAD1 WILD-TYPE
  R0             15              212
  R1              0               10
  R2              0               10
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D215V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AKNAD1 MUTATED       4                         1    11
  AKNAD1 WILD-TYPE    72                         3   157
D215V12, multiclass
                           clus
vv                          AKNAD1 MUTATED AKNAD1 WILD-TYPE
  ASIAN                                  4               72
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                 11              157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(216) Variable = ERBB3 MUTATION ANALYSIS
D216V1, survival
                 sevent
clus2               0   1
  ERBB3 MUTATED    14   8
  ERBB3 WILD-TYPE 167  72
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             22             239 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
              8              72 
$`ERBB3 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6563 TCGA-BR-6706 TCGA-BR-8059 TCGA-BR-8078 
        6.97        34.68        39.12        18.05        14.43        12.26 
TCGA-BR-8363 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-8527 
        0.26         0.26        15.85        11.57         5.13         0.07 
TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-EQ-8122 TCGA-FP-7735 
        6.02        28.96        16.44         5.92         7.99         3.48 
TCGA-HU-8602 TCGA-HU-A4G9 TCGA-HU-A4GU TCGA-HU-A4H8 
       11.41        24.20         6.25         8.88 

$`ERBB3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       17.29        13.68        19.33        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       25.61        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8080 
        9.07        12.76        18.71        17.49         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40         6.18        19.50        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       19.17        14.79         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 
        0.39         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 
        1.02         0.99         0.99       105.07        12.03        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       20.91        14.27        15.16        13.78        14.76         0.62 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7829 TCGA-FP-7916 
       16.24        14.47        72.23        21.27        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       11.84         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
       12.95        19.36        23.84        12.30         9.67        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  ERBB3 MUTATED ERBB3 WILD-TYPE 
           0.07            0.00 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
          39.12          105.07 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
         10.145          12.790 
[1] "0.1 - 39.1 (10.1)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.4"
D216V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ERBB3 MUTATED         0        2        4        2         2         7
  ERBB3 WILD-TYPE       1        7       23       24        29        37
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ERBB3 MUTATED           1          4          2          1        1
  ERBB3 WILD-TYPE         2         45         34         23       23
D216V3, multiclass
            clus
vv           ERBB3 MUTATED ERBB3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               2               7
  STAGE IB               4              23
  STAGE II               2              24
  STAGE IIA              2              29
  STAGE IIB              7              37
  STAGE III              1               2
  STAGE IIIA             4              45
  STAGE IIIB             2              34
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ERBB3 MUTATED     3   5  13   6
  ERBB3 WILD-TYPE   8  67 109  69
D216V4, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  T1             3               8
  T2             5              67
  T3            13             109
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ERBB3 MUTATED   10 14  1  3
  ERBB3 WILD-TYPE 83 67 49 50
D216V5, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  N0            10              83
  N1            14              67
  N2             1              49
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D216V6, binary
                 cls
clus                0   1
  ERBB3 MUTATED    27   0
  ERBB3 WILD-TYPE 230  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     27    0
  ERBB3 WILD-TYPE  230   18
   clus
vv  ERBB3 MUTATED ERBB3 WILD-TYPE
  0            27             230
  1             0              18
[1] 2 2
[1] FALSE
D216V7, binary
                 cls
clus                0   1
  ERBB3 MUTATED    14  17
  ERBB3 WILD-TYPE  96 162
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     14   17
  ERBB3 WILD-TYPE   96  162
        clus
vv       ERBB3 MUTATED ERBB3 WILD-TYPE
  FEMALE            14              96
  MALE              17             162
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ERBB3 MUTATED                                       2
  ERBB3 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ERBB3 MUTATED                                                       18
  ERBB3 WILD-TYPE                                                    117
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ERBB3 MUTATED                                                                   6
  ERBB3 WILD-TYPE                                                                34
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ERBB3 MUTATED                                                  4
  ERBB3 WILD-TYPE                                               34
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ERBB3 MUTATED                                                          1
  ERBB3 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ERBB3 MUTATED                                                           0
  ERBB3 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ERBB3 MUTATED                                          0
  ERBB3 WILD-TYPE                                        3
D216V8, multiclass
                                                                   clus
vv                                                                  ERBB3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       18
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ERBB3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        117
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D216V9, binary
                 cls
clus                0   1
  ERBB3 MUTATED     1  30
  ERBB3 WILD-TYPE   4 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED      1   30
  ERBB3 WILD-TYPE    4  254
     clus
vv    ERBB3 MUTATED ERBB3 WILD-TYPE
  NO              1               4
  YES            30             254
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ERBB3 MUTATED    23   0   0   7
  ERBB3 WILD-TYPE 204  10  10  17
D216V10, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  R0            23             204
  R1             0              10
  R2             0              10
  RX             7              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D216V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERBB3 MUTATED       5                         1    21
  ERBB3 WILD-TYPE    71                         3   147
D216V12, multiclass
                           clus
vv                          ERBB3 MUTATED ERBB3 WILD-TYPE
  ASIAN                                 5              71
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                21             147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(217) Variable = RSF1 MUTATION ANALYSIS
D217V1, survival
                sevent
clus2              0   1
  RSF1 MUTATED    11   4
  RSF1 WILD-TYPE 170  76
  RSF1 MUTATED RSF1 WILD-TYPE 
            15            246 
  RSF1 MUTATED RSF1 WILD-TYPE 
             4             76 
$`RSF1 MUTATED`
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6565 TCGA-BR-6852 TCGA-BR-8081 
        7.43        30.90        34.68         9.17        32.94        20.55 
TCGA-BR-8361 TCGA-BR-8680 TCGA-CG-4305 TCGA-CG-4437 TCGA-D7-6815 TCGA-FP-7916 
       19.50        15.81        15.95         8.05        15.98        14.07 
TCGA-HU-A4G3 TCGA-HU-A4GX TCGA-IP-7968 
        5.59        10.19         2.53 

$`RSF1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 
       26.70        11.70         6.61         6.97         4.64        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.68        19.33        39.12        26.10        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       12.82         9.21        24.76        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        9.60         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 
       20.02         3.02        27.02         1.02         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       13.35        17.19        10.26        15.22        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 
       11.41        12.10        10.62         0.76        24.30        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51         6.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 

  RSF1 MUTATED RSF1 WILD-TYPE 
          2.53           0.00 
  RSF1 MUTATED RSF1 WILD-TYPE 
         34.68         105.07 
  RSF1 MUTATED RSF1 WILD-TYPE 
        15.810         12.575 
[1] "2.5 - 34.7 (15.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D217V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RSF1 MUTATED         0        0        1        2         2         4
  RSF1 WILD-TYPE       1        9       26       24        29        40
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RSF1 MUTATED           0          0          1          3        1
  RSF1 WILD-TYPE         3         49         35         21       23
D217V3, multiclass
            clus
vv           RSF1 MUTATED RSF1 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              2             24
  STAGE IIA             2             29
  STAGE IIB             4             40
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            1             35
  STAGE IIIC            3             21
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RSF1 MUTATED     0   6   3   6
  RSF1 WILD-TYPE  11  66 119  69
D217V4, multiclass
    clus
vv   RSF1 MUTATED RSF1 WILD-TYPE
  T1            0             11
  T2            6             66
  T3            3            119
  T4            6             69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  RSF1 MUTATED    5  4  6  1
  RSF1 WILD-TYPE 88 77 44 52
D217V5, multiclass
    clus
vv   RSF1 MUTATED RSF1 WILD-TYPE
  N0            5             88
  N1            4             77
  N2            6             44
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D217V6, binary
                cls
clus               0   1
  RSF1 MUTATED    14   1
  RSF1 WILD-TYPE 243  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  RSF1 MUTATED     14    1
  RSF1 WILD-TYPE  243   17
   clus
vv  RSF1 MUTATED RSF1 WILD-TYPE
  0           14            243
  1            1             17
[1] 2 2
[1] FALSE
D217V7, binary
                cls
clus               0   1
  RSF1 MUTATED     9   8
  RSF1 WILD-TYPE 101 171
[1] "tbl2"
                cls
clus             [,1] [,2]
  RSF1 MUTATED      9    8
  RSF1 WILD-TYPE  101  171
        clus
vv       RSF1 MUTATED RSF1 WILD-TYPE
  FEMALE            9            101
  MALE              8            171
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RSF1 MUTATED                                       2
  RSF1 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RSF1 MUTATED                                                       10
  RSF1 WILD-TYPE                                                    125
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RSF1 MUTATED                                                                   2
  RSF1 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RSF1 MUTATED                                                  3
  RSF1 WILD-TYPE                                               35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RSF1 MUTATED                                                          0
  RSF1 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RSF1 MUTATED                                                           0
  RSF1 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RSF1 MUTATED                                          0
  RSF1 WILD-TYPE                                        3
D217V8, multiclass
                                                                   clus
vv                                                                  RSF1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  RSF1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D217V9, binary
                cls
clus               0   1
  RSF1 MUTATED     0  17
  RSF1 WILD-TYPE   5 267
[1] "tbl2"
                cls
clus             [,1] [,2]
  RSF1 MUTATED      0   17
  RSF1 WILD-TYPE    5  267
     clus
vv    RSF1 MUTATED RSF1 WILD-TYPE
  NO             0              5
  YES           17            267
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RSF1 MUTATED    13   0   0   3
  RSF1 WILD-TYPE 214  10  10  21
D217V10, multiclass
    clus
vv   RSF1 MUTATED RSF1 WILD-TYPE
  R0           13            214
  R1            0             10
  R2            0             10
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D217V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RSF1 MUTATED       4                         0    10
  RSF1 WILD-TYPE    72                         4   158
D217V12, multiclass
                           clus
vv                          RSF1 MUTATED RSF1 WILD-TYPE
  ASIAN                                4             72
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               10            158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(218) Variable = KBTBD10 MUTATION ANALYSIS
D218V1, survival
                   sevent
clus2                 0   1
  KBTBD10 MUTATED     6   0
  KBTBD10 WILD-TYPE 175  80
  KBTBD10 MUTATED KBTBD10 WILD-TYPE 
                6               255 
  KBTBD10 MUTATED KBTBD10 WILD-TYPE 
                0                80 
$`KBTBD10 MUTATED`
TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8678 TCGA-CG-4437 TCGA-HU-A4GP TCGA-HU-A4GT 
        1.12        13.45        11.54         8.05         8.98         6.51 

$`KBTBD10 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
        9.34         6.28         7.53         0.49        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GU 
       22.75        25.81        11.77        29.98         0.10         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  KBTBD10 MUTATED KBTBD10 WILD-TYPE 
             1.12              0.00 
  KBTBD10 MUTATED KBTBD10 WILD-TYPE 
            13.45            105.07 
  KBTBD10 MUTATED KBTBD10 WILD-TYPE 
            8.515            12.760 
[1] "1.1 - 13.4 (8.5)"   "0.0 - 105.1 (12.8)"
[1] "hr="     "9200000"
D218V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KBTBD10 MUTATED         0        0        1        1         3         0
  KBTBD10 WILD-TYPE       1        9       26       25        28        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KBTBD10 MUTATED           0          0          0          1        0
  KBTBD10 WILD-TYPE         3         49         36         23       24
D218V3, multiclass
            clus
vv           KBTBD10 MUTATED KBTBD10 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 1                25
  STAGE IIA                3                28
  STAGE IIB                0                44
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               0                36
  STAGE IIIC               1                23
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  KBTBD10 MUTATED     0   3   2   1
  KBTBD10 WILD-TYPE  11  69 120  74
D218V4, multiclass
    clus
vv   KBTBD10 MUTATED KBTBD10 WILD-TYPE
  T1               0                11
  T2               3                69
  T3               2               120
  T4               1                74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  KBTBD10 MUTATED    3  2  0  1
  KBTBD10 WILD-TYPE 90 79 50 52
D218V5, multiclass
    clus
vv   KBTBD10 MUTATED KBTBD10 WILD-TYPE
  N0               3                90
  N1               2                79
  N2               0                50
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D218V6, binary
                   cls
clus                  0   1
  KBTBD10 MUTATED     7   0
  KBTBD10 WILD-TYPE 250  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KBTBD10 MUTATED      7    0
  KBTBD10 WILD-TYPE  250   18
   clus
vv  KBTBD10 MUTATED KBTBD10 WILD-TYPE
  0               7               250
  1               0                18
[1] 2 2
[1] FALSE
D218V7, binary
                   cls
clus                  0   1
  KBTBD10 MUTATED     4   3
  KBTBD10 WILD-TYPE 106 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KBTBD10 MUTATED      4    3
  KBTBD10 WILD-TYPE  106  176
        clus
vv       KBTBD10 MUTATED KBTBD10 WILD-TYPE
  FEMALE               4               106
  MALE                 3               176
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KBTBD10 MUTATED                                       1
  KBTBD10 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KBTBD10 MUTATED                                                        4
  KBTBD10 WILD-TYPE                                                    131
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KBTBD10 MUTATED                                                                   1
  KBTBD10 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KBTBD10 MUTATED                                                  1
  KBTBD10 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KBTBD10 MUTATED                                                          0
  KBTBD10 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KBTBD10 MUTATED                                                           0
  KBTBD10 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KBTBD10 MUTATED                                          0
  KBTBD10 WILD-TYPE                                        3
D218V8, multiclass
                                                                   clus
vv                                                                  KBTBD10 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  KBTBD10 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D218V9, binary
                   cls
clus                  0   1
  KBTBD10 MUTATED     0   7
  KBTBD10 WILD-TYPE   5 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KBTBD10 MUTATED      0    7
  KBTBD10 WILD-TYPE    5  277
     clus
vv    KBTBD10 MUTATED KBTBD10 WILD-TYPE
  NO                0                 5
  YES               7               277
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  KBTBD10 MUTATED     6   0   0   1
  KBTBD10 WILD-TYPE 221  10  10  23
D218V10, multiclass
    clus
vv   KBTBD10 MUTATED KBTBD10 WILD-TYPE
  R0               6               221
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D218V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KBTBD10 MUTATED       2                         0     4
  KBTBD10 WILD-TYPE    74                         4   164
D218V12, multiclass
                           clus
vv                          KBTBD10 MUTATED KBTBD10 WILD-TYPE
  ASIAN                                   2                74
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   4               164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(219) Variable = OSBP2 MUTATION ANALYSIS
D219V1, survival
                 sevent
clus2               0   1
  OSBP2 MUTATED     9   1
  OSBP2 WILD-TYPE 172  79
  OSBP2 MUTATED OSBP2 WILD-TYPE 
             10             251 
  OSBP2 MUTATED OSBP2 WILD-TYPE 
              1              79 
$`OSBP2 MUTATED`
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8382 TCGA-BR-A4QL 
       34.68        32.78        32.94        23.93        15.85        11.57 
TCGA-CG-4306 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GX 
        1.02        11.41        11.84        10.19 

$`OSBP2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 
       30.90        31.20        12.82         9.21        24.76        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        5.52        26.47         5.92        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  OSBP2 MUTATED OSBP2 WILD-TYPE 
           1.02            0.00 
  OSBP2 MUTATED OSBP2 WILD-TYPE 
          34.68          105.07 
  OSBP2 MUTATED OSBP2 WILD-TYPE 
         13.845          12.620 
[1] "1.0 - 34.7 (13.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "4.5"
D219V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OSBP2 MUTATED         0        0        1        0         3         2
  OSBP2 WILD-TYPE       1        9       26       26        28        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OSBP2 MUTATED           0          0          1          2        2
  OSBP2 WILD-TYPE         3         49         35         22       22
D219V3, multiclass
            clus
vv           OSBP2 MUTATED OSBP2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              3              28
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             2              22
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OSBP2 MUTATED     0   1   6   4
  OSBP2 WILD-TYPE  11  71 116  71
D219V4, multiclass
    clus
vv   OSBP2 MUTATED OSBP2 WILD-TYPE
  T1             0              11
  T2             1              71
  T3             6             116
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  OSBP2 MUTATED    5  1  3  2
  OSBP2 WILD-TYPE 88 80 47 51
D219V5, multiclass
    clus
vv   OSBP2 MUTATED OSBP2 WILD-TYPE
  N0             5              88
  N1             1              80
  N2             3              47
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D219V6, binary
                 cls
clus                0   1
  OSBP2 MUTATED    10   1
  OSBP2 WILD-TYPE 247  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OSBP2 MUTATED     10    1
  OSBP2 WILD-TYPE  247   17
   clus
vv  OSBP2 MUTATED OSBP2 WILD-TYPE
  0            10             247
  1             1              17
[1] 2 2
[1] FALSE
D219V7, binary
                 cls
clus                0   1
  OSBP2 MUTATED    10   1
  OSBP2 WILD-TYPE 100 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OSBP2 MUTATED     10    1
  OSBP2 WILD-TYPE  100  178
        clus
vv       OSBP2 MUTATED OSBP2 WILD-TYPE
  FEMALE            10             100
  MALE               1             178
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  OSBP2 MUTATED                                       3
  OSBP2 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OSBP2 MUTATED                                                        8
  OSBP2 WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OSBP2 MUTATED                                                                   0
  OSBP2 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  OSBP2 MUTATED                                                  0
  OSBP2 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  OSBP2 MUTATED                                                          0
  OSBP2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  OSBP2 MUTATED                                                           0
  OSBP2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  OSBP2 MUTATED                                          0
  OSBP2 WILD-TYPE                                        3
D219V8, multiclass
                                                                   clus
vv                                                                  OSBP2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  OSBP2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D219V9, binary
                 cls
clus                0   1
  OSBP2 MUTATED     0  11
  OSBP2 WILD-TYPE   5 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OSBP2 MUTATED      0   11
  OSBP2 WILD-TYPE    5  273
     clus
vv    OSBP2 MUTATED OSBP2 WILD-TYPE
  NO              0               5
  YES            11             273
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OSBP2 MUTATED     8   0   1   1
  OSBP2 WILD-TYPE 219  10   9  23
D219V10, multiclass
    clus
vv   OSBP2 MUTATED OSBP2 WILD-TYPE
  R0             8             219
  R1             0              10
  R2             1               9
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D219V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OSBP2 MUTATED       3                         0     7
  OSBP2 WILD-TYPE    73                         4   161
D219V12, multiclass
                           clus
vv                          OSBP2 MUTATED OSBP2 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 7             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(220) Variable = EBF3 MUTATION ANALYSIS
D220V1, survival
                sevent
clus2              0   1
  EBF3 MUTATED    10   2
  EBF3 WILD-TYPE 171  78
  EBF3 MUTATED EBF3 WILD-TYPE 
            12            249 
  EBF3 MUTATED EBF3 WILD-TYPE 
             2             78 
$`EBF3 MUTATED`
TCGA-BR-6452 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MJ 
       34.68         1.12        13.45        15.81        11.57        12.62 
TCGA-CG-5721 TCGA-D7-A4YY TCGA-FP-7829 TCGA-FP-7916 TCGA-HU-A4GQ TCGA-HU-A4GT 
        6.02        13.78        19.53        14.07         0.10         6.51 

$`EBF3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        13.64         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       21.27         3.48        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU 
       22.75        25.81        11.77        29.98         8.98         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  EBF3 MUTATED EBF3 WILD-TYPE 
           0.1            0.0 
  EBF3 MUTATED EBF3 WILD-TYPE 
         34.68         105.07 
  EBF3 MUTATED EBF3 WILD-TYPE 
        13.035         12.590 
[1] "0.1 - 34.7 (13.0)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.6"
D220V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EBF3 MUTATED         0        0        1        0         3         1
  EBF3 WILD-TYPE       1        9       26       26        28        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EBF3 MUTATED           0          0          2          3        2
  EBF3 WILD-TYPE         3         49         34         21       22
D220V3, multiclass
            clus
vv           EBF3 MUTATED EBF3 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             3             28
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            2             34
  STAGE IIIC            3             21
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EBF3 MUTATED     0   1   6   5
  EBF3 WILD-TYPE  11  71 116  70
D220V4, multiclass
    clus
vv   EBF3 MUTATED EBF3 WILD-TYPE
  T1            0             11
  T2            1             71
  T3            6            116
  T4            5             70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  EBF3 MUTATED    4  2  2  4
  EBF3 WILD-TYPE 89 79 48 49
D220V5, multiclass
    clus
vv   EBF3 MUTATED EBF3 WILD-TYPE
  N0            4             89
  N1            2             79
  N2            2             48
  N3            4             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D220V6, binary
                cls
clus               0   1
  EBF3 MUTATED    10   1
  EBF3 WILD-TYPE 247  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  EBF3 MUTATED     10    1
  EBF3 WILD-TYPE  247   17
   clus
vv  EBF3 MUTATED EBF3 WILD-TYPE
  0           10            247
  1            1             17
[1] 2 2
[1] FALSE
D220V7, binary
                cls
clus               0   1
  EBF3 MUTATED     4   8
  EBF3 WILD-TYPE 106 171
[1] "tbl2"
                cls
clus             [,1] [,2]
  EBF3 MUTATED      4    8
  EBF3 WILD-TYPE  106  171
        clus
vv       EBF3 MUTATED EBF3 WILD-TYPE
  FEMALE            4            106
  MALE              8            171
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  EBF3 MUTATED                                       1
  EBF3 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EBF3 MUTATED                                                        6
  EBF3 WILD-TYPE                                                    129
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EBF3 MUTATED                                                                   1
  EBF3 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  EBF3 MUTATED                                                  3
  EBF3 WILD-TYPE                                               35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  EBF3 MUTATED                                                          1
  EBF3 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  EBF3 MUTATED                                                           0
  EBF3 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  EBF3 MUTATED                                          0
  EBF3 WILD-TYPE                                        3
D220V8, multiclass
                                                                   clus
vv                                                                  EBF3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  EBF3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D220V9, binary
                cls
clus               0   1
  EBF3 MUTATED     0  12
  EBF3 WILD-TYPE   5 272
[1] "tbl2"
                cls
clus             [,1] [,2]
  EBF3 MUTATED      0   12
  EBF3 WILD-TYPE    5  272
     clus
vv    EBF3 MUTATED EBF3 WILD-TYPE
  NO             0              5
  YES           12            272
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EBF3 MUTATED    10   0   0   0
  EBF3 WILD-TYPE 217  10  10  24
D220V10, multiclass
    clus
vv   EBF3 MUTATED EBF3 WILD-TYPE
  R0           10            217
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D220V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EBF3 MUTATED       5                         0     6
  EBF3 WILD-TYPE    71                         4   162
D220V12, multiclass
                           clus
vv                          EBF3 MUTATED EBF3 WILD-TYPE
  ASIAN                                5             71
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                6            162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(221) Variable = LRP1 MUTATION ANALYSIS
D221V1, survival
                sevent
clus2              0   1
  LRP1 MUTATED    20   6
  LRP1 WILD-TYPE 161  74
  LRP1 MUTATED LRP1 WILD-TYPE 
            26            235 
  LRP1 MUTATED LRP1 WILD-TYPE 
             6             74 
$`LRP1 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-7851 
        6.97        30.90         6.61        34.68        24.76        12.43 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       12.26        20.55         7.40         6.18        19.50         0.26 
TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5723 
        3.32        19.17         1.12         6.58         6.02       105.07 
TCGA-CG-5728 TCGA-D7-6822 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-HJ-7597 TCGA-HU-8602 
       65.10        12.33        16.24        14.47        26.47        11.41 
TCGA-HU-A4GT TCGA-HU-A4GX 
        6.51        10.19 

$`LRP1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       32.94        12.82         9.21        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 
       18.71        17.49        14.43         0.69         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8364 
       12.95         2.66        16.31         2.20        15.58        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 
       17.52         0.95        26.33         4.31        14.04        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
        6.97        36.00         1.02         0.99         0.99        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       15.22        15.98        12.79        10.55        11.31        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
       14.76         0.62         7.99        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56        11.08         5.52         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY 
       11.77        29.98         8.98         0.10         6.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  LRP1 MUTATED LRP1 WILD-TYPE 
          0.26           0.00 
  LRP1 MUTATED LRP1 WILD-TYPE 
        105.07          79.07 
  LRP1 MUTATED LRP1 WILD-TYPE 
        12.295         12.760 
[1] "0.3 - 105.1 (12.3)" "0.0 - 79.1 (12.8)" 
[1] "hr=" "1.7"
D221V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LRP1 MUTATED         0        1        5        1         5         4
  LRP1 WILD-TYPE       1        8       22       25        26        40
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRP1 MUTATED           1          2          2          4        2
  LRP1 WILD-TYPE         2         47         34         20       22
D221V3, multiclass
            clus
vv           LRP1 MUTATED LRP1 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              5             22
  STAGE II              1             25
  STAGE IIA             5             26
  STAGE IIB             4             40
  STAGE III             1              2
  STAGE IIIA            2             47
  STAGE IIIB            2             34
  STAGE IIIC            4             20
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LRP1 MUTATED     2   8   7  12
  LRP1 WILD-TYPE   9  64 115  63
D221V4, multiclass
    clus
vv   LRP1 MUTATED LRP1 WILD-TYPE
  T1            2              9
  T2            8             64
  T3            7            115
  T4           12             63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  LRP1 MUTATED   16  6  3  3
  LRP1 WILD-TYPE 77 75 47 50
D221V5, multiclass
    clus
vv   LRP1 MUTATED LRP1 WILD-TYPE
  N0           16             77
  N1            6             75
  N2            3             47
  N3            3             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D221V6, binary
                cls
clus               0   1
  LRP1 MUTATED    27   0
  LRP1 WILD-TYPE 230  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRP1 MUTATED     27    0
  LRP1 WILD-TYPE  230   18
   clus
vv  LRP1 MUTATED LRP1 WILD-TYPE
  0           27            230
  1            0             18
[1] 2 2
[1] FALSE
D221V7, binary
                cls
clus               0   1
  LRP1 MUTATED    17  13
  LRP1 WILD-TYPE  93 166
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRP1 MUTATED     17   13
  LRP1 WILD-TYPE   93  166
        clus
vv       LRP1 MUTATED LRP1 WILD-TYPE
  FEMALE           17             93
  MALE             13            166
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  LRP1 MUTATED                                       5
  LRP1 WILD-TYPE                                    45
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LRP1 MUTATED                                                       16
  LRP1 WILD-TYPE                                                    119
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LRP1 MUTATED                                                                   5
  LRP1 WILD-TYPE                                                                35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  LRP1 MUTATED                                                  2
  LRP1 WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  LRP1 MUTATED                                                          0
  LRP1 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  LRP1 MUTATED                                                           1
  LRP1 WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  LRP1 MUTATED                                          1
  LRP1 WILD-TYPE                                        2
D221V8, multiclass
                                                                   clus
vv                                                                  LRP1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  LRP1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       119
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D221V9, binary
                cls
clus               0   1
  LRP1 MUTATED     0  30
  LRP1 WILD-TYPE   5 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRP1 MUTATED      0   30
  LRP1 WILD-TYPE    5  254
     clus
vv    LRP1 MUTATED LRP1 WILD-TYPE
  NO             0              5
  YES           30            254
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LRP1 MUTATED    22   0   0   7
  LRP1 WILD-TYPE 205  10  10  17
D221V10, multiclass
    clus
vv   LRP1 MUTATED LRP1 WILD-TYPE
  R0           22            205
  R1            0             10
  R2            0             10
  RX            7             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D221V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LRP1 MUTATED       4                         0    23
  LRP1 WILD-TYPE    72                         4   145
D221V12, multiclass
                           clus
vv                          LRP1 MUTATED LRP1 WILD-TYPE
  ASIAN                                4             72
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               23            145
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(222) Variable = PHKB MUTATION ANALYSIS
D222V1, survival
                sevent
clus2              0   1
  PHKB MUTATED     5   1
  PHKB WILD-TYPE 176  79
  PHKB MUTATED PHKB WILD-TYPE 
             6            255 
  PHKB MUTATED PHKB WILD-TYPE 
             1             79 
$`PHKB MUTATED`
TCGA-BR-8361 TCGA-BR-8680 TCGA-BR-8682 TCGA-CD-A4MG TCGA-HU-A4GC TCGA-HU-A4GN 
       19.50        15.81        16.44         6.58         3.25        29.98 

$`PHKB WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD 
       24.30         5.59        12.30        11.84        24.20        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  PHKB MUTATED PHKB WILD-TYPE 
          3.25           0.00 
  PHKB MUTATED PHKB WILD-TYPE 
         29.98         105.07 
  PHKB MUTATED PHKB WILD-TYPE 
        16.125         12.590 
[1] "3.2 - 30.0 (16.1)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.1"
D222V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PHKB MUTATED         0        0        0        0         2         1
  PHKB WILD-TYPE       1        9       27       26        29        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PHKB MUTATED           0          0          1          1        1
  PHKB WILD-TYPE         3         49         35         23       23
D222V3, multiclass
            clus
vv           PHKB MUTATED PHKB WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              0             26
  STAGE IIA             2             29
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            1             35
  STAGE IIIC            1             23
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PHKB MUTATED     0   1   1   4
  PHKB WILD-TYPE  11  71 121  71
D222V4, multiclass
    clus
vv   PHKB MUTATED PHKB WILD-TYPE
  T1            0             11
  T2            1             71
  T3            1            121
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  PHKB MUTATED    2  2  3  0
  PHKB WILD-TYPE 91 79 47 53
D222V5, multiclass
    clus
vv   PHKB MUTATED PHKB WILD-TYPE
  N0            2             91
  N1            2             79
  N2            3             47
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D222V6, binary
                cls
clus               0   1
  PHKB MUTATED     6   1
  PHKB WILD-TYPE 251  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHKB MUTATED      6    1
  PHKB WILD-TYPE  251   17
   clus
vv  PHKB MUTATED PHKB WILD-TYPE
  0            6            251
  1            1             17
[1] 2 2
[1] FALSE
D222V7, binary
                cls
clus               0   1
  PHKB MUTATED     2   5
  PHKB WILD-TYPE 108 174
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHKB MUTATED      2    5
  PHKB WILD-TYPE  108  174
        clus
vv       PHKB MUTATED PHKB WILD-TYPE
  FEMALE            2            108
  MALE              5            174
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PHKB MUTATED                                       2
  PHKB WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PHKB MUTATED                                                        2
  PHKB WILD-TYPE                                                    133
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PHKB MUTATED                                                                   0
  PHKB WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PHKB MUTATED                                                  2
  PHKB WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PHKB MUTATED                                                          1
  PHKB WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PHKB MUTATED                                                           0
  PHKB WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PHKB MUTATED                                          0
  PHKB WILD-TYPE                                        3
D222V8, multiclass
                                                                   clus
vv                                                                  PHKB MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  PHKB WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D222V9, binary
                cls
clus               0   1
  PHKB MUTATED     0   7
  PHKB WILD-TYPE   5 277
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHKB MUTATED      0    7
  PHKB WILD-TYPE    5  277
     clus
vv    PHKB MUTATED PHKB WILD-TYPE
  NO             0              5
  YES            7            277
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PHKB MUTATED     5   0   0   1
  PHKB WILD-TYPE 222  10  10  23
D222V10, multiclass
    clus
vv   PHKB MUTATED PHKB WILD-TYPE
  R0            5            222
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D222V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHKB MUTATED       5                         0     2
  PHKB WILD-TYPE    71                         4   166
D222V12, multiclass
                           clus
vv                          PHKB MUTATED PHKB WILD-TYPE
  ASIAN                                5             71
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                2            166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(223) Variable = ABCB6 MUTATION ANALYSIS
D223V1, survival
                 sevent
clus2               0   1
  ABCB6 MUTATED     5   3
  ABCB6 WILD-TYPE 176  77
  ABCB6 MUTATED ABCB6 WILD-TYPE 
              8             253 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
              3              77 
$`ABCB6 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7958 TCGA-BR-8360 TCGA-CG-4306 TCGA-CG-5721 
       30.90        34.68        12.76         6.18         1.02         6.02 
TCGA-CG-5733 TCGA-F1-6874 
       21.07        14.47 

$`ABCB6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       18.35         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         3.45         9.07        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        2.66        16.31         2.20        15.58         7.40        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       28.96        79.07        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
       13.78        14.76         0.62         7.99        16.24        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  ABCB6 MUTATED ABCB6 WILD-TYPE 
           1.02            0.00 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
          34.68          105.07 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
         13.615          12.590 
[1] "1.0 - 34.7 (13.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1"  
D223V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCB6 MUTATED         0        0        1        0         2         0
  ABCB6 WILD-TYPE       1        9       26       26        29        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ABCB6 MUTATED           0          1          1          0        2
  ABCB6 WILD-TYPE         3         48         35         24       22
D223V3, multiclass
            clus
vv           ABCB6 MUTATED ABCB6 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCB6 MUTATED     0   3   3   2
  ABCB6 WILD-TYPE  11  69 119  73
D223V4, multiclass
    clus
vv   ABCB6 MUTATED ABCB6 WILD-TYPE
  T1             0              11
  T2             3              69
  T3             3             119
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ABCB6 MUTATED    4  1  2  0
  ABCB6 WILD-TYPE 89 80 48 53
D223V5, multiclass
    clus
vv   ABCB6 MUTATED ABCB6 WILD-TYPE
  N0             4              89
  N1             1              80
  N2             2              48
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D223V6, binary
                 cls
clus                0   1
  ABCB6 MUTATED     7   1
  ABCB6 WILD-TYPE 250  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB6 MUTATED      7    1
  ABCB6 WILD-TYPE  250   17
   clus
vv  ABCB6 MUTATED ABCB6 WILD-TYPE
  0             7             250
  1             1              17
[1] 2 2
[1] FALSE
D223V7, binary
                 cls
clus                0   1
  ABCB6 MUTATED     3   5
  ABCB6 WILD-TYPE 107 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB6 MUTATED      3    5
  ABCB6 WILD-TYPE  107  174
        clus
vv       ABCB6 MUTATED ABCB6 WILD-TYPE
  FEMALE             3             107
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ABCB6 MUTATED                                       0
  ABCB6 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ABCB6 MUTATED                                                        4
  ABCB6 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ABCB6 MUTATED                                                                   4
  ABCB6 WILD-TYPE                                                                36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ABCB6 MUTATED                                                  0
  ABCB6 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ABCB6 MUTATED                                                          0
  ABCB6 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ABCB6 MUTATED                                                           0
  ABCB6 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ABCB6 MUTATED                                          0
  ABCB6 WILD-TYPE                                        3
D223V8, multiclass
                                                                   clus
vv                                                                  ABCB6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ABCB6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D223V9, binary
                 cls
clus                0   1
  ABCB6 MUTATED     0   8
  ABCB6 WILD-TYPE   5 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB6 MUTATED      0    8
  ABCB6 WILD-TYPE    5  276
     clus
vv    ABCB6 MUTATED ABCB6 WILD-TYPE
  NO              0               5
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ABCB6 MUTATED     6   0   1   1
  ABCB6 WILD-TYPE 221  10   9  23
D223V10, multiclass
    clus
vv   ABCB6 MUTATED ABCB6 WILD-TYPE
  R0             6             221
  R1             0              10
  R2             1               9
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D223V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ABCB6 MUTATED       0                         0     5
  ABCB6 WILD-TYPE    76                         4   163
D223V12, multiclass
                           clus
vv                          ABCB6 MUTATED ABCB6 WILD-TYPE
  ASIAN                                 0              76
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(224) Variable = DNAJC18 MUTATION ANALYSIS
D224V1, survival
                   sevent
clus2                 0   1
  DNAJC18 MUTATED     8   3
  DNAJC18 WILD-TYPE 173  77
  DNAJC18 MUTATED DNAJC18 WILD-TYPE 
               11               250 
  DNAJC18 MUTATED DNAJC18 WILD-TYPE 
                3                77 
$`DNAJC18 MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8382 TCGA-CD-8536 TCGA-CG-4306 TCGA-D7-A4YV 
       34.68        12.26        15.85         0.10         1.02         5.92 
TCGA-HU-8608 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4H3 TCGA-HU-A4H8 
       10.62        11.84         0.10        19.36         8.88 

$`DNAJC18 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       11.41        12.10         0.76        24.30         5.59        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
       12.95        23.84        12.30         9.67        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  DNAJC18 MUTATED DNAJC18 WILD-TYPE 
              0.1               0.0 
  DNAJC18 MUTATED DNAJC18 WILD-TYPE 
            34.68            105.07 
  DNAJC18 MUTATED DNAJC18 WILD-TYPE 
           10.620            12.775 
[1] "0.1 - 34.7 (10.6)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.1"
D224V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DNAJC18 MUTATED         0        0        1        1         1         3
  DNAJC18 WILD-TYPE       1        9       26       25        30        41
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJC18 MUTATED           0          0          1          3        1
  DNAJC18 WILD-TYPE         3         49         35         21       23
D224V3, multiclass
            clus
vv           DNAJC18 MUTATED DNAJC18 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 1                25
  STAGE IIA                1                30
  STAGE IIB                3                41
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               1                35
  STAGE IIIC               3                21
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  DNAJC18 MUTATED     1   0   5   5
  DNAJC18 WILD-TYPE  10  72 117  70
D224V4, multiclass
    clus
vv   DNAJC18 MUTATED DNAJC18 WILD-TYPE
  T1               1                10
  T2               0                72
  T3               5               117
  T4               5                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  DNAJC18 MUTATED    3  4  3  2
  DNAJC18 WILD-TYPE 90 77 47 51
D224V5, multiclass
    clus
vv   DNAJC18 MUTATED DNAJC18 WILD-TYPE
  N0               3                90
  N1               4                77
  N2               3                47
  N3               2                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D224V6, binary
                   cls
clus                  0   1
  DNAJC18 MUTATED    12   1
  DNAJC18 WILD-TYPE 245  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC18 MUTATED     12    1
  DNAJC18 WILD-TYPE  245   17
   clus
vv  DNAJC18 MUTATED DNAJC18 WILD-TYPE
  0              12               245
  1               1                17
[1] 2 2
[1] FALSE
D224V7, binary
                   cls
clus                  0   1
  DNAJC18 MUTATED     7   6
  DNAJC18 WILD-TYPE 103 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC18 MUTATED      7    6
  DNAJC18 WILD-TYPE  103  173
        clus
vv       DNAJC18 MUTATED DNAJC18 WILD-TYPE
  FEMALE               7               103
  MALE                 6               173
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DNAJC18 MUTATED                                       3
  DNAJC18 WILD-TYPE                                    47
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DNAJC18 MUTATED                                                        7
  DNAJC18 WILD-TYPE                                                    128
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DNAJC18 MUTATED                                                                   0
  DNAJC18 WILD-TYPE                                                                40
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DNAJC18 MUTATED                                                  3
  DNAJC18 WILD-TYPE                                               35
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DNAJC18 MUTATED                                                          0
  DNAJC18 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DNAJC18 MUTATED                                                           0
  DNAJC18 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DNAJC18 MUTATED                                          0
  DNAJC18 WILD-TYPE                                        3
D224V8, multiclass
                                                                   clus
vv                                                                  DNAJC18 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  DNAJC18 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D224V9, binary
                   cls
clus                  0   1
  DNAJC18 MUTATED     0  13
  DNAJC18 WILD-TYPE   5 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC18 MUTATED      0   13
  DNAJC18 WILD-TYPE    5  271
     clus
vv    DNAJC18 MUTATED DNAJC18 WILD-TYPE
  NO                0                 5
  YES              13               271
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  DNAJC18 MUTATED     9   0   1   2
  DNAJC18 WILD-TYPE 218  10   9  22
D224V10, multiclass
    clus
vv   DNAJC18 MUTATED DNAJC18 WILD-TYPE
  R0               9               218
  R1               0                10
  R2               1                 9
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D224V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DNAJC18 MUTATED       6                         0     6
  DNAJC18 WILD-TYPE    70                         4   162
D224V12, multiclass
                           clus
vv                          DNAJC18 MUTATED DNAJC18 WILD-TYPE
  ASIAN                                   6                70
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   6               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(225) Variable = IDH2 MUTATION ANALYSIS
D225V1, survival
                sevent
clus2              0   1
  IDH2 MUTATED     4   0
  IDH2 WILD-TYPE 177  80
  IDH2 MUTATED IDH2 WILD-TYPE 
             4            257 
  IDH2 MUTATED IDH2 WILD-TYPE 
             0             80 
$`IDH2 MUTATED`
TCGA-BR-A4IY TCGA-CG-5723 TCGA-HU-A4G9 TCGA-HU-A4GT 
       12.89       105.07        24.20         6.51 

$`IDH2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        1.48        13.41        13.51         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         6.02         0.99        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  IDH2 MUTATED IDH2 WILD-TYPE 
          6.51           0.00 
  IDH2 MUTATED IDH2 WILD-TYPE 
        105.07          79.07 
  IDH2 MUTATED IDH2 WILD-TYPE 
        18.545         12.590 
[1] "6.5 - 105.1 (18.5)" "0.0 - 79.1 (12.6)" 
[1] "hr="     "2.9e+07"
D225V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IDH2 MUTATED         0        1        0        1         1         1
  IDH2 WILD-TYPE       1        8       27       25        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IDH2 MUTATED           0          0          0          0        0
  IDH2 WILD-TYPE         3         49         36         24       24
D225V3, multiclass
            clus
vv           IDH2 MUTATED IDH2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              0             27
  STAGE II              1             25
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IDH2 MUTATED     1   1   1   1
  IDH2 WILD-TYPE  10  71 121  74
D225V4, multiclass
    clus
vv   IDH2 MUTATED IDH2 WILD-TYPE
  T1            1             10
  T2            1             71
  T3            1            121
  T4            1             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  IDH2 MUTATED    3  1  0  0
  IDH2 WILD-TYPE 90 80 50 53
D225V5, multiclass
    clus
vv   IDH2 MUTATED IDH2 WILD-TYPE
  N0            3             90
  N1            1             80
  N2            0             50
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D225V6, binary
                cls
clus               0   1
  IDH2 MUTATED     4   0
  IDH2 WILD-TYPE 253  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED      4    0
  IDH2 WILD-TYPE  253   18
   clus
vv  IDH2 MUTATED IDH2 WILD-TYPE
  0            4            253
  1            0             18
[1] 2 2
[1] FALSE
D225V7, binary
                cls
clus               0   1
  IDH2 MUTATED     2   2
  IDH2 WILD-TYPE 108 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED      2    2
  IDH2 WILD-TYPE  108  177
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  FEMALE            2            108
  MALE              2            177
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  IDH2 MUTATED                                       0
  IDH2 WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IDH2 MUTATED                                                        2
  IDH2 WILD-TYPE                                                    133
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IDH2 MUTATED                                                                   0
  IDH2 WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  IDH2 MUTATED                                                  2
  IDH2 WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  IDH2 MUTATED                                                          0
  IDH2 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  IDH2 MUTATED                                                           0
  IDH2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  IDH2 MUTATED                                          0
  IDH2 WILD-TYPE                                        3
D225V8, multiclass
                                                                   clus
vv                                                                  IDH2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  IDH2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D225V9, binary
                cls
clus               0   1
  IDH2 MUTATED     0   4
  IDH2 WILD-TYPE   5 280
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED      0    4
  IDH2 WILD-TYPE    5  280
     clus
vv    IDH2 MUTATED IDH2 WILD-TYPE
  NO             0              5
  YES            4            280
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IDH2 MUTATED     4   0   0   0
  IDH2 WILD-TYPE 223  10  10  24
D225V10, multiclass
    clus
vv   IDH2 MUTATED IDH2 WILD-TYPE
  R0            4            223
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D225V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IDH2 MUTATED       3                         0     0
  IDH2 WILD-TYPE    73                         4   168
D225V12, multiclass
                           clus
vv                          IDH2 MUTATED IDH2 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                0            168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(226) Variable = DLGAP3 MUTATION ANALYSIS
D226V1, survival
                  sevent
clus2                0   1
  DLGAP3 MUTATED    14   1
  DLGAP3 WILD-TYPE 167  79
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
              15              246 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
               1               79 
$`DLGAP3 MUTATED`
TCGA-BR-4201 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8680 TCGA-BR-A4J7 TCGA-CG-5721 
       30.90        12.26        19.50        15.81        19.36         6.02 
TCGA-CG-5728 TCGA-D7-6822 TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H4 
       65.10        12.33        29.98         6.51         6.25        23.84 
TCGA-HU-A4H8 TCGA-IN-8462 TCGA-IP-7968 
        8.88        18.81         2.53 

$`DLGAP3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J8 
        8.98         0.72        14.17         0.53         0.66        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       15.22        15.98        12.79        10.55        11.31        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       24.20         3.25        22.75        25.81        11.77         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 
       12.30         9.67        27.42        21.21         3.45         3.39 

  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
            2.53             0.00 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
           65.10           105.07 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
          15.810           12.605 
[1] "2.5 - 65.1 (15.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "6.3"
D226V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DLGAP3 MUTATED         0        0        3        1         2         5
  DLGAP3 WILD-TYPE       1        9       24       25        29        39
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DLGAP3 MUTATED           0          0          1          1        2
  DLGAP3 WILD-TYPE         3         49         35         23       22
D226V3, multiclass
            clus
vv           DLGAP3 MUTATED DLGAP3 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                3               24
  STAGE II                1               25
  STAGE IIA               2               29
  STAGE IIB               5               39
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              1               35
  STAGE IIIC              1               23
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DLGAP3 MUTATED     1   7   3   5
  DLGAP3 WILD-TYPE  10  65 119  70
D226V4, multiclass
    clus
vv   DLGAP3 MUTATED DLGAP3 WILD-TYPE
  T1              1               10
  T2              7               65
  T3              3              119
  T4              5               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  DLGAP3 MUTATED    4  6  4  0
  DLGAP3 WILD-TYPE 89 75 46 53
D226V5, multiclass
    clus
vv   DLGAP3 MUTATED DLGAP3 WILD-TYPE
  N0              4               89
  N1              6               75
  N2              4               46
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D226V6, binary
                  cls
clus                 0   1
  DLGAP3 MUTATED    14   1
  DLGAP3 WILD-TYPE 243  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP3 MUTATED     14    1
  DLGAP3 WILD-TYPE  243   17
   clus
vv  DLGAP3 MUTATED DLGAP3 WILD-TYPE
  0             14              243
  1              1               17
[1] 2 2
[1] FALSE
D226V7, binary
                  cls
clus                 0   1
  DLGAP3 MUTATED     6  10
  DLGAP3 WILD-TYPE 104 169
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP3 MUTATED      6   10
  DLGAP3 WILD-TYPE  104  169
        clus
vv       DLGAP3 MUTATED DLGAP3 WILD-TYPE
  FEMALE              6              104
  MALE               10              169
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DLGAP3 MUTATED                                       1
  DLGAP3 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DLGAP3 MUTATED                                                        5
  DLGAP3 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DLGAP3 MUTATED                                                                   2
  DLGAP3 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DLGAP3 MUTATED                                                  6
  DLGAP3 WILD-TYPE                                               32
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DLGAP3 MUTATED                                                          2
  DLGAP3 WILD-TYPE                                                       14
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DLGAP3 MUTATED                                                           0
  DLGAP3 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DLGAP3 MUTATED                                          0
  DLGAP3 WILD-TYPE                                        3
D226V8, multiclass
                                                                   clus
vv                                                                  DLGAP3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  DLGAP3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D226V9, binary
                  cls
clus                 0   1
  DLGAP3 MUTATED     1  15
  DLGAP3 WILD-TYPE   4 269
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP3 MUTATED      1   15
  DLGAP3 WILD-TYPE    4  269
     clus
vv    DLGAP3 MUTATED DLGAP3 WILD-TYPE
  NO               1                4
  YES             15              269
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DLGAP3 MUTATED    15   0   0   1
  DLGAP3 WILD-TYPE 212  10  10  23
D226V10, multiclass
    clus
vv   DLGAP3 MUTATED DLGAP3 WILD-TYPE
  R0             15              212
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D226V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DLGAP3 MUTATED       7                         0     6
  DLGAP3 WILD-TYPE    69                         4   162
D226V12, multiclass
                           clus
vv                          DLGAP3 MUTATED DLGAP3 WILD-TYPE
  ASIAN                                  7               69
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(227) Variable = KIAA0240 MUTATION ANALYSIS
D227V1, survival
                    sevent
clus2                  0   1
  KIAA0240 MUTATED     8   1
  KIAA0240 WILD-TYPE 173  79
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                 9                252 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                 1                 79 
$`KIAA0240 MUTATED`
TCGA-BR-7851 TCGA-BR-8382 TCGA-BR-8487 TCGA-CD-8529 TCGA-CG-5721 TCGA-CG-5723 
       12.43        15.85         1.12         0.13         6.02       105.07 
TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GQ 
       24.20        11.77         0.10 

$`KIAA0240 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       19.17        14.79         0.26         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.07         0.10         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
        6.97        36.00         1.02         0.99         0.99        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN 
       12.30        11.84         3.25        22.75        25.81        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
               0.1                0.0 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
            105.07              79.07 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
             11.77              12.71 
[1] "0.1 - 105.1 (11.8)" "0.0 - 79.1 (12.7)" 
[1] "hr=" "3.4"
D227V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0240 MUTATED         0        2        0        1         1         1
  KIAA0240 WILD-TYPE       1        7       27       25        30        43
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0240 MUTATED           0          1          0          2        2
  KIAA0240 WILD-TYPE         3         48         36         22       22
D227V3, multiclass
            clus
vv           KIAA0240 MUTATED KIAA0240 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  2                  7
  STAGE IB                  0                 27
  STAGE II                  1                 25
  STAGE IIA                 1                 30
  STAGE IIB                 1                 43
  STAGE III                 0                  3
  STAGE IIIA                1                 48
  STAGE IIIB                0                 36
  STAGE IIIC                2                 22
  STAGE IV                  2                 22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0240 MUTATED     3   1   1   6
  KIAA0240 WILD-TYPE   8  71 121  69
D227V4, multiclass
    clus
vv   KIAA0240 MUTATED KIAA0240 WILD-TYPE
  T1                3                  8
  T2                1                 71
  T3                1                121
  T4                6                 69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  KIAA0240 MUTATED    6  3  1  1
  KIAA0240 WILD-TYPE 87 78 49 52
D227V5, multiclass
    clus
vv   KIAA0240 MUTATED KIAA0240 WILD-TYPE
  N0                6                 87
  N1                3                 78
  N2                1                 49
  N3                1                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D227V6, binary
                    cls
clus                   0   1
  KIAA0240 MUTATED    11   1
  KIAA0240 WILD-TYPE 246  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0240 MUTATED     11    1
  KIAA0240 WILD-TYPE  246   17
   clus
vv  KIAA0240 MUTATED KIAA0240 WILD-TYPE
  0               11                246
  1                1                 17
[1] 2 2
[1] FALSE
D227V7, binary
                    cls
clus                   0   1
  KIAA0240 MUTATED     6   6
  KIAA0240 WILD-TYPE 104 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0240 MUTATED      6    6
  KIAA0240 WILD-TYPE  104  173
        clus
vv       KIAA0240 MUTATED KIAA0240 WILD-TYPE
  FEMALE                6                104
  MALE                  6                173
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KIAA0240 MUTATED                                       0
  KIAA0240 WILD-TYPE                                    50
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA0240 MUTATED                                                        6
  KIAA0240 WILD-TYPE                                                    129
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA0240 MUTATED                                                                   2
  KIAA0240 WILD-TYPE                                                                38
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KIAA0240 MUTATED                                                  3
  KIAA0240 WILD-TYPE                                               35
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KIAA0240 MUTATED                                                          1
  KIAA0240 WILD-TYPE                                                       15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KIAA0240 MUTATED                                                           0
  KIAA0240 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KIAA0240 MUTATED                                          0
  KIAA0240 WILD-TYPE                                        3
D227V8, multiclass
                                                                   clus
vv                                                                  KIAA0240 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  KIAA0240 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D227V9, binary
                    cls
clus                   0   1
  KIAA0240 MUTATED     0  12
  KIAA0240 WILD-TYPE   5 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0240 MUTATED      0   12
  KIAA0240 WILD-TYPE    5  272
     clus
vv    KIAA0240 MUTATED KIAA0240 WILD-TYPE
  NO                 0                  5
  YES               12                272
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0240 MUTATED     9   0   0   3
  KIAA0240 WILD-TYPE 218  10  10  21
D227V10, multiclass
    clus
vv   KIAA0240 MUTATED KIAA0240 WILD-TYPE
  R0                9                218
  R1                0                 10
  R2                0                 10
  RX                3                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D227V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA0240 MUTATED       4                         0     6
  KIAA0240 WILD-TYPE    72                         4   162
D227V12, multiclass
                           clus
vv                          KIAA0240 MUTATED KIAA0240 WILD-TYPE
  ASIAN                                    4                 72
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    6                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(228) Variable = ATXN2L MUTATION ANALYSIS
D228V1, survival
                  sevent
clus2                0   1
  ATXN2L MUTATED    12   3
  ATXN2L WILD-TYPE 169  77
  ATXN2L MUTATED ATXN2L WILD-TYPE 
              15              246 
  ATXN2L MUTATED ATXN2L WILD-TYPE 
               3               77 
$`ATXN2L MUTATED`
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8286 TCGA-BR-8372 
       34.68        32.78        14.43        12.26        12.95        19.17 
TCGA-BR-8487 TCGA-CD-5813 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4465 
        1.12         0.39         0.10        12.62        20.02         9.01 
TCGA-HU-8602 TCGA-HU-A4GN TCGA-HU-A4GT 
       11.41        29.98         6.51 

$`ATXN2L WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8289 TCGA-BR-8291 
        0.69         9.60        20.55         8.05         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4304 
       12.43        11.61         6.58        12.20         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  ATXN2L MUTATED ATXN2L WILD-TYPE 
             0.1              0.0 
  ATXN2L MUTATED ATXN2L WILD-TYPE 
           34.68           105.07 
  ATXN2L MUTATED ATXN2L WILD-TYPE 
          12.620           12.625 
[1] "0.1 - 34.7 (12.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.7"
D228V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATXN2L MUTATED         0        0        1        2         5         2
  ATXN2L WILD-TYPE       1        9       26       24        26        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATXN2L MUTATED           1          0          2          1        1
  ATXN2L WILD-TYPE         2         49         34         23       23
D228V3, multiclass
            clus
vv           ATXN2L MUTATED ATXN2L WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                2               24
  STAGE IIA               5               26
  STAGE IIB               2               42
  STAGE III               1                2
  STAGE IIIA              0               49
  STAGE IIIB              2               34
  STAGE IIIC              1               23
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATXN2L MUTATED     1   2   8   5
  ATXN2L WILD-TYPE  10  70 114  70
D228V4, multiclass
    clus
vv   ATXN2L MUTATED ATXN2L WILD-TYPE
  T1              1               10
  T2              2               70
  T3              8              114
  T4              5               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ATXN2L MUTATED    9  4  1  2
  ATXN2L WILD-TYPE 84 77 49 51
D228V5, multiclass
    clus
vv   ATXN2L MUTATED ATXN2L WILD-TYPE
  N0              9               84
  N1              4               77
  N2              1               49
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D228V6, binary
                  cls
clus                 0   1
  ATXN2L MUTATED    16   1
  ATXN2L WILD-TYPE 241  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN2L MUTATED     16    1
  ATXN2L WILD-TYPE  241   17
   clus
vv  ATXN2L MUTATED ATXN2L WILD-TYPE
  0             16              241
  1              1               17
[1] 2 2
[1] FALSE
D228V7, binary
                  cls
clus                 0   1
  ATXN2L MUTATED     9   8
  ATXN2L WILD-TYPE 101 171
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN2L MUTATED      9    8
  ATXN2L WILD-TYPE  101  171
        clus
vv       ATXN2L MUTATED ATXN2L WILD-TYPE
  FEMALE              9              101
  MALE                8              171
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ATXN2L MUTATED                                       2
  ATXN2L WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ATXN2L MUTATED                                                       11
  ATXN2L WILD-TYPE                                                    124
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ATXN2L MUTATED                                                                   1
  ATXN2L WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ATXN2L MUTATED                                                  2
  ATXN2L WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ATXN2L MUTATED                                                          1
  ATXN2L WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ATXN2L MUTATED                                                           0
  ATXN2L WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ATXN2L MUTATED                                          0
  ATXN2L WILD-TYPE                                        3
D228V8, multiclass
                                                                   clus
vv                                                                  ATXN2L MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ATXN2L WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D228V9, binary
                  cls
clus                 0   1
  ATXN2L MUTATED     0  17
  ATXN2L WILD-TYPE   5 267
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN2L MUTATED      0   17
  ATXN2L WILD-TYPE    5  267
     clus
vv    ATXN2L MUTATED ATXN2L WILD-TYPE
  NO               0                5
  YES             17              267
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ATXN2L MUTATED    11   0   1   2
  ATXN2L WILD-TYPE 216  10   9  22
D228V10, multiclass
    clus
vv   ATXN2L MUTATED ATXN2L WILD-TYPE
  R0             11              216
  R1              0               10
  R2              1                9
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D228V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATXN2L MUTATED       6                         0     9
  ATXN2L WILD-TYPE    70                         4   159
D228V12, multiclass
                           clus
vv                          ATXN2L MUTATED ATXN2L WILD-TYPE
  ASIAN                                  6               70
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  9              159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(229) Variable = ZNF608 MUTATION ANALYSIS
D229V1, survival
                  sevent
clus2                0   1
  ZNF608 MUTATED     8   4
  ZNF608 WILD-TYPE 173  76
  ZNF608 MUTATED ZNF608 WILD-TYPE 
              12              249 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               4               76 
$`ZNF608 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8372 TCGA-BR-8680 
        6.97        30.90        34.68        32.94        19.17        15.81 
TCGA-BR-A4QL TCGA-CG-4305 TCGA-CG-5733 TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HU-8602 
       11.57        15.95        21.07         5.92        11.08        11.41 

$`ZNF608 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       31.20        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       14.27        16.44        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  ZNF608 MUTATED ZNF608 WILD-TYPE 
            5.92             0.00 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
           34.68           105.07 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
           15.88            12.59 
[1] "5.9 - 34.7 (15.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D229V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF608 MUTATED         0        0        0        1         3         2
  ZNF608 WILD-TYPE       1        9       27       25        28        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF608 MUTATED           0          2          1          1        1
  ZNF608 WILD-TYPE         3         47         35         23       23
D229V3, multiclass
            clus
vv           ZNF608 MUTATED ZNF608 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                1               25
  STAGE IIA               3               28
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              1               35
  STAGE IIIC              1               23
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF608 MUTATED     1   3   6   3
  ZNF608 WILD-TYPE  10  69 116  72
D229V4, multiclass
    clus
vv   ZNF608 MUTATED ZNF608 WILD-TYPE
  T1              1               10
  T2              3               69
  T3              6              116
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZNF608 MUTATED    4  4  2  2
  ZNF608 WILD-TYPE 89 77 48 51
D229V5, multiclass
    clus
vv   ZNF608 MUTATED ZNF608 WILD-TYPE
  N0              4               89
  N1              4               77
  N2              2               48
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D229V6, binary
                  cls
clus                 0   1
  ZNF608 MUTATED    13   1
  ZNF608 WILD-TYPE 244  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED     13    1
  ZNF608 WILD-TYPE  244   17
   clus
vv  ZNF608 MUTATED ZNF608 WILD-TYPE
  0             13              244
  1              1               17
[1] 2 2
[1] FALSE
D229V7, binary
                  cls
clus                 0   1
  ZNF608 MUTATED     9   6
  ZNF608 WILD-TYPE 101 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED      9    6
  ZNF608 WILD-TYPE  101  173
        clus
vv       ZNF608 MUTATED ZNF608 WILD-TYPE
  FEMALE              9              101
  MALE                6              173
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZNF608 MUTATED                                       1
  ZNF608 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF608 MUTATED                                                       11
  ZNF608 WILD-TYPE                                                    124
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF608 MUTATED                                                                   1
  ZNF608 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZNF608 MUTATED                                                  2
  ZNF608 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZNF608 MUTATED                                                          0
  ZNF608 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZNF608 MUTATED                                                           0
  ZNF608 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZNF608 MUTATED                                          0
  ZNF608 WILD-TYPE                                        3
D229V8, multiclass
                                                                   clus
vv                                                                  ZNF608 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ZNF608 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D229V9, binary
                  cls
clus                 0   1
  ZNF608 MUTATED     0  15
  ZNF608 WILD-TYPE   5 269
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED      0   15
  ZNF608 WILD-TYPE    5  269
     clus
vv    ZNF608 MUTATED ZNF608 WILD-TYPE
  NO               0                5
  YES             15              269
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF608 MUTATED    10   0   0   5
  ZNF608 WILD-TYPE 217  10  10  19
D229V10, multiclass
    clus
vv   ZNF608 MUTATED ZNF608 WILD-TYPE
  R0             10              217
  R1              0               10
  R2              0               10
  RX              5               19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D229V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF608 MUTATED       2                         1    10
  ZNF608 WILD-TYPE    74                         3   158
D229V12, multiclass
                           clus
vv                          ZNF608 MUTATED ZNF608 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                 10              158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(230) Variable = KIAA0406 MUTATION ANALYSIS
D230V1, survival
                    sevent
clus2                  0   1
  KIAA0406 MUTATED     8   2
  KIAA0406 WILD-TYPE 173  78
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                10                251 
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                 2                 78 
$`KIAA0406 MUTATED`
TCGA-BR-6452 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4CS TCGA-BR-A4QL 
       34.68        15.81        13.45        15.81         1.48        11.57 
TCGA-CD-A4MG TCGA-CG-4475 TCGA-HU-A4GN TCGA-HU-A4GX 
        6.58        22.98        29.98        10.19 

$`KIAA0406 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 
       25.18         9.21        20.22         1.12        12.79         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08        22.26        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       24.20         3.25        22.75        25.81        11.77         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
              1.48               0.00 
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
             34.68             105.07 
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
             14.63              12.59 
[1] "1.5 - 34.7 (14.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.9"
D230V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0406 MUTATED         0        0        1        0         3         1
  KIAA0406 WILD-TYPE       1        9       26       26        28        43
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0406 MUTATED           0          0          2          3        1
  KIAA0406 WILD-TYPE         3         49         34         21       23
D230V3, multiclass
            clus
vv           KIAA0406 MUTATED KIAA0406 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  1                 26
  STAGE II                  0                 26
  STAGE IIA                 3                 28
  STAGE IIB                 1                 43
  STAGE III                 0                  3
  STAGE IIIA                0                 49
  STAGE IIIB                2                 34
  STAGE IIIC                3                 21
  STAGE IV                  1                 23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0406 MUTATED     0   2   4   5
  KIAA0406 WILD-TYPE  11  70 118  70
D230V4, multiclass
    clus
vv   KIAA0406 MUTATED KIAA0406 WILD-TYPE
  T1                0                 11
  T2                2                 70
  T3                4                118
  T4                5                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  KIAA0406 MUTATED    3  4  2  3
  KIAA0406 WILD-TYPE 90 77 48 50
D230V5, multiclass
    clus
vv   KIAA0406 MUTATED KIAA0406 WILD-TYPE
  N0                3                 90
  N1                4                 77
  N2                2                 48
  N3                3                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D230V6, binary
                    cls
clus                   0   1
  KIAA0406 MUTATED    11   1
  KIAA0406 WILD-TYPE 246  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0406 MUTATED     11    1
  KIAA0406 WILD-TYPE  246   17
   clus
vv  KIAA0406 MUTATED KIAA0406 WILD-TYPE
  0               11                246
  1                1                 17
[1] 2 2
[1] FALSE
D230V7, binary
                    cls
clus                   0   1
  KIAA0406 MUTATED     3   9
  KIAA0406 WILD-TYPE 107 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0406 MUTATED      3    9
  KIAA0406 WILD-TYPE  107  170
        clus
vv       KIAA0406 MUTATED KIAA0406 WILD-TYPE
  FEMALE                3                107
  MALE                  9                170
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KIAA0406 MUTATED                                       2
  KIAA0406 WILD-TYPE                                    48
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA0406 MUTATED                                                        6
  KIAA0406 WILD-TYPE                                                    129
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA0406 MUTATED                                                                   1
  KIAA0406 WILD-TYPE                                                                39
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KIAA0406 MUTATED                                                  2
  KIAA0406 WILD-TYPE                                               36
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KIAA0406 MUTATED                                                          0
  KIAA0406 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KIAA0406 MUTATED                                                           0
  KIAA0406 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KIAA0406 MUTATED                                          0
  KIAA0406 WILD-TYPE                                        3
D230V8, multiclass
                                                                   clus
vv                                                                  KIAA0406 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  KIAA0406 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D230V9, binary
                    cls
clus                   0   1
  KIAA0406 MUTATED     0  12
  KIAA0406 WILD-TYPE   5 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0406 MUTATED      0   12
  KIAA0406 WILD-TYPE    5  272
     clus
vv    KIAA0406 MUTATED KIAA0406 WILD-TYPE
  NO                 0                  5
  YES               12                272
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0406 MUTATED    10   0   0   1
  KIAA0406 WILD-TYPE 217  10  10  23
D230V10, multiclass
    clus
vv   KIAA0406 MUTATED KIAA0406 WILD-TYPE
  R0               10                217
  R1                0                 10
  R2                0                 10
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D230V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA0406 MUTATED       4                         0     6
  KIAA0406 WILD-TYPE    72                         4   162
D230V12, multiclass
                           clus
vv                          KIAA0406 MUTATED KIAA0406 WILD-TYPE
  ASIAN                                    4                 72
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    6                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(231) Variable = KIAA1967 MUTATION ANALYSIS
D231V1, survival
                    sevent
clus2                  0   1
  KIAA1967 MUTATED    12   3
  KIAA1967 WILD-TYPE 169  77
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
                15                246 
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
                 3                 77 
$`KIAA1967 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8081 
        6.97        30.90        34.68        32.94        23.93        20.55 
TCGA-BR-8372 TCGA-CD-A4MI TCGA-CG-4305 TCGA-CG-5733 TCGA-F1-A448 TCGA-HU-8602 
       19.17         0.10        15.95        21.07        21.27        11.41 
TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-HU-A4H3 
       11.84         6.51        19.36 

$`KIAA1967 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 
       31.20        12.82         9.21        24.76        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        9.60         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        7.99        16.24        14.47        72.23         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
               0.1                0.0 
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
             34.68             105.07 
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
            19.360             12.495 
[1] "0.1 - 34.7 (19.4)"  "0.0 - 105.1 (12.5)"
[1] "hr=" "2.3"
D231V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1967 MUTATED         0        0        1        1         3         3
  KIAA1967 WILD-TYPE       1        9       26       25        28        41
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1967 MUTATED           0          2          2          2        0
  KIAA1967 WILD-TYPE         3         47         34         22       24
D231V3, multiclass
            clus
vv           KIAA1967 MUTATED KIAA1967 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  1                 26
  STAGE II                  1                 25
  STAGE IIA                 3                 28
  STAGE IIB                 3                 41
  STAGE III                 0                  3
  STAGE IIIA                2                 47
  STAGE IIIB                2                 34
  STAGE IIIC                2                 22
  STAGE IV                  0                 24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1967 MUTATED     0   4   7   4
  KIAA1967 WILD-TYPE  11  68 115  71
D231V4, multiclass
    clus
vv   KIAA1967 MUTATED KIAA1967 WILD-TYPE
  T1                0                 11
  T2                4                 68
  T3                7                115
  T4                4                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  KIAA1967 MUTATED    6  5  1  3
  KIAA1967 WILD-TYPE 87 76 49 50
D231V5, multiclass
    clus
vv   KIAA1967 MUTATED KIAA1967 WILD-TYPE
  N0                6                 87
  N1                5                 76
  N2                1                 49
  N3                3                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D231V6, binary
                    cls
clus                   0   1
  KIAA1967 MUTATED    16   0
  KIAA1967 WILD-TYPE 241  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1967 MUTATED     16    0
  KIAA1967 WILD-TYPE  241   18
   clus
vv  KIAA1967 MUTATED KIAA1967 WILD-TYPE
  0               16                241
  1                0                 18
[1] 2 2
[1] FALSE
D231V7, binary
                    cls
clus                   0   1
  KIAA1967 MUTATED    12   5
  KIAA1967 WILD-TYPE  98 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1967 MUTATED     12    5
  KIAA1967 WILD-TYPE   98  174
        clus
vv       KIAA1967 MUTATED KIAA1967 WILD-TYPE
  FEMALE               12                 98
  MALE                  5                174
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KIAA1967 MUTATED                                       3
  KIAA1967 WILD-TYPE                                    47
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA1967 MUTATED                                                       11
  KIAA1967 WILD-TYPE                                                    124
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA1967 MUTATED                                                                   1
  KIAA1967 WILD-TYPE                                                                39
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KIAA1967 MUTATED                                                  1
  KIAA1967 WILD-TYPE                                               37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KIAA1967 MUTATED                                                          1
  KIAA1967 WILD-TYPE                                                       15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KIAA1967 MUTATED                                                           0
  KIAA1967 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KIAA1967 MUTATED                                          0
  KIAA1967 WILD-TYPE                                        3
D231V8, multiclass
                                                                   clus
vv                                                                  KIAA1967 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  KIAA1967 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D231V9, binary
                    cls
clus                   0   1
  KIAA1967 MUTATED     0  17
  KIAA1967 WILD-TYPE   5 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1967 MUTATED      0   17
  KIAA1967 WILD-TYPE    5  267
     clus
vv    KIAA1967 MUTATED KIAA1967 WILD-TYPE
  NO                 0                  5
  YES               17                267
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA1967 MUTATED    11   0   0   4
  KIAA1967 WILD-TYPE 216  10  10  20
D231V10, multiclass
    clus
vv   KIAA1967 MUTATED KIAA1967 WILD-TYPE
  R0               11                216
  R1                0                 10
  R2                0                 10
  RX                4                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D231V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA1967 MUTATED       5                         0    10
  KIAA1967 WILD-TYPE    71                         4   158
D231V12, multiclass
                           clus
vv                          KIAA1967 MUTATED KIAA1967 WILD-TYPE
  ASIAN                                    5                 71
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                   10                158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(232) Variable = CBLL1 MUTATION ANALYSIS
D232V1, survival
                 sevent
clus2               0   1
  CBLL1 MUTATED     3   1
  CBLL1 WILD-TYPE 178  79
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              4             257 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              1              79 
$`CBLL1 MUTATED`
TCGA-BR-7703 TCGA-BR-8289 TCGA-BR-8686 TCGA-CG-4305 
       24.76         2.66        15.68        15.95 

$`CBLL1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        8.05        12.95        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         9.86         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  CBLL1 MUTATED CBLL1 WILD-TYPE 
           2.66            0.00 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
          24.76          105.07 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
         15.815          12.590 
[1] "2.7 - 24.8 (15.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D232V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CBLL1 MUTATED         1        1        0        1         0         0
  CBLL1 WILD-TYPE       0        8       27       25        31        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CBLL1 MUTATED           0          0          1          0        1
  CBLL1 WILD-TYPE         3         49         35         24       23
D232V3, multiclass
            clus
vv           CBLL1 MUTATED CBLL1 WILD-TYPE
  STAGE I                1               0
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              0              31
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CBLL1 MUTATED     2   1   0   2
  CBLL1 WILD-TYPE   9  71 122  73
D232V4, multiclass
    clus
vv   CBLL1 MUTATED CBLL1 WILD-TYPE
  T1             2               9
  T2             1              71
  T3             0             122
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CBLL1 MUTATED    1  4  0  1
  CBLL1 WILD-TYPE 92 77 50 52
D232V5, multiclass
    clus
vv   CBLL1 MUTATED CBLL1 WILD-TYPE
  N0             1              92
  N1             4              77
  N2             0              50
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D232V6, binary
                 cls
clus                0   1
  CBLL1 MUTATED     4   1
  CBLL1 WILD-TYPE 253  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      4    1
  CBLL1 WILD-TYPE  253   17
   clus
vv  CBLL1 MUTATED CBLL1 WILD-TYPE
  0             4             253
  1             1              17
[1] 2 2
[1] FALSE
D232V7, binary
                 cls
clus                0   1
  CBLL1 MUTATED     0   6
  CBLL1 WILD-TYPE 110 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      0    6
  CBLL1 WILD-TYPE  110  173
        clus
vv       CBLL1 MUTATED CBLL1 WILD-TYPE
  FEMALE             0             110
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CBLL1 MUTATED                                       0
  CBLL1 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CBLL1 MUTATED                                                        3
  CBLL1 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CBLL1 MUTATED                                                                   1
  CBLL1 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CBLL1 MUTATED                                                  1
  CBLL1 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CBLL1 MUTATED                                                          0
  CBLL1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CBLL1 MUTATED                                                           1
  CBLL1 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CBLL1 MUTATED                                          0
  CBLL1 WILD-TYPE                                        3
D232V8, multiclass
                                                                   clus
vv                                                                  CBLL1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  CBLL1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D232V9, binary
                 cls
clus                0   1
  CBLL1 MUTATED     0   6
  CBLL1 WILD-TYPE   5 278
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      0    6
  CBLL1 WILD-TYPE    5  278
     clus
vv    CBLL1 MUTATED CBLL1 WILD-TYPE
  NO              0               5
  YES             6             278
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CBLL1 MUTATED     5   0   0   1
  CBLL1 WILD-TYPE 222  10  10  23
D232V10, multiclass
    clus
vv   CBLL1 MUTATED CBLL1 WILD-TYPE
  R0             5             222
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D232V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CBLL1 MUTATED       1                         1     3
  CBLL1 WILD-TYPE    75                         3   165
D232V12, multiclass
                           clus
vv                          CBLL1 MUTATED CBLL1 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(233) Variable = TENC1 MUTATION ANALYSIS
D233V1, survival
                 sevent
clus2               0   1
  TENC1 MUTATED     7   3
  TENC1 WILD-TYPE 174  77
  TENC1 MUTATED TENC1 WILD-TYPE 
             10             251 
  TENC1 MUTATED TENC1 WILD-TYPE 
              3              77 
$`TENC1 MUTATED`
TCGA-B7-5816 TCGA-BR-6852 TCGA-BR-8297 TCGA-CD-A4MG TCGA-CG-5721 TCGA-D7-6526 
       26.70        32.94         7.40         6.58         6.02        17.19 
TCGA-D7-A4YV TCGA-HJ-7597 TCGA-HU-A4GX TCGA-HU-A4H3 
        5.92        26.47        10.19        19.36 

$`TENC1 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 
       12.95         2.66        16.31         2.20        15.58         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.52         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       12.95        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  TENC1 MUTATED TENC1 WILD-TYPE 
           5.92            0.00 
  TENC1 MUTATED TENC1 WILD-TYPE 
          32.94          105.07 
  TENC1 MUTATED TENC1 WILD-TYPE 
          13.69           12.62 
[1] "5.9 - 32.9 (13.7)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D233V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TENC1 MUTATED         0        0        1        0         2         2
  TENC1 WILD-TYPE       1        9       26       26        29        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TENC1 MUTATED           0          1          0          3        1
  TENC1 WILD-TYPE         3         48         36         21       23
D233V3, multiclass
            clus
vv           TENC1 MUTATED TENC1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             3              21
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TENC1 MUTATED     0   1   4   5
  TENC1 WILD-TYPE  11  71 118  70
D233V4, multiclass
    clus
vv   TENC1 MUTATED TENC1 WILD-TYPE
  T1             0              11
  T2             1              71
  T3             4             118
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  TENC1 MUTATED    4  2  2  2
  TENC1 WILD-TYPE 89 79 48 51
D233V5, multiclass
    clus
vv   TENC1 MUTATED TENC1 WILD-TYPE
  N0             4              89
  N1             2              79
  N2             2              48
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D233V6, binary
                 cls
clus                0   1
  TENC1 MUTATED    10   0
  TENC1 WILD-TYPE 247  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TENC1 MUTATED     10    0
  TENC1 WILD-TYPE  247   18
   clus
vv  TENC1 MUTATED TENC1 WILD-TYPE
  0            10             247
  1             0              18
[1] 2 2
[1] FALSE
D233V7, binary
                 cls
clus                0   1
  TENC1 MUTATED     8   3
  TENC1 WILD-TYPE 102 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TENC1 MUTATED      8    3
  TENC1 WILD-TYPE  102  176
        clus
vv       TENC1 MUTATED TENC1 WILD-TYPE
  FEMALE             8             102
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TENC1 MUTATED                                       5
  TENC1 WILD-TYPE                                    45
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TENC1 MUTATED                                                        2
  TENC1 WILD-TYPE                                                    133
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TENC1 MUTATED                                                                   1
  TENC1 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TENC1 MUTATED                                                  2
  TENC1 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TENC1 MUTATED                                                          0
  TENC1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TENC1 MUTATED                                                           0
  TENC1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TENC1 MUTATED                                          1
  TENC1 WILD-TYPE                                        2
D233V8, multiclass
                                                                   clus
vv                                                                  TENC1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  TENC1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D233V9, binary
                 cls
clus                0   1
  TENC1 MUTATED     0  11
  TENC1 WILD-TYPE   5 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TENC1 MUTATED      0   11
  TENC1 WILD-TYPE    5  273
     clus
vv    TENC1 MUTATED TENC1 WILD-TYPE
  NO              0               5
  YES            11             273
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TENC1 MUTATED     9   0   0   1
  TENC1 WILD-TYPE 218  10  10  23
D233V10, multiclass
    clus
vv   TENC1 MUTATED TENC1 WILD-TYPE
  R0             9             218
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D233V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TENC1 MUTATED       3                         0     7
  TENC1 WILD-TYPE    73                         4   161
D233V12, multiclass
                           clus
vv                          TENC1 MUTATED TENC1 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 7             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(234) Variable = C1QA MUTATION ANALYSIS
D234V1, survival
                sevent
clus2              0   1
  C1QA MUTATED     5   0
  C1QA WILD-TYPE 176  80
  C1QA MUTATED C1QA WILD-TYPE 
             5            256 
  C1QA MUTATED C1QA WILD-TYPE 
             0             80 
$`C1QA MUTATED`
TCGA-BR-8078 TCGA-BR-8487 TCGA-CG-5723 TCGA-CG-5728 TCGA-HU-A4GT 
       12.26         1.12       105.07        65.10         6.51 

$`C1QA WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        6.02         0.99        12.03        28.96        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  C1QA MUTATED C1QA WILD-TYPE 
          1.12           0.00 
  C1QA MUTATED C1QA WILD-TYPE 
        105.07          79.07 
  C1QA MUTATED C1QA WILD-TYPE 
         12.26          12.64 
[1] "1.1 - 105.1 (12.3)" "0.0 - 79.1 (12.6)" 
[1] "hr="     "3.1e+07"
D234V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C1QA MUTATED         0        0        1        1         2         1
  C1QA WILD-TYPE       1        9       26       25        29        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1QA MUTATED           0          0          0          0        0
  C1QA WILD-TYPE         3         49         36         24       24
D234V3, multiclass
            clus
vv           C1QA MUTATED C1QA WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              1             25
  STAGE IIA             2             29
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  C1QA MUTATED     0   2   2   1
  C1QA WILD-TYPE  11  70 120  74
D234V4, multiclass
    clus
vv   C1QA MUTATED C1QA WILD-TYPE
  T1            0             11
  T2            2             70
  T3            2            120
  T4            1             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  C1QA MUTATED    4  1  0  0
  C1QA WILD-TYPE 89 80 50 53
D234V5, multiclass
    clus
vv   C1QA MUTATED C1QA WILD-TYPE
  N0            4             89
  N1            1             80
  N2            0             50
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D234V6, binary
                cls
clus               0   1
  C1QA MUTATED     5   0
  C1QA WILD-TYPE 252  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1QA MUTATED      5    0
  C1QA WILD-TYPE  252   18
   clus
vv  C1QA MUTATED C1QA WILD-TYPE
  0            5            252
  1            0             18
[1] 2 2
[1] FALSE
D234V7, binary
                cls
clus               0   1
  C1QA MUTATED     4   1
  C1QA WILD-TYPE 106 178
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1QA MUTATED      4    1
  C1QA WILD-TYPE  106  178
        clus
vv       C1QA MUTATED C1QA WILD-TYPE
  FEMALE            4            106
  MALE              1            178
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C1QA MUTATED                                       0
  C1QA WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C1QA MUTATED                                                        3
  C1QA WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C1QA MUTATED                                                                   1
  C1QA WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C1QA MUTATED                                                  1
  C1QA WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C1QA MUTATED                                                          0
  C1QA WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C1QA MUTATED                                                           0
  C1QA WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C1QA MUTATED                                          0
  C1QA WILD-TYPE                                        3
D234V8, multiclass
                                                                   clus
vv                                                                  C1QA MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  C1QA WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D234V9, binary
                cls
clus               0   1
  C1QA MUTATED     0   5
  C1QA WILD-TYPE   5 279
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1QA MUTATED      0    5
  C1QA WILD-TYPE    5  279
     clus
vv    C1QA MUTATED C1QA WILD-TYPE
  NO             0              5
  YES            5            279
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  C1QA MUTATED     5   0   0   0
  C1QA WILD-TYPE 222  10  10  24
D234V10, multiclass
    clus
vv   C1QA MUTATED C1QA WILD-TYPE
  R0            5            222
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D234V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C1QA MUTATED       1                         0     2
  C1QA WILD-TYPE    75                         4   166
D234V12, multiclass
                           clus
vv                          C1QA MUTATED C1QA WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                2            166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(235) Variable = PLAU MUTATION ANALYSIS
D235V1, survival
                sevent
clus2              0   1
  PLAU MUTATED     4   1
  PLAU WILD-TYPE 177  79
  PLAU MUTATED PLAU WILD-TYPE 
             5            256 
  PLAU MUTATED PLAU WILD-TYPE 
             1             79 
$`PLAU MUTATED`
TCGA-BR-4201 TCGA-BR-8487 TCGA-CG-5723 TCGA-F1-6874 TCGA-HU-A4GN 
       30.90         1.12       105.07        14.47        29.98 

$`PLAU WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        0.62         7.99        16.24        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       22.75        25.81        11.77         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  PLAU MUTATED PLAU WILD-TYPE 
          1.12           0.00 
  PLAU MUTATED PLAU WILD-TYPE 
        105.07          79.07 
  PLAU MUTATED PLAU WILD-TYPE 
        29.980         12.575 
[1] "1.1 - 105.1 (30.0)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "4"  
D235V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLAU MUTATED         0        0        1        1         2         0
  PLAU WILD-TYPE       1        9       26       25        29        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLAU MUTATED           0          0          0          0        0
  PLAU WILD-TYPE         3         49         36         24       24
D235V3, multiclass
            clus
vv           PLAU MUTATED PLAU WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              1             25
  STAGE IIA             2             29
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PLAU MUTATED     0   4   1   0
  PLAU WILD-TYPE  11  68 121  75
D235V4, multiclass
    clus
vv   PLAU MUTATED PLAU WILD-TYPE
  T1            0             11
  T2            4             68
  T3            1            121
  T4            0             75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  PLAU MUTATED    2  3  0  0
  PLAU WILD-TYPE 91 78 50 53
D235V5, multiclass
    clus
vv   PLAU MUTATED PLAU WILD-TYPE
  N0            2             91
  N1            3             78
  N2            0             50
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D235V6, binary
                cls
clus               0   1
  PLAU MUTATED     7   0
  PLAU WILD-TYPE 250  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLAU MUTATED      7    0
  PLAU WILD-TYPE  250   18
   clus
vv  PLAU MUTATED PLAU WILD-TYPE
  0            7            250
  1            0             18
[1] 2 2
[1] FALSE
D235V7, binary
                cls
clus               0   1
  PLAU MUTATED     4   3
  PLAU WILD-TYPE 106 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLAU MUTATED      4    3
  PLAU WILD-TYPE  106  176
        clus
vv       PLAU MUTATED PLAU WILD-TYPE
  FEMALE            4            106
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PLAU MUTATED                                       0
  PLAU WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLAU MUTATED                                                        5
  PLAU WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLAU MUTATED                                                                   1
  PLAU WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PLAU MUTATED                                                  1
  PLAU WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PLAU MUTATED                                                          0
  PLAU WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PLAU MUTATED                                                           0
  PLAU WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PLAU MUTATED                                          0
  PLAU WILD-TYPE                                        3
D235V8, multiclass
                                                                   clus
vv                                                                  PLAU MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  PLAU WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D235V9, binary
                cls
clus               0   1
  PLAU MUTATED     0   7
  PLAU WILD-TYPE   5 277
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLAU MUTATED      0    7
  PLAU WILD-TYPE    5  277
     clus
vv    PLAU MUTATED PLAU WILD-TYPE
  NO             0              5
  YES            7            277
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PLAU MUTATED     4   0   0   3
  PLAU WILD-TYPE 223  10  10  21
D235V10, multiclass
    clus
vv   PLAU MUTATED PLAU WILD-TYPE
  R0            4            223
  R1            0             10
  R2            0             10
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D235V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLAU MUTATED       1                         0     5
  PLAU WILD-TYPE    75                         4   163
D235V12, multiclass
                           clus
vv                          PLAU MUTATED PLAU WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                5            163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(236) Variable = ALG10 MUTATION ANALYSIS
D236V1, survival
                 sevent
clus2               0   1
  ALG10 MUTATED     7   4
  ALG10 WILD-TYPE 174  76
  ALG10 MUTATED ALG10 WILD-TYPE 
             11             250 
  ALG10 MUTATED ALG10 WILD-TYPE 
              4              76 
$`ALG10 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6455 TCGA-BR-7851 TCGA-CD-A4MI TCGA-CG-5726 
        6.97        30.90        13.87        12.43         0.10        28.96 
TCGA-D7-6818 TCGA-D7-A4YY TCGA-HU-8602 TCGA-HU-A4GU TCGA-HU-A4H3 
       10.55        13.78        11.41         6.25        19.36 

$`ALG10 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6456 
        6.18         9.57         6.61        34.68        15.95        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       15.42        28.01        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.22        15.98        12.79        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       26.47         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  ALG10 MUTATED ALG10 WILD-TYPE 
            0.1             0.0 
  ALG10 MUTATED ALG10 WILD-TYPE 
          30.90          105.07 
  ALG10 MUTATED ALG10 WILD-TYPE 
          12.43           12.64 
[1] "0.1 - 30.9 (12.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D236V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ALG10 MUTATED         0        1        0        0         0         4
  ALG10 WILD-TYPE       1        8       27       26        31        40
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ALG10 MUTATED           0          2          2          1        0
  ALG10 WILD-TYPE         3         47         34         23       24
D236V3, multiclass
            clus
vv           ALG10 MUTATED ALG10 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              0              31
  STAGE IIB              4              40
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             2              34
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ALG10 MUTATED     1   2   5   3
  ALG10 WILD-TYPE  10  70 117  72
D236V4, multiclass
    clus
vv   ALG10 MUTATED ALG10 WILD-TYPE
  T1             1              10
  T2             2              70
  T3             5             117
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ALG10 MUTATED    3  4  0  3
  ALG10 WILD-TYPE 90 77 50 50
D236V5, multiclass
    clus
vv   ALG10 MUTATED ALG10 WILD-TYPE
  N0             3              90
  N1             4              77
  N2             0              50
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D236V6, binary
                 cls
clus                0   1
  ALG10 MUTATED    10   0
  ALG10 WILD-TYPE 247  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALG10 MUTATED     10    0
  ALG10 WILD-TYPE  247   18
   clus
vv  ALG10 MUTATED ALG10 WILD-TYPE
  0            10             247
  1             0              18
[1] 2 2
[1] FALSE
D236V7, binary
                 cls
clus                0   1
  ALG10 MUTATED     3   8
  ALG10 WILD-TYPE 107 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALG10 MUTATED      3    8
  ALG10 WILD-TYPE  107  171
        clus
vv       ALG10 MUTATED ALG10 WILD-TYPE
  FEMALE             3             107
  MALE               8             171
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ALG10 MUTATED                                       4
  ALG10 WILD-TYPE                                    46
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ALG10 MUTATED                                                        5
  ALG10 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ALG10 MUTATED                                                                   2
  ALG10 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ALG10 MUTATED                                                  0
  ALG10 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ALG10 MUTATED                                                          0
  ALG10 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ALG10 MUTATED                                                           0
  ALG10 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ALG10 MUTATED                                          0
  ALG10 WILD-TYPE                                        3
D236V8, multiclass
                                                                   clus
vv                                                                  ALG10 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ALG10 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D236V9, binary
                 cls
clus                0   1
  ALG10 MUTATED     1  10
  ALG10 WILD-TYPE   4 274
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALG10 MUTATED      1   10
  ALG10 WILD-TYPE    4  274
     clus
vv    ALG10 MUTATED ALG10 WILD-TYPE
  NO              1               4
  YES            10             274
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ALG10 MUTATED     8   0   0   2
  ALG10 WILD-TYPE 219  10  10  22
D236V10, multiclass
    clus
vv   ALG10 MUTATED ALG10 WILD-TYPE
  R0             8             219
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D236V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ALG10 MUTATED       4                         0     6
  ALG10 WILD-TYPE    72                         4   162
D236V12, multiclass
                           clus
vv                          ALG10 MUTATED ALG10 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(237) Variable = DAO MUTATION ANALYSIS
D237V1, survival
               sevent
clus2             0   1
  DAO MUTATED     9   1
  DAO WILD-TYPE 172  79
  DAO MUTATED DAO WILD-TYPE 
           10           251 
  DAO MUTATED DAO WILD-TYPE 
            1            79 
$`DAO MUTATED`
TCGA-BR-6563 TCGA-BR-6706 TCGA-BR-7851 TCGA-BR-8680 TCGA-BR-A4PE TCGA-CG-4466 
       39.12        18.05        12.43        15.81        20.42        18.97 
TCGA-F1-A448 TCGA-HU-A4G9 TCGA-HU-A4GX TCGA-HU-A4H6 
       21.27        24.20        10.19         9.67 

$`DAO WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        19.33        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        32.78        25.61        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51        20.65         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        72.23         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       11.84         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HD 
       12.95        19.36        23.84        12.30         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  DAO MUTATED DAO WILD-TYPE 
         9.67          0.00 
  DAO MUTATED DAO WILD-TYPE 
        39.12        105.07 
  DAO MUTATED DAO WILD-TYPE 
        18.51         12.56 
[1] "9.7 - 39.1 (18.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "4.5"
D237V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DAO MUTATED         1        1        2        0         0         2
  DAO WILD-TYPE       0        8       25       26        31        42
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DAO MUTATED           0          2          1          1        1
  DAO WILD-TYPE         3         47         35         23       23
D237V3, multiclass
            clus
vv           DAO MUTATED DAO WILD-TYPE
  STAGE I              1             0
  STAGE IA             1             8
  STAGE IB             2            25
  STAGE II             0            26
  STAGE IIA            0            31
  STAGE IIB            2            42
  STAGE III            0             3
  STAGE IIIA           2            47
  STAGE IIIB           1            35
  STAGE IIIC           1            23
  STAGE IV             1            23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  DAO MUTATED     2   2   4   3
  DAO WILD-TYPE   9  70 118  72
D237V4, multiclass
    clus
vv   DAO MUTATED DAO WILD-TYPE
  T1           2             9
  T2           2            70
  T3           4           118
  T4           3            72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  DAO MUTATED    4  3  3  1
  DAO WILD-TYPE 89 78 47 52
D237V5, multiclass
    clus
vv   DAO MUTATED DAO WILD-TYPE
  N0           4            89
  N1           3            78
  N2           3            47
  N3           1            52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D237V6, binary
               cls
clus              0   1
  DAO MUTATED     9   1
  DAO WILD-TYPE 248  17
[1] "tbl2"
               cls
clus            [,1] [,2]
  DAO MUTATED      9    1
  DAO WILD-TYPE  248   17
   clus
vv  DAO MUTATED DAO WILD-TYPE
  0           9           248
  1           1            17
[1] 2 2
[1] FALSE
D237V7, binary
               cls
clus              0   1
  DAO MUTATED     5   6
  DAO WILD-TYPE 105 173
[1] "tbl2"
               cls
clus            [,1] [,2]
  DAO MUTATED      5    6
  DAO WILD-TYPE  105  173
        clus
vv       DAO MUTATED DAO WILD-TYPE
  FEMALE           5           105
  MALE             6           173
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DAO MUTATED                                       1
  DAO WILD-TYPE                                    49
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DAO MUTATED                                                        4
  DAO WILD-TYPE                                                    131
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DAO MUTATED                                                                   2
  DAO WILD-TYPE                                                                38
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DAO MUTATED                                                  3
  DAO WILD-TYPE                                               35
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DAO MUTATED                                                          1
  DAO WILD-TYPE                                                       15
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DAO MUTATED                                                           0
  DAO WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DAO MUTATED                                          0
  DAO WILD-TYPE                                        3
D237V8, multiclass
                                                                   clus
vv                                                                  DAO MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  DAO WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D237V9, binary
               cls
clus              0   1
  DAO MUTATED     0  11
  DAO WILD-TYPE   5 273
[1] "tbl2"
               cls
clus            [,1] [,2]
  DAO MUTATED      0   11
  DAO WILD-TYPE    5  273
     clus
vv    DAO MUTATED DAO WILD-TYPE
  NO            0             5
  YES          11           273
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  DAO MUTATED    11   0   0   0
  DAO WILD-TYPE 216  10  10  24
D237V10, multiclass
    clus
vv   DAO MUTATED DAO WILD-TYPE
  R0          11           216
  R1           0            10
  R2           0            10
  RX           0            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D237V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DAO MUTATED       4                         1     5
  DAO WILD-TYPE    72                         3   163
D237V12, multiclass
                           clus
vv                          DAO MUTATED DAO WILD-TYPE
  ASIAN                               4            72
  BLACK OR AFRICAN AMERICAN           1             3
  WHITE                               5           163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(238) Variable = CDKL3 MUTATION ANALYSIS
D238V1, survival
                 sevent
clus2               0   1
  CDKL3 MUTATED     6   1
  CDKL3 WILD-TYPE 175  79
  CDKL3 MUTATED CDKL3 WILD-TYPE 
              7             254 
  CDKL3 MUTATED CDKL3 WILD-TYPE 
              1              79 
$`CDKL3 MUTATED`
TCGA-BR-4184 TCGA-BR-6566 TCGA-BR-8589 TCGA-BR-8591 TCGA-CG-5721 TCGA-CG-5723 
        6.97        32.78        15.81        13.45         6.02       105.07 
TCGA-HU-A4H8 
        8.88 

$`CDKL3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 
        9.21        20.22         1.12        12.79         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
        6.97        36.00         1.02         0.99         0.99        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       12.30         9.67        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  CDKL3 MUTATED CDKL3 WILD-TYPE 
           6.02            0.00 
  CDKL3 MUTATED CDKL3 WILD-TYPE 
         105.07           79.07 
  CDKL3 MUTATED CDKL3 WILD-TYPE 
         13.450          12.605 
[1] "6.0 - 105.1 (13.4)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "3.8"
D238V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDKL3 MUTATED         0        0        1        1         1         0
  CDKL3 WILD-TYPE       1        9       26       25        30        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDKL3 MUTATED           0          1          1          1        1
  CDKL3 WILD-TYPE         3         48         35         23       23
D238V3, multiclass
            clus
vv           CDKL3 MUTATED CDKL3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDKL3 MUTATED     1   1   2   3
  CDKL3 WILD-TYPE  10  71 120  72
D238V4, multiclass
    clus
vv   CDKL3 MUTATED CDKL3 WILD-TYPE
  T1             1              10
  T2             1              71
  T3             2             120
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CDKL3 MUTATED    1  5  0  1
  CDKL3 WILD-TYPE 92 76 50 52
D238V5, multiclass
    clus
vv   CDKL3 MUTATED CDKL3 WILD-TYPE
  N0             1              92
  N1             5              76
  N2             0              50
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D238V6, binary
                 cls
clus                0   1
  CDKL3 MUTATED     6   0
  CDKL3 WILD-TYPE 251  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL3 MUTATED      6    0
  CDKL3 WILD-TYPE  251   18
   clus
vv  CDKL3 MUTATED CDKL3 WILD-TYPE
  0             6             251
  1             0              18
[1] 2 2
[1] FALSE
D238V7, binary
                 cls
clus                0   1
  CDKL3 MUTATED     1   6
  CDKL3 WILD-TYPE 109 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL3 MUTATED      1    6
  CDKL3 WILD-TYPE  109  173
        clus
vv       CDKL3 MUTATED CDKL3 WILD-TYPE
  FEMALE             1             109
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CDKL3 MUTATED                                       0
  CDKL3 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CDKL3 MUTATED                                                        5
  CDKL3 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CDKL3 MUTATED                                                                   1
  CDKL3 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CDKL3 MUTATED                                                  1
  CDKL3 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CDKL3 MUTATED                                                          0
  CDKL3 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CDKL3 MUTATED                                                           0
  CDKL3 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CDKL3 MUTATED                                          0
  CDKL3 WILD-TYPE                                        3
D238V8, multiclass
                                                                   clus
vv                                                                  CDKL3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  CDKL3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D238V9, binary
                 cls
clus                0   1
  CDKL3 MUTATED     0   7
  CDKL3 WILD-TYPE   5 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL3 MUTATED      0    7
  CDKL3 WILD-TYPE    5  277
     clus
vv    CDKL3 MUTATED CDKL3 WILD-TYPE
  NO              0               5
  YES             7             277
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDKL3 MUTATED     6   0   0   1
  CDKL3 WILD-TYPE 221  10  10  23
D238V10, multiclass
    clus
vv   CDKL3 MUTATED CDKL3 WILD-TYPE
  R0             6             221
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D238V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDKL3 MUTATED       1                         0     4
  CDKL3 WILD-TYPE    75                         4   164
D238V12, multiclass
                           clus
vv                          CDKL3 MUTATED CDKL3 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(239) Variable = GLIPR1L2 MUTATION ANALYSIS
D239V1, survival
                    sevent
clus2                  0   1
  GLIPR1L2 MUTATED     4   6
  GLIPR1L2 WILD-TYPE 177  74
  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE 
                10                251 
  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE 
                 6                 74 
$`GLIPR1L2 MUTATED`
TCGA-BR-4201 TCGA-BR-6566 TCGA-BR-A4QL TCGA-CD-5801 TCGA-CD-8536 TCGA-CG-4465 
       30.90        32.78        11.57        13.18         0.10         9.01 
TCGA-CG-5717 TCGA-D7-6527 TCGA-FP-A4BE TCGA-HU-A4GQ 
        6.97        10.26        11.08         0.10 

$`GLIPR1L2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
       13.64         5.13         2.83         3.25        13.15         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        22.98        30.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
       18.54        18.61        17.85        13.35        17.19        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 
       59.54         5.03        13.58         0.56         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE 
               0.1                0.0 
  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE 
             32.78             105.07 
  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE 
             10.67              12.76 
[1] "0.1 - 32.8 (10.7)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "2.2"
D239V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GLIPR1L2 MUTATED         0        0        0        3         2         0
  GLIPR1L2 WILD-TYPE       1        9       27       23        29        44
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLIPR1L2 MUTATED           0          1          1          1        1
  GLIPR1L2 WILD-TYPE         3         48         35         23       23
D239V3, multiclass
            clus
vv           GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  0                 27
  STAGE II                  3                 23
  STAGE IIA                 2                 29
  STAGE IIB                 0                 44
  STAGE III                 0                  3
  STAGE IIIA                1                 48
  STAGE IIIB                1                 35
  STAGE IIIC                1                 23
  STAGE IV                  1                 23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  GLIPR1L2 MUTATED     0   3   5   2
  GLIPR1L2 WILD-TYPE  11  69 117  73
D239V4, multiclass
    clus
vv   GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  T1                0                 11
  T2                3                 69
  T3                5                117
  T4                2                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  GLIPR1L2 MUTATED    3  3  1  2
  GLIPR1L2 WILD-TYPE 90 78 49 51
D239V5, multiclass
    clus
vv   GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  N0                3                 90
  N1                3                 78
  N2                1                 49
  N3                2                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D239V6, binary
                    cls
clus                   0   1
  GLIPR1L2 MUTATED     9   1
  GLIPR1L2 WILD-TYPE 248  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  GLIPR1L2 MUTATED      9    1
  GLIPR1L2 WILD-TYPE  248   17
   clus
vv  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  0                9                248
  1                1                 17
[1] 2 2
[1] FALSE
D239V7, binary
                    cls
clus                   0   1
  GLIPR1L2 MUTATED     4   6
  GLIPR1L2 WILD-TYPE 106 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  GLIPR1L2 MUTATED      4    6
  GLIPR1L2 WILD-TYPE  106  173
        clus
vv       GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  FEMALE                4                106
  MALE                  6                173
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GLIPR1L2 MUTATED                                       1
  GLIPR1L2 WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GLIPR1L2 MUTATED                                                        7
  GLIPR1L2 WILD-TYPE                                                    128
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GLIPR1L2 MUTATED                                                                   0
  GLIPR1L2 WILD-TYPE                                                                40
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GLIPR1L2 MUTATED                                                  1
  GLIPR1L2 WILD-TYPE                                               37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GLIPR1L2 MUTATED                                                          0
  GLIPR1L2 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GLIPR1L2 MUTATED                                                           1
  GLIPR1L2 WILD-TYPE                                                         5
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GLIPR1L2 MUTATED                                          0
  GLIPR1L2 WILD-TYPE                                        3
D239V8, multiclass
                                                                   clus
vv                                                                  GLIPR1L2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  GLIPR1L2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D239V9, binary
                    cls
clus                   0   1
  GLIPR1L2 MUTATED     0  10
  GLIPR1L2 WILD-TYPE   5 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  GLIPR1L2 MUTATED      0   10
  GLIPR1L2 WILD-TYPE    5  274
     clus
vv    GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  NO                 0                  5
  YES               10                274
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  GLIPR1L2 MUTATED     8   0   1   1
  GLIPR1L2 WILD-TYPE 219  10   9  23
D239V10, multiclass
    clus
vv   GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  R0                8                219
  R1                0                 10
  R2                1                  9
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D239V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GLIPR1L2 MUTATED       3                         1     4
  GLIPR1L2 WILD-TYPE    73                         3   164
D239V12, multiclass
                           clus
vv                          GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  ASIAN                                    3                 73
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                    4                164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(240) Variable = FZD3 MUTATION ANALYSIS
D240V1, survival
                sevent
clus2              0   1
  FZD3 MUTATED     7   2
  FZD3 WILD-TYPE 174  78
  FZD3 MUTATED FZD3 WILD-TYPE 
             9            252 
  FZD3 MUTATED FZD3 WILD-TYPE 
             2             78 
$`FZD3 MUTATED`
TCGA-BR-4184 TCGA-BR-6458 TCGA-BR-7703 TCGA-BR-7851 TCGA-BR-8078 TCGA-BR-8360 
        6.97        19.33        24.76        12.43        12.26         6.18 
TCGA-BR-8368 TCGA-BR-A4QL TCGA-CG-5723 
        4.31        11.57       105.07 

$`FZD3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 
       30.90        31.20        32.94        12.82         9.21        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       15.42        28.01        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        20.55         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20        15.58         7.40        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  FZD3 MUTATED FZD3 WILD-TYPE 
          4.31           0.00 
  FZD3 MUTATED FZD3 WILD-TYPE 
        105.07          79.07 
  FZD3 MUTATED FZD3 WILD-TYPE 
         12.26          12.71 
[1] "4.3 - 105.1 (12.3)" "0.0 - 79.1 (12.7)" 
[1] "hr=" "1.9"
D240V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FZD3 MUTATED         0        1        1        1         1         3
  FZD3 WILD-TYPE       1        8       26       25        30        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FZD3 MUTATED           0          1          1          0        0
  FZD3 WILD-TYPE         3         48         35         24       24
D240V3, multiclass
            clus
vv           FZD3 MUTATED FZD3 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              1             26
  STAGE II              1             25
  STAGE IIA             1             30
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FZD3 MUTATED     1   2   4   2
  FZD3 WILD-TYPE  10  70 118  73
D240V4, multiclass
    clus
vv   FZD3 MUTATED FZD3 WILD-TYPE
  T1            1             10
  T2            2             70
  T3            4            118
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  FZD3 MUTATED    5  3  0  1
  FZD3 WILD-TYPE 88 78 50 52
D240V5, multiclass
    clus
vv   FZD3 MUTATED FZD3 WILD-TYPE
  N0            5             88
  N1            3             78
  N2            0             50
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D240V6, binary
                cls
clus               0   1
  FZD3 MUTATED     9   0
  FZD3 WILD-TYPE 248  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD3 MUTATED      9    0
  FZD3 WILD-TYPE  248   18
   clus
vv  FZD3 MUTATED FZD3 WILD-TYPE
  0            9            248
  1            0             18
[1] 2 2
[1] FALSE
D240V7, binary
                cls
clus               0   1
  FZD3 MUTATED     5   5
  FZD3 WILD-TYPE 105 174
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD3 MUTATED      5    5
  FZD3 WILD-TYPE  105  174
        clus
vv       FZD3 MUTATED FZD3 WILD-TYPE
  FEMALE            5            105
  MALE              5            174
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FZD3 MUTATED                                       0
  FZD3 WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FZD3 MUTATED                                                        7
  FZD3 WILD-TYPE                                                    128
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FZD3 MUTATED                                                                   2
  FZD3 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FZD3 MUTATED                                                  0
  FZD3 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FZD3 MUTATED                                                          0
  FZD3 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FZD3 MUTATED                                                           1
  FZD3 WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FZD3 MUTATED                                          0
  FZD3 WILD-TYPE                                        3
D240V8, multiclass
                                                                   clus
vv                                                                  FZD3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  FZD3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D240V9, binary
                cls
clus               0   1
  FZD3 MUTATED     0  10
  FZD3 WILD-TYPE   5 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD3 MUTATED      0   10
  FZD3 WILD-TYPE    5  274
     clus
vv    FZD3 MUTATED FZD3 WILD-TYPE
  NO             0              5
  YES           10            274
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FZD3 MUTATED     8   0   0   2
  FZD3 WILD-TYPE 219  10  10  22
D240V10, multiclass
    clus
vv   FZD3 MUTATED FZD3 WILD-TYPE
  R0            8            219
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D240V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FZD3 MUTATED       0                         0     9
  FZD3 WILD-TYPE    76                         4   159
D240V12, multiclass
                           clus
vv                          FZD3 MUTATED FZD3 WILD-TYPE
  ASIAN                                0             76
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                9            159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(241) Variable = CETN3 MUTATION ANALYSIS
D241V1, survival
                 sevent
clus2               0   1
  CETN3 MUTATED     5   0
  CETN3 WILD-TYPE 176  80
  CETN3 MUTATED CETN3 WILD-TYPE 
              5             256 
  CETN3 MUTATED CETN3 WILD-TYPE 
              0              80 
$`CETN3 MUTATED`
TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-5721 TCGA-CG-5728 TCGA-HU-A4GT 
       15.81        11.57         6.02        65.10         6.51 

$`CETN3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        0.99       105.07        12.03        28.96        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  CETN3 MUTATED CETN3 WILD-TYPE 
           6.02            0.00 
  CETN3 MUTATED CETN3 WILD-TYPE 
          65.10          105.07 
  CETN3 MUTATED CETN3 WILD-TYPE 
          11.57           12.64 
[1] "6.0 - 65.1 (11.6)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "9500000"
D241V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CETN3 MUTATED         0        0        1        0         1         0
  CETN3 WILD-TYPE       1        9       26       26        30        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CETN3 MUTATED           0          0          1          0        3
  CETN3 WILD-TYPE         3         49         35         24       21
D241V3, multiclass
            clus
vv           CETN3 MUTATED CETN3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               3              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CETN3 MUTATED     1   1   2   3
  CETN3 WILD-TYPE  10  71 120  72
D241V4, multiclass
    clus
vv   CETN3 MUTATED CETN3 WILD-TYPE
  T1             1              10
  T2             1              71
  T3             2             120
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CETN3 MUTATED    2  1  2  1
  CETN3 WILD-TYPE 91 80 48 52
D241V5, multiclass
    clus
vv   CETN3 MUTATED CETN3 WILD-TYPE
  N0             2              91
  N1             1              80
  N2             2              48
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D241V6, binary
                 cls
clus                0   1
  CETN3 MUTATED     6   1
  CETN3 WILD-TYPE 251  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CETN3 MUTATED      6    1
  CETN3 WILD-TYPE  251   17
   clus
vv  CETN3 MUTATED CETN3 WILD-TYPE
  0             6             251
  1             1              17
[1] 2 2
[1] FALSE
D241V7, binary
                 cls
clus                0   1
  CETN3 MUTATED     5   2
  CETN3 WILD-TYPE 105 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CETN3 MUTATED      5    2
  CETN3 WILD-TYPE  105  177
        clus
vv       CETN3 MUTATED CETN3 WILD-TYPE
  FEMALE             5             105
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CETN3 MUTATED                                       0
  CETN3 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CETN3 MUTATED                                                        3
  CETN3 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CETN3 MUTATED                                                                   2
  CETN3 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CETN3 MUTATED                                                  2
  CETN3 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CETN3 MUTATED                                                          0
  CETN3 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CETN3 MUTATED                                                           0
  CETN3 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CETN3 MUTATED                                          0
  CETN3 WILD-TYPE                                        3
D241V8, multiclass
                                                                   clus
vv                                                                  CETN3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  CETN3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D241V9, binary
                 cls
clus                0   1
  CETN3 MUTATED     0   7
  CETN3 WILD-TYPE   5 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CETN3 MUTATED      0    7
  CETN3 WILD-TYPE    5  277
     clus
vv    CETN3 MUTATED CETN3 WILD-TYPE
  NO              0               5
  YES             7             277
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CETN3 MUTATED     5   0   0   2
  CETN3 WILD-TYPE 222  10  10  22
D241V10, multiclass
    clus
vv   CETN3 MUTATED CETN3 WILD-TYPE
  R0             5             222
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D241V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CETN3 MUTATED       2                         0     3
  CETN3 WILD-TYPE    74                         4   165
D241V12, multiclass
                           clus
vv                          CETN3 MUTATED CETN3 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(242) Variable = PSME4 MUTATION ANALYSIS
D242V1, survival
                 sevent
clus2               0   1
  PSME4 MUTATED    22   5
  PSME4 WILD-TYPE 159  75
  PSME4 MUTATED PSME4 WILD-TYPE 
             27             234 
  PSME4 MUTATED PSME4 WILD-TYPE 
              5              75 
$`PSME4 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8078 
       26.70         6.97        30.90        34.68        23.93        12.26 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A44U TCGA-BR-A4QL 
       19.50         0.26         1.12        15.81        13.87        11.57 
TCGA-CD-8524 TCGA-CD-8536 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4465 TCGA-CG-5723 
        0.07         0.10         0.10        12.62         9.01       105.07 
TCGA-CG-5728 TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GH TCGA-HU-A4GT 
       65.10        11.08        11.41        11.84        11.77         6.51 
TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H8 
        6.25        19.36         8.88 

$`PSME4 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 
       11.70         6.61         4.64         7.43        18.35         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 
       32.94        12.82         9.21        24.76        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 
       12.76        18.71        17.49        14.43         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       15.58         7.40         6.18        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
       15.68         8.22        10.68        12.56         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.13         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 
       12.43        11.61         6.58        12.20        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       26.47         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX 
       22.75        25.81        29.98         8.98         0.10        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  PSME4 MUTATED PSME4 WILD-TYPE 
           0.07            0.00 
  PSME4 MUTATED PSME4 WILD-TYPE 
         105.07           79.07 
  PSME4 MUTATED PSME4 WILD-TYPE 
          11.77           12.79 
[1] "0.1 - 105.1 (11.8)" "0.0 - 79.1 (12.8)" 
[1] "hr=" "2.1"
D242V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PSME4 MUTATED         0        1        6        4         4         5
  PSME4 WILD-TYPE       1        8       21       22        27        39
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PSME4 MUTATED           0          2          3          2        3
  PSME4 WILD-TYPE         3         47         33         22       21
D242V3, multiclass
            clus
vv           PSME4 MUTATED PSME4 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               6              21
  STAGE II               4              22
  STAGE IIA              4              27
  STAGE IIB              5              39
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             3              33
  STAGE IIIC             2              22
  STAGE IV               3              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PSME4 MUTATED     2   8  12   9
  PSME4 WILD-TYPE   9  64 110  66
D242V4, multiclass
    clus
vv   PSME4 MUTATED PSME4 WILD-TYPE
  T1             2               9
  T2             8              64
  T3            12             110
  T4             9              66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PSME4 MUTATED   16  9  3  4
  PSME4 WILD-TYPE 77 72 47 49
D242V5, multiclass
    clus
vv   PSME4 MUTATED PSME4 WILD-TYPE
  N0            16              77
  N1             9              72
  N2             3              47
  N3             4              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D242V6, binary
                 cls
clus                0   1
  PSME4 MUTATED    32   2
  PSME4 WILD-TYPE 225  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSME4 MUTATED     32    2
  PSME4 WILD-TYPE  225   16
   clus
vv  PSME4 MUTATED PSME4 WILD-TYPE
  0            32             225
  1             2              16
[1] 2 2
[1] FALSE
D242V7, binary
                 cls
clus                0   1
  PSME4 MUTATED    21  14
  PSME4 WILD-TYPE  89 165
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSME4 MUTATED     21   14
  PSME4 WILD-TYPE   89  165
        clus
vv       PSME4 MUTATED PSME4 WILD-TYPE
  FEMALE            21              89
  MALE              14             165
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PSME4 MUTATED                                       6
  PSME4 WILD-TYPE                                    44
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PSME4 MUTATED                                                       21
  PSME4 WILD-TYPE                                                    114
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PSME4 MUTATED                                                                   3
  PSME4 WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PSME4 MUTATED                                                  4
  PSME4 WILD-TYPE                                               34
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PSME4 MUTATED                                                          1
  PSME4 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PSME4 MUTATED                                                           0
  PSME4 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PSME4 MUTATED                                          0
  PSME4 WILD-TYPE                                        3
D242V8, multiclass
                                                                   clus
vv                                                                  PSME4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       21
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  PSME4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          44
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        114
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D242V9, binary
                 cls
clus                0   1
  PSME4 MUTATED     1  34
  PSME4 WILD-TYPE   4 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSME4 MUTATED      1   34
  PSME4 WILD-TYPE    4  250
     clus
vv    PSME4 MUTATED PSME4 WILD-TYPE
  NO              1               4
  YES            34             250
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PSME4 MUTATED    23   0   1   8
  PSME4 WILD-TYPE 204  10   9  16
D242V10, multiclass
    clus
vv   PSME4 MUTATED PSME4 WILD-TYPE
  R0            23             204
  R1             0              10
  R2             1               9
  RX             8              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D242V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PSME4 MUTATED      12                         1    17
  PSME4 WILD-TYPE    64                         3   151
D242V12, multiclass
                           clus
vv                          PSME4 MUTATED PSME4 WILD-TYPE
  ASIAN                                12              64
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                17             151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(243) Variable = GNPNAT1 MUTATION ANALYSIS
D243V1, survival
                   sevent
clus2                 0   1
  GNPNAT1 MUTATED     3   0
  GNPNAT1 WILD-TYPE 178  80
  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE 
                3               258 
  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE 
                0                80 
$`GNPNAT1 MUTATED`
TCGA-CG-5721 TCGA-CG-5728 TCGA-IN-8462 
        6.02        65.10        18.81 

$`GNPNAT1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IP-7968 
        8.88        27.42        21.21         3.45         3.39         2.53 

  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE 
             6.02              0.00 
  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE 
            65.10            105.07 
  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE 
           18.810            12.605 
[1] "6.0 - 65.1 (18.8)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "9500000"
D243V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GNPNAT1 MUTATED         0        0        1        0         0         1
  GNPNAT1 WILD-TYPE       1        9       26       26        31        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GNPNAT1 MUTATED           0          1          0          0        1
  GNPNAT1 WILD-TYPE         3         48         36         24       23
D243V3, multiclass
            clus
vv           GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 0                26
  STAGE IIA                0                31
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               0                36
  STAGE IIIC               0                24
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GNPNAT1 MUTATED     0   2   0   2
  GNPNAT1 WILD-TYPE  11  70 122  73
D243V4, multiclass
    clus
vv   GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  T1               0                11
  T2               2                70
  T3               0               122
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  GNPNAT1 MUTATED    2  2  0  0
  GNPNAT1 WILD-TYPE 91 79 50 53
D243V5, multiclass
    clus
vv   GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  N0               2                91
  N1               2                79
  N2               0                50
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D243V6, binary
                   cls
clus                  0   1
  GNPNAT1 MUTATED     4   0
  GNPNAT1 WILD-TYPE 253  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GNPNAT1 MUTATED      4    0
  GNPNAT1 WILD-TYPE  253   18
   clus
vv  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  0               4               253
  1               0                18
[1] 2 2
[1] FALSE
D243V7, binary
                   cls
clus                  0   1
  GNPNAT1 MUTATED     2   2
  GNPNAT1 WILD-TYPE 108 177
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GNPNAT1 MUTATED      2    2
  GNPNAT1 WILD-TYPE  108  177
        clus
vv       GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  FEMALE               2               108
  MALE                 2               177
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GNPNAT1 MUTATED                                       0
  GNPNAT1 WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GNPNAT1 MUTATED                                                        2
  GNPNAT1 WILD-TYPE                                                    133
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GNPNAT1 MUTATED                                                                   2
  GNPNAT1 WILD-TYPE                                                                38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GNPNAT1 MUTATED                                                  0
  GNPNAT1 WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GNPNAT1 MUTATED                                                          0
  GNPNAT1 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GNPNAT1 MUTATED                                                           0
  GNPNAT1 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GNPNAT1 MUTATED                                          0
  GNPNAT1 WILD-TYPE                                        3
D243V8, multiclass
                                                                   clus
vv                                                                  GNPNAT1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  GNPNAT1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D243V9, binary
                   cls
clus                  0   1
  GNPNAT1 MUTATED     0   4
  GNPNAT1 WILD-TYPE   5 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GNPNAT1 MUTATED      0    4
  GNPNAT1 WILD-TYPE    5  280
     clus
vv    GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  NO                0                 5
  YES               4               280
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  GNPNAT1 MUTATED     3   0   0   1
  GNPNAT1 WILD-TYPE 224  10  10  23
D243V10, multiclass
    clus
vv   GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  R0               3               224
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D243V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GNPNAT1 MUTATED       0                         0     2
  GNPNAT1 WILD-TYPE    76                         4   166
D243V12, multiclass
[1] "Remove cluster labels:" "GNPNAT1 MUTATED"       
clus
  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE 
                2               246 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-4187        TCGA-BR-4188        TCGA-BR-4191        TCGA-BR-4201 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-4294        TCGA-BR-4357        TCGA-BR-4362        TCGA-BR-4363 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-4366        TCGA-BR-4368        TCGA-BR-4369        TCGA-BR-4370 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-4371        TCGA-BR-6452        TCGA-BR-6453        TCGA-BR-6454 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457        TCGA-BR-6458 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565        TCGA-BR-6566 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707        TCGA-BR-6710 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-7196        TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7707 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8058        TCGA-BR-8059 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297        TCGA-BR-8360 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-8361        TCGA-BR-8363        TCGA-BR-8364        TCGA-BR-8365 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-8366        TCGA-BR-8367        TCGA-BR-8368        TCGA-BR-8369 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-8370        TCGA-BR-8371        TCGA-BR-8372        TCGA-BR-8373 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-8380        TCGA-BR-8381        TCGA-BR-8382        TCGA-BR-8384 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-8483        TCGA-BR-8484        TCGA-BR-8485        TCGA-BR-8486 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-8487        TCGA-BR-8588        TCGA-BR-8589        TCGA-BR-8590 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-8591        TCGA-BR-8592        TCGA-BR-8676        TCGA-BR-8677 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-8678        TCGA-BR-8679        TCGA-BR-8680        TCGA-BR-8682 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-8683        TCGA-BR-8686        TCGA-BR-8687        TCGA-BR-8690 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-A44T        TCGA-BR-A44U        TCGA-BR-A452        TCGA-BR-A453 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-A4CQ        TCGA-BR-A4CR        TCGA-BR-A4CS        TCGA-BR-A4IU 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-A4IV        TCGA-BR-A4IY        TCGA-BR-A4IZ        TCGA-BR-A4J1 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-A4J2        TCGA-BR-A4J4        TCGA-BR-A4J6        TCGA-BR-A4J7 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-A4J8        TCGA-BR-A4PD        TCGA-BR-A4PE        TCGA-BR-A4PF 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-BR-A4QM        TCGA-CD-5798 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-CD-5803        TCGA-CD-5804        TCGA-CD-5813        TCGA-CD-8524 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-CD-8525        TCGA-CD-8526        TCGA-CD-8527        TCGA-CD-8528 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-CD-8529        TCGA-CD-8530        TCGA-CD-8531        TCGA-CD-8532 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-CD-8534        TCGA-CD-8535        TCGA-CD-8536        TCGA-CD-A486 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-CD-A487        TCGA-CD-A489        TCGA-CD-A48A        TCGA-CD-A48C 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-CD-A4MG        TCGA-CD-A4MH        TCGA-CD-A4MI        TCGA-CD-A4MJ 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-D7-8570        TCGA-D7-8572 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-D7-8573        TCGA-D7-8574        TCGA-D7-8575        TCGA-D7-8576 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-D7-8578        TCGA-D7-8579        TCGA-D7-A4YT        TCGA-D7-A4YU 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-D7-A4YV        TCGA-D7-A4YX        TCGA-D7-A4YY        TCGA-D7-A4Z0 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-EQ-A4SO        TCGA-F1-6177 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-F1-A448        TCGA-FP-7735 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8211        TCGA-FP-8631 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-FP-A4BE        TCGA-FP-A4BF        TCGA-HJ-7597        TCGA-HU-8243 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-HU-8245        TCGA-HU-8249        TCGA-HU-8602        TCGA-HU-8604 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-HU-8608        TCGA-HU-8610        TCGA-HU-A4G2        TCGA-HU-A4G3 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-HU-A4G6        TCGA-HU-A4G8        TCGA-HU-A4G9        TCGA-HU-A4GC 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-HU-A4GD        TCGA-HU-A4GF        TCGA-HU-A4GH        TCGA-HU-A4GN 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-HU-A4GP        TCGA-HU-A4GQ        TCGA-HU-A4GT        TCGA-HU-A4GU 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-HU-A4GX        TCGA-HU-A4GY        TCGA-HU-A4H0        TCGA-HU-A4H2 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-HU-A4H3        TCGA-HU-A4H4        TCGA-HU-A4H5        TCGA-HU-A4H6 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-HU-A4H8        TCGA-HU-A4HD        TCGA-IN-7806        TCGA-IN-7808 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 
       TCGA-IN-8663        TCGA-IP-7968 
"GNPNAT1 WILD-TYPE" "GNPNAT1 WILD-TYPE" 

Clustering(244) Variable = ZDHHC7 MUTATION ANALYSIS
D244V1, survival
                  sevent
clus2                0   1
  ZDHHC7 MUTATED     4   0
  ZDHHC7 WILD-TYPE 177  80
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
               4              257 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
               0               80 
$`ZDHHC7 MUTATED`
TCGA-BR-6452 TCGA-BR-8487 TCGA-BR-8591 TCGA-HU-A4G8 
       34.68         1.12        13.45        11.84 

$`ZDHHC7 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
            1.12             0.00 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
           34.68           105.07 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
          12.645           12.620 
[1] "1.1 - 34.7 (12.6)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "9200000"
D244V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZDHHC7 MUTATED         0        0        1        1         2         1
  ZDHHC7 WILD-TYPE       1        9       26       25        29        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZDHHC7 MUTATED           0          0          0          1        0
  ZDHHC7 WILD-TYPE         3         49         36         23       24
D244V3, multiclass
            clus
vv           ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                1               25
  STAGE IIA               2               29
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZDHHC7 MUTATED     0   2   3   1
  ZDHHC7 WILD-TYPE  11  70 119  74
D244V4, multiclass
    clus
vv   ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  T1              0               11
  T2              2               70
  T3              3              119
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZDHHC7 MUTATED    3  2  0  1
  ZDHHC7 WILD-TYPE 90 79 50 52
D244V5, multiclass
    clus
vv   ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  N0              3               90
  N1              2               79
  N2              0               50
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D244V6, binary
                  cls
clus                 0   1
  ZDHHC7 MUTATED     6   0
  ZDHHC7 WILD-TYPE 251  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC7 MUTATED      6    0
  ZDHHC7 WILD-TYPE  251   18
   clus
vv  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  0              6              251
  1              0               18
[1] 2 2
[1] FALSE
D244V7, binary
                  cls
clus                 0   1
  ZDHHC7 MUTATED     3   3
  ZDHHC7 WILD-TYPE 107 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC7 MUTATED      3    3
  ZDHHC7 WILD-TYPE  107  176
        clus
vv       ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  FEMALE              3              107
  MALE                3              176
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZDHHC7 MUTATED                                       1
  ZDHHC7 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZDHHC7 MUTATED                                                        3
  ZDHHC7 WILD-TYPE                                                    132
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZDHHC7 MUTATED                                                                   1
  ZDHHC7 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZDHHC7 MUTATED                                                  0
  ZDHHC7 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZDHHC7 MUTATED                                                          1
  ZDHHC7 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZDHHC7 MUTATED                                                           0
  ZDHHC7 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZDHHC7 MUTATED                                          0
  ZDHHC7 WILD-TYPE                                        3
D244V8, multiclass
                                                                   clus
vv                                                                  ZDHHC7 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ZDHHC7 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D244V9, binary
                  cls
clus                 0   1
  ZDHHC7 MUTATED     1   5
  ZDHHC7 WILD-TYPE   4 279
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC7 MUTATED      1    5
  ZDHHC7 WILD-TYPE    4  279
     clus
vv    ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  NO               1                4
  YES              5              279
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZDHHC7 MUTATED     5   0   0   0
  ZDHHC7 WILD-TYPE 222  10  10  24
D244V10, multiclass
    clus
vv   ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  R0              5              222
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D244V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZDHHC7 MUTATED       1                         0     3
  ZDHHC7 WILD-TYPE    75                         4   165
D244V12, multiclass
                           clus
vv                          ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  3              165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(245) Variable = PANK1 MUTATION ANALYSIS
D245V1, survival
                 sevent
clus2               0   1
  PANK1 MUTATED     4   3
  PANK1 WILD-TYPE 177  77
  PANK1 MUTATED PANK1 WILD-TYPE 
              7             254 
  PANK1 MUTATED PANK1 WILD-TYPE 
              3              77 
$`PANK1 MUTATED`
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7851 TCGA-BR-8363 TCGA-CD-A4MG TCGA-CG-4306 
       12.82        24.76        12.43         0.26         6.58         1.02 
TCGA-CG-5723 
      105.07 

$`PANK1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 
        8.98        21.11        30.90        31.20        32.94         9.21 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       19.50        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         6.02         0.99        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  PANK1 MUTATED PANK1 WILD-TYPE 
           0.26            0.00 
  PANK1 MUTATED PANK1 WILD-TYPE 
         105.07           79.07 
  PANK1 MUTATED PANK1 WILD-TYPE 
          12.43           12.64 
[1] "0.3 - 105.1 (12.4)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.1"
D245V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PANK1 MUTATED         0        1        2        1         1         1
  PANK1 WILD-TYPE       1        8       25       25        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PANK1 MUTATED           0          0          0          0        2
  PANK1 WILD-TYPE         3         49         36         24       22
D245V3, multiclass
            clus
vv           PANK1 MUTATED PANK1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               2              25
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PANK1 MUTATED     1   3   3   1
  PANK1 WILD-TYPE  10  69 119  74
D245V4, multiclass
    clus
vv   PANK1 MUTATED PANK1 WILD-TYPE
  T1             1              10
  T2             3              69
  T3             3             119
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PANK1 MUTATED    5  1  1  1
  PANK1 WILD-TYPE 88 80 49 52
D245V5, multiclass
    clus
vv   PANK1 MUTATED PANK1 WILD-TYPE
  N0             5              88
  N1             1              80
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D245V6, binary
                 cls
clus                0   1
  PANK1 MUTATED     6   2
  PANK1 WILD-TYPE 251  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK1 MUTATED      6    2
  PANK1 WILD-TYPE  251   16
   clus
vv  PANK1 MUTATED PANK1 WILD-TYPE
  0             6             251
  1             2              16
[1] 2 2
[1] FALSE
D245V7, binary
                 cls
clus                0   1
  PANK1 MUTATED     1   7
  PANK1 WILD-TYPE 109 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK1 MUTATED      1    7
  PANK1 WILD-TYPE  109  172
        clus
vv       PANK1 MUTATED PANK1 WILD-TYPE
  FEMALE             1             109
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PANK1 MUTATED                                       1
  PANK1 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PANK1 MUTATED                                                        4
  PANK1 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PANK1 MUTATED                                                                   2
  PANK1 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PANK1 MUTATED                                                  0
  PANK1 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PANK1 MUTATED                                                          0
  PANK1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PANK1 MUTATED                                                           1
  PANK1 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PANK1 MUTATED                                          0
  PANK1 WILD-TYPE                                        3
D245V8, multiclass
                                                                   clus
vv                                                                  PANK1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  PANK1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D245V9, binary
                 cls
clus                0   1
  PANK1 MUTATED     0   8
  PANK1 WILD-TYPE   5 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK1 MUTATED      0    8
  PANK1 WILD-TYPE    5  276
     clus
vv    PANK1 MUTATED PANK1 WILD-TYPE
  NO              0               5
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PANK1 MUTATED     6   0   1   0
  PANK1 WILD-TYPE 221  10   9  24
D245V10, multiclass
    clus
vv   PANK1 MUTATED PANK1 WILD-TYPE
  R0             6             221
  R1             0              10
  R2             1               9
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D245V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PANK1 MUTATED       1                         0     4
  PANK1 WILD-TYPE    75                         4   164
D245V12, multiclass
                           clus
vv                          PANK1 MUTATED PANK1 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(246) Variable = FAM116A MUTATION ANALYSIS
D246V1, survival
                   sevent
clus2                 0   1
  FAM116A MUTATED     5   0
  FAM116A WILD-TYPE 176  80
  FAM116A MUTATED FAM116A WILD-TYPE 
                5               256 
  FAM116A MUTATED FAM116A WILD-TYPE 
                0                80 
$`FAM116A MUTATED`
TCGA-BR-8680 TCGA-CD-A4MI TCGA-CG-4305 TCGA-HU-A4GT TCGA-HU-A4GX 
       15.81         0.10        15.95         6.51        10.19 

$`FAM116A WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10         6.25         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  FAM116A MUTATED FAM116A WILD-TYPE 
              0.1               0.0 
  FAM116A MUTATED FAM116A WILD-TYPE 
            15.95            105.07 
  FAM116A MUTATED FAM116A WILD-TYPE 
            10.19             12.64 
[1] "0.1 - 15.9 (10.2)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "9100000"
D246V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM116A MUTATED         0        0        1        1         1         0
  FAM116A WILD-TYPE       1        9       26       25        30        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM116A MUTATED           0          0          1          1        1
  FAM116A WILD-TYPE         3         49         35         23       23
D246V3, multiclass
            clus
vv           FAM116A MUTATED FAM116A WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 1                25
  STAGE IIA                1                30
  STAGE IIB                0                44
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               1                35
  STAGE IIIC               1                23
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM116A MUTATED     0   2   2   2
  FAM116A WILD-TYPE  11  70 120  73
D246V4, multiclass
    clus
vv   FAM116A MUTATED FAM116A WILD-TYPE
  T1               0                11
  T2               2                70
  T3               2               120
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  FAM116A MUTATED    2  2  2  0
  FAM116A WILD-TYPE 91 79 48 53
D246V5, multiclass
    clus
vv   FAM116A MUTATED FAM116A WILD-TYPE
  N0               2                91
  N1               2                79
  N2               2                48
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D246V6, binary
                   cls
clus                  0   1
  FAM116A MUTATED     5   1
  FAM116A WILD-TYPE 252  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM116A MUTATED      5    1
  FAM116A WILD-TYPE  252   17
   clus
vv  FAM116A MUTATED FAM116A WILD-TYPE
  0               5               252
  1               1                17
[1] 2 2
[1] FALSE
D246V7, binary
                   cls
clus                  0   1
  FAM116A MUTATED     2   4
  FAM116A WILD-TYPE 108 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM116A MUTATED      2    4
  FAM116A WILD-TYPE  108  175
        clus
vv       FAM116A MUTATED FAM116A WILD-TYPE
  FEMALE               2               108
  MALE                 4               175
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FAM116A MUTATED                                       1
  FAM116A WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAM116A MUTATED                                                        2
  FAM116A WILD-TYPE                                                    133
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAM116A MUTATED                                                                   1
  FAM116A WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FAM116A MUTATED                                                  2
  FAM116A WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FAM116A MUTATED                                                          0
  FAM116A WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FAM116A MUTATED                                                           0
  FAM116A WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FAM116A MUTATED                                          0
  FAM116A WILD-TYPE                                        3
D246V8, multiclass
                                                                   clus
vv                                                                  FAM116A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  FAM116A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D246V9, binary
                   cls
clus                  0   1
  FAM116A MUTATED     0   6
  FAM116A WILD-TYPE   5 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM116A MUTATED      0    6
  FAM116A WILD-TYPE    5  278
     clus
vv    FAM116A MUTATED FAM116A WILD-TYPE
  NO                0                 5
  YES               6               278
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM116A MUTATED     5   0   0   0
  FAM116A WILD-TYPE 222  10  10  24
D246V10, multiclass
    clus
vv   FAM116A MUTATED FAM116A WILD-TYPE
  R0               5               222
  R1               0                10
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D246V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM116A MUTATED       4                         0     0
  FAM116A WILD-TYPE    72                         4   168
D246V12, multiclass
                           clus
vv                          FAM116A MUTATED FAM116A WILD-TYPE
  ASIAN                                   4                72
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   0               168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(247) Variable = C11ORF9 MUTATION ANALYSIS
D247V1, survival
                   sevent
clus2                 0   1
  C11ORF9 MUTATED     4   1
  C11ORF9 WILD-TYPE 177  79
  C11ORF9 MUTATED C11ORF9 WILD-TYPE 
                5               256 
  C11ORF9 MUTATED C11ORF9 WILD-TYPE 
                1                79 
$`C11ORF9 MUTATED`
TCGA-BR-6457 TCGA-BR-6566 TCGA-BR-7851 TCGA-BR-8363 TCGA-HU-A4GT 
       13.68        32.78        12.43         0.26         6.51 

$`C11ORF9 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        17.29        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       19.50        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  C11ORF9 MUTATED C11ORF9 WILD-TYPE 
             0.26              0.00 
  C11ORF9 MUTATED C11ORF9 WILD-TYPE 
            32.78            105.07 
  C11ORF9 MUTATED C11ORF9 WILD-TYPE 
            12.43             12.64 
[1] "0.3 - 32.8 (12.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.5"
D247V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C11ORF9 MUTATED         0        0        1        1         3         1
  C11ORF9 WILD-TYPE       1        9       26       25        28        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C11ORF9 MUTATED           0          0          0          0        1
  C11ORF9 WILD-TYPE         3         49         36         24       23
D247V3, multiclass
            clus
vv           C11ORF9 MUTATED C11ORF9 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 1                25
  STAGE IIA                3                28
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               0                36
  STAGE IIIC               0                24
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C11ORF9 MUTATED     0   2   3   2
  C11ORF9 WILD-TYPE  11  70 119  73
D247V4, multiclass
    clus
vv   C11ORF9 MUTATED C11ORF9 WILD-TYPE
  T1               0                11
  T2               2                70
  T3               3               119
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  C11ORF9 MUTATED    5  2  1  0
  C11ORF9 WILD-TYPE 88 79 49 53
D247V5, multiclass
    clus
vv   C11ORF9 MUTATED C11ORF9 WILD-TYPE
  N0               5                88
  N1               2                79
  N2               1                49
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D247V6, binary
                   cls
clus                  0   1
  C11ORF9 MUTATED     8   0
  C11ORF9 WILD-TYPE 249  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C11ORF9 MUTATED      8    0
  C11ORF9 WILD-TYPE  249   18
   clus
vv  C11ORF9 MUTATED C11ORF9 WILD-TYPE
  0               8               249
  1               0                18
[1] 2 2
[1] FALSE
D247V7, binary
                   cls
clus                  0   1
  C11ORF9 MUTATED     5   3
  C11ORF9 WILD-TYPE 105 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C11ORF9 MUTATED      5    3
  C11ORF9 WILD-TYPE  105  176
        clus
vv       C11ORF9 MUTATED C11ORF9 WILD-TYPE
  FEMALE               5               105
  MALE                 3               176
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C11ORF9 MUTATED                                       0
  C11ORF9 WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C11ORF9 MUTATED                                                        5
  C11ORF9 WILD-TYPE                                                    130
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C11ORF9 MUTATED                                                                   1
  C11ORF9 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C11ORF9 MUTATED                                                  1
  C11ORF9 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C11ORF9 MUTATED                                                          1
  C11ORF9 WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C11ORF9 MUTATED                                                           0
  C11ORF9 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C11ORF9 MUTATED                                          0
  C11ORF9 WILD-TYPE                                        3
D247V8, multiclass
                                                                   clus
vv                                                                  C11ORF9 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  C11ORF9 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D247V9, binary
                   cls
clus                  0   1
  C11ORF9 MUTATED     1   7
  C11ORF9 WILD-TYPE   4 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C11ORF9 MUTATED      1    7
  C11ORF9 WILD-TYPE    4  277
     clus
vv    C11ORF9 MUTATED C11ORF9 WILD-TYPE
  NO                1                 4
  YES               7               277
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C11ORF9 MUTATED     6   0   0   2
  C11ORF9 WILD-TYPE 221  10  10  22
D247V10, multiclass
    clus
vv   C11ORF9 MUTATED C11ORF9 WILD-TYPE
  R0               6               221
  R1               0                10
  R2               0                10
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D247V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C11ORF9 MUTATED       1                         0     6
  C11ORF9 WILD-TYPE    75                         4   162
D247V12, multiclass
                           clus
vv                          C11ORF9 MUTATED C11ORF9 WILD-TYPE
  ASIAN                                   1                75
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   6               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(248) Variable = KIAA0195 MUTATION ANALYSIS
D248V1, survival
                    sevent
clus2                  0   1
  KIAA0195 MUTATED    10   3
  KIAA0195 WILD-TYPE 171  77
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                13                248 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                 3                 77 
$`KIAA0195 MUTATED`
TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-A4QL TCGA-CD-8536 
       12.26         4.31        19.17         1.12        11.57         0.10 
TCGA-CD-A4MG TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4GT 
        6.58        11.08        26.47        11.41         0.10         6.51 
TCGA-HU-A4GU 
        6.25 

$`KIAA0195 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
        0.95        26.33        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        13.64         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 
        0.13         0.16         0.10         0.10         0.13         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GX 
       22.75        25.81        11.77        29.98         8.98        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
               0.1                0.0 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
             26.47             105.07 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
             6.580             12.805 
[1] "0.1 - 26.5 (6.6)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.2"
D248V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0195 MUTATED         1        0        2        1         4         3
  KIAA0195 WILD-TYPE       0        9       25       25        27        41
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0195 MUTATED           0          1          1          2        0
  KIAA0195 WILD-TYPE         3         48         35         22       24
D248V3, multiclass
            clus
vv           KIAA0195 MUTATED KIAA0195 WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                  0                  9
  STAGE IB                  2                 25
  STAGE II                  1                 25
  STAGE IIA                 4                 27
  STAGE IIB                 3                 41
  STAGE III                 0                  3
  STAGE IIIA                1                 48
  STAGE IIIB                1                 35
  STAGE IIIC                2                 22
  STAGE IV                  0                 24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0195 MUTATED     1   2   7   5
  KIAA0195 WILD-TYPE  10  70 115  70
D248V4, multiclass
    clus
vv   KIAA0195 MUTATED KIAA0195 WILD-TYPE
  T1                1                 10
  T2                2                 70
  T3                7                115
  T4                5                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  KIAA0195 MUTATED   10  2  1  2
  KIAA0195 WILD-TYPE 83 79 49 51
D248V5, multiclass
    clus
vv   KIAA0195 MUTATED KIAA0195 WILD-TYPE
  N0               10                 83
  N1                2                 79
  N2                1                 49
  N3                2                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D248V6, binary
                    cls
clus                   0   1
  KIAA0195 MUTATED    14   0
  KIAA0195 WILD-TYPE 243  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0195 MUTATED     14    0
  KIAA0195 WILD-TYPE  243   18
   clus
vv  KIAA0195 MUTATED KIAA0195 WILD-TYPE
  0               14                243
  1                0                 18
[1] 2 2
[1] FALSE
D248V7, binary
                    cls
clus                   0   1
  KIAA0195 MUTATED     9   7
  KIAA0195 WILD-TYPE 101 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0195 MUTATED      9    7
  KIAA0195 WILD-TYPE  101  172
        clus
vv       KIAA0195 MUTATED KIAA0195 WILD-TYPE
  FEMALE                9                101
  MALE                  7                172
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KIAA0195 MUTATED                                       3
  KIAA0195 WILD-TYPE                                    47
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA0195 MUTATED                                                       10
  KIAA0195 WILD-TYPE                                                    125
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA0195 MUTATED                                                                   0
  KIAA0195 WILD-TYPE                                                                40
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KIAA0195 MUTATED                                                  2
  KIAA0195 WILD-TYPE                                               36
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KIAA0195 MUTATED                                                          0
  KIAA0195 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KIAA0195 MUTATED                                                           0
  KIAA0195 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KIAA0195 MUTATED                                          1
  KIAA0195 WILD-TYPE                                        2
D248V8, multiclass
                                                                   clus
vv                                                                  KIAA0195 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  KIAA0195 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D248V9, binary
                    cls
clus                   0   1
  KIAA0195 MUTATED     0  16
  KIAA0195 WILD-TYPE   5 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0195 MUTATED      0   16
  KIAA0195 WILD-TYPE    5  268
     clus
vv    KIAA0195 MUTATED KIAA0195 WILD-TYPE
  NO                 0                  5
  YES               16                268
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0195 MUTATED    13   0   0   2
  KIAA0195 WILD-TYPE 214  10  10  22
D248V10, multiclass
    clus
vv   KIAA0195 MUTATED KIAA0195 WILD-TYPE
  R0               13                214
  R1                0                 10
  R2                0                 10
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D248V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA0195 MUTATED       6                         2     8
  KIAA0195 WILD-TYPE    70                         2   160
D248V12, multiclass
                           clus
vv                          KIAA0195 MUTATED KIAA0195 WILD-TYPE
  ASIAN                                    6                 70
  BLACK OR AFRICAN AMERICAN                2                  2
  WHITE                                    8                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(249) Variable = TRIP10 MUTATION ANALYSIS
D249V1, survival
                  sevent
clus2                0   1
  TRIP10 MUTATED     7   1
  TRIP10 WILD-TYPE 174  79
  TRIP10 MUTATED TRIP10 WILD-TYPE 
               8              253 
  TRIP10 MUTATED TRIP10 WILD-TYPE 
               1               79 
$`TRIP10 MUTATED`
TCGA-BR-6452 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-FP-A4BE TCGA-HU-A4GT 
       34.68         6.02       105.07        28.96        11.08         6.51 
TCGA-HU-A4GU TCGA-HU-A4H3 
        6.25        19.36 

$`TRIP10 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99         0.99        12.03        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX 
       25.81        11.77        29.98         8.98         0.10        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  TRIP10 MUTATED TRIP10 WILD-TYPE 
            6.02             0.00 
  TRIP10 MUTATED TRIP10 WILD-TYPE 
          105.07            79.07 
  TRIP10 MUTATED TRIP10 WILD-TYPE 
           15.22            12.62 
[1] "6.0 - 105.1 (15.2)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "4.6"
D249V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRIP10 MUTATED         0        1        0        1         3         1
  TRIP10 WILD-TYPE       1        8       27       25        28        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIP10 MUTATED           0          0          0          1        1
  TRIP10 WILD-TYPE         3         49         36         23       23
D249V3, multiclass
            clus
vv           TRIP10 MUTATED TRIP10 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                0               27
  STAGE II                1               25
  STAGE IIA               3               28
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIP10 MUTATED     1   1   4   2
  TRIP10 WILD-TYPE  10  71 118  73
D249V4, multiclass
    clus
vv   TRIP10 MUTATED TRIP10 WILD-TYPE
  T1              1               10
  T2              1               71
  T3              4              118
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  TRIP10 MUTATED    4  3  0  1
  TRIP10 WILD-TYPE 89 78 50 52
D249V5, multiclass
    clus
vv   TRIP10 MUTATED TRIP10 WILD-TYPE
  N0              4               89
  N1              3               78
  N2              0               50
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D249V6, binary
                  cls
clus                 0   1
  TRIP10 MUTATED     8   0
  TRIP10 WILD-TYPE 249  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP10 MUTATED      8    0
  TRIP10 WILD-TYPE  249   18
   clus
vv  TRIP10 MUTATED TRIP10 WILD-TYPE
  0              8              249
  1              0               18
[1] 2 2
[1] FALSE
D249V7, binary
                  cls
clus                 0   1
  TRIP10 MUTATED     3   5
  TRIP10 WILD-TYPE 107 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP10 MUTATED      3    5
  TRIP10 WILD-TYPE  107  174
        clus
vv       TRIP10 MUTATED TRIP10 WILD-TYPE
  FEMALE              3              107
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TRIP10 MUTATED                                       2
  TRIP10 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TRIP10 MUTATED                                                        3
  TRIP10 WILD-TYPE                                                    132
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TRIP10 MUTATED                                                                   2
  TRIP10 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TRIP10 MUTATED                                                  1
  TRIP10 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TRIP10 MUTATED                                                          0
  TRIP10 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TRIP10 MUTATED                                                           0
  TRIP10 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TRIP10 MUTATED                                          0
  TRIP10 WILD-TYPE                                        3
D249V8, multiclass
                                                                   clus
vv                                                                  TRIP10 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  TRIP10 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D249V9, binary
                  cls
clus                 0   1
  TRIP10 MUTATED     0   8
  TRIP10 WILD-TYPE   5 276
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP10 MUTATED      0    8
  TRIP10 WILD-TYPE    5  276
     clus
vv    TRIP10 MUTATED TRIP10 WILD-TYPE
  NO               0                5
  YES              8              276
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRIP10 MUTATED     8   0   0   0
  TRIP10 WILD-TYPE 219  10  10  24
D249V10, multiclass
    clus
vv   TRIP10 MUTATED TRIP10 WILD-TYPE
  R0              8              219
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D249V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TRIP10 MUTATED       3                         1     1
  TRIP10 WILD-TYPE    73                         3   167
D249V12, multiclass
                           clus
vv                          TRIP10 MUTATED TRIP10 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  1              167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(250) Variable = PRKAB1 MUTATION ANALYSIS
D250V1, survival
                  sevent
clus2                0   1
  PRKAB1 MUTATED     2   2
  PRKAB1 WILD-TYPE 179  78
  PRKAB1 MUTATED PRKAB1 WILD-TYPE 
               4              257 
  PRKAB1 MUTATED PRKAB1 WILD-TYPE 
               2               78 
$`PRKAB1 MUTATED`
TCGA-BR-8289 TCGA-BR-8485 TCGA-BR-8591 TCGA-HU-A4GQ 
        2.66         9.21        13.45         0.10 

$`PRKAB1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
       20.55         8.05        12.95        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  PRKAB1 MUTATED PRKAB1 WILD-TYPE 
             0.1              0.0 
  PRKAB1 MUTATED PRKAB1 WILD-TYPE 
           13.45           105.07 
  PRKAB1 MUTATED PRKAB1 WILD-TYPE 
           5.935           12.660 
[1] "0.1 - 13.4 (5.9)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "4"  
D250V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRKAB1 MUTATED         0        0        0        0         0         0
  PRKAB1 WILD-TYPE       1        9       27       26        31        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRKAB1 MUTATED           0          0          0          3        2
  PRKAB1 WILD-TYPE         3         49         36         21       22
D250V3, multiclass
            clus
vv           PRKAB1 MUTATED PRKAB1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               0               31
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              3               21
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PRKAB1 MUTATED     1   0   0   5
  PRKAB1 WILD-TYPE  10  72 122  70
D250V4, multiclass
    clus
vv   PRKAB1 MUTATED PRKAB1 WILD-TYPE
  T1              1               10
  T2              0               72
  T3              0              122
  T4              5               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  PRKAB1 MUTATED    0  0  2  3
  PRKAB1 WILD-TYPE 93 81 48 50
D250V5, multiclass
    clus
vv   PRKAB1 MUTATED PRKAB1 WILD-TYPE
  N0              0               93
  N1              0               81
  N2              2               48
  N3              3               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D250V6, binary
                  cls
clus                 0   1
  PRKAB1 MUTATED     5   1
  PRKAB1 WILD-TYPE 252  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAB1 MUTATED      5    1
  PRKAB1 WILD-TYPE  252   17
   clus
vv  PRKAB1 MUTATED PRKAB1 WILD-TYPE
  0              5              252
  1              1               17
[1] 2 2
[1] FALSE
D250V7, binary
                  cls
clus                 0   1
  PRKAB1 MUTATED     3   3
  PRKAB1 WILD-TYPE 107 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAB1 MUTATED      3    3
  PRKAB1 WILD-TYPE  107  176
        clus
vv       PRKAB1 MUTATED PRKAB1 WILD-TYPE
  FEMALE              3              107
  MALE                3              176
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PRKAB1 MUTATED                                       0
  PRKAB1 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PRKAB1 MUTATED                                                        4
  PRKAB1 WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PRKAB1 MUTATED                                                                   1
  PRKAB1 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PRKAB1 MUTATED                                                  1
  PRKAB1 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PRKAB1 MUTATED                                                          0
  PRKAB1 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PRKAB1 MUTATED                                                           0
  PRKAB1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PRKAB1 MUTATED                                          0
  PRKAB1 WILD-TYPE                                        3
D250V8, multiclass
                                                                   clus
vv                                                                  PRKAB1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  PRKAB1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D250V9, binary
                  cls
clus                 0   1
  PRKAB1 MUTATED     0   6
  PRKAB1 WILD-TYPE   5 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAB1 MUTATED      0    6
  PRKAB1 WILD-TYPE    5  278
     clus
vv    PRKAB1 MUTATED PRKAB1 WILD-TYPE
  NO               0                5
  YES              6              278
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PRKAB1 MUTATED     4   0   0   2
  PRKAB1 WILD-TYPE 223  10  10  22
D250V10, multiclass
    clus
vv   PRKAB1 MUTATED PRKAB1 WILD-TYPE
  R0              4              223
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D250V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRKAB1 MUTATED       1                         0     5
  PRKAB1 WILD-TYPE    75                         4   163
D250V12, multiclass
                           clus
vv                          PRKAB1 MUTATED PRKAB1 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  5              163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(251) Variable = FAM193A MUTATION ANALYSIS
D251V1, survival
                   sevent
clus2                 0   1
  FAM193A MUTATED     6   6
  FAM193A WILD-TYPE 175  74
  FAM193A MUTATED FAM193A WILD-TYPE 
               12               249 
  FAM193A MUTATED FAM193A WILD-TYPE 
                6                74 
$`FAM193A MUTATED`
TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-7851 TCGA-BR-8059 TCGA-BR-8680 TCGA-CD-A4MH 
       30.90         6.61        12.43        14.43        15.81        12.20 
TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4465 TCGA-D7-6527 TCGA-HU-A4G9 TCGA-HU-A4H8 
       12.62         1.02         9.01        10.26        24.20         8.88 

$`FAM193A WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       18.35         6.18         9.57        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 
        3.45         9.07        12.76        18.71        17.49         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
        0.10        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       19.07        12.03         0.00        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        11.84         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  FAM193A MUTATED FAM193A WILD-TYPE 
             1.02              0.00 
  FAM193A MUTATED FAM193A WILD-TYPE 
            30.90            105.07 
  FAM193A MUTATED FAM193A WILD-TYPE 
           12.315            12.760 
[1] "1.0 - 30.9 (12.3)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.8"
D251V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM193A MUTATED         0        1        3        2         1         1
  FAM193A WILD-TYPE       1        8       24       24        30        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM193A MUTATED           2          1          0          0        3
  FAM193A WILD-TYPE         1         48         36         24       21
D251V3, multiclass
            clus
vv           FAM193A MUTATED FAM193A WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 1                 8
  STAGE IB                 3                24
  STAGE II                 2                24
  STAGE IIA                1                30
  STAGE IIB                1                43
  STAGE III                2                 1
  STAGE IIIA               1                48
  STAGE IIIB               0                36
  STAGE IIIC               0                24
  STAGE IV                 3                21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM193A MUTATED     2   6   2   5
  FAM193A WILD-TYPE   9  66 120  70
D251V4, multiclass
    clus
vv   FAM193A MUTATED FAM193A WILD-TYPE
  T1               2                 9
  T2               6                66
  T3               2               120
  T4               5                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  FAM193A MUTATED    6  5  2  1
  FAM193A WILD-TYPE 87 76 48 52
D251V5, multiclass
    clus
vv   FAM193A MUTATED FAM193A WILD-TYPE
  N0               6                87
  N1               5                76
  N2               2                48
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D251V6, binary
                   cls
clus                  0   1
  FAM193A MUTATED    12   3
  FAM193A WILD-TYPE 245  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM193A MUTATED     12    3
  FAM193A WILD-TYPE  245   15
   clus
vv  FAM193A MUTATED FAM193A WILD-TYPE
  0              12               245
  1               3                15
[1] 2 2
[1] FALSE
D251V7, binary
                   cls
clus                  0   1
  FAM193A MUTATED     6   9
  FAM193A WILD-TYPE 104 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM193A MUTATED      6    9
  FAM193A WILD-TYPE  104  170
        clus
vv       FAM193A MUTATED FAM193A WILD-TYPE
  FEMALE               6               104
  MALE                 9               170
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FAM193A MUTATED                                       1
  FAM193A WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAM193A MUTATED                                                        6
  FAM193A WILD-TYPE                                                    129
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAM193A MUTATED                                                                   3
  FAM193A WILD-TYPE                                                                37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FAM193A MUTATED                                                  3
  FAM193A WILD-TYPE                                               35
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FAM193A MUTATED                                                          1
  FAM193A WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FAM193A MUTATED                                                           1
  FAM193A WILD-TYPE                                                         5
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FAM193A MUTATED                                          0
  FAM193A WILD-TYPE                                        3
D251V8, multiclass
                                                                   clus
vv                                                                  FAM193A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  FAM193A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D251V9, binary
                   cls
clus                  0   1
  FAM193A MUTATED     1  14
  FAM193A WILD-TYPE   4 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM193A MUTATED      1   14
  FAM193A WILD-TYPE    4  270
     clus
vv    FAM193A MUTATED FAM193A WILD-TYPE
  NO                1                 4
  YES              14               270
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM193A MUTATED     8   0   2   3
  FAM193A WILD-TYPE 219  10   8  21
D251V10, multiclass
    clus
vv   FAM193A MUTATED FAM193A WILD-TYPE
  R0               8               219
  R1               0                10
  R2               2                 8
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D251V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM193A MUTATED       5                         0     6
  FAM193A WILD-TYPE    71                         4   162
D251V12, multiclass
                           clus
vv                          FAM193A MUTATED FAM193A WILD-TYPE
  ASIAN                                   5                71
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   6               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(252) Variable = AXIN2 MUTATION ANALYSIS
D252V1, survival
                 sevent
clus2               0   1
  AXIN2 MUTATED    10   4
  AXIN2 WILD-TYPE 171  76
  AXIN2 MUTATED AXIN2 WILD-TYPE 
             14             247 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
              4              76 
$`AXIN2 MUTATED`
TCGA-BR-6452 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8487 
       34.68        12.43         9.07        12.26        19.50         1.12 
TCGA-BR-A4CQ TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-4465 
       22.26        11.57         0.10         6.58        15.95         9.01 
TCGA-CG-5723 TCGA-D7-A4YV 
      105.07         5.92 

$`AXIN2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       28.73         3.45        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
       16.31         2.20        15.58         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       10.68        12.56        13.87         7.53         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         6.02         0.99        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  AXIN2 MUTATED AXIN2 WILD-TYPE 
            0.1             0.0 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
         105.07           79.07 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
         11.915          12.760 
[1] "0.1 - 105.1 (11.9)" "0.0 - 79.1 (12.8)" 
[1] "hr=" "1.3"
D252V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AXIN2 MUTATED         0        0        0        3         3         3
  AXIN2 WILD-TYPE       1        9       27       23        28        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AXIN2 MUTATED           0          2          1          1        2
  AXIN2 WILD-TYPE         3         47         35         23       22
D252V3, multiclass
            clus
vv           AXIN2 MUTATED AXIN2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               3              23
  STAGE IIA              3              28
  STAGE IIB              3              41
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AXIN2 MUTATED     0   2   7   6
  AXIN2 WILD-TYPE  11  70 115  69
D252V4, multiclass
    clus
vv   AXIN2 MUTATED AXIN2 WILD-TYPE
  T1             0              11
  T2             2              70
  T3             7             115
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  AXIN2 MUTATED    7  4  1  3
  AXIN2 WILD-TYPE 86 77 49 50
D252V5, multiclass
    clus
vv   AXIN2 MUTATED AXIN2 WILD-TYPE
  N0             7              86
  N1             4              77
  N2             1              49
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D252V6, binary
                 cls
clus                0   1
  AXIN2 MUTATED    13   2
  AXIN2 WILD-TYPE 244  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN2 MUTATED     13    2
  AXIN2 WILD-TYPE  244   16
   clus
vv  AXIN2 MUTATED AXIN2 WILD-TYPE
  0            13             244
  1             2              16
[1] 2 2
[1] FALSE
D252V7, binary
                 cls
clus                0   1
  AXIN2 MUTATED     9   6
  AXIN2 WILD-TYPE 101 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN2 MUTATED      9    6
  AXIN2 WILD-TYPE  101  173
        clus
vv       AXIN2 MUTATED AXIN2 WILD-TYPE
  FEMALE             9             101
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AXIN2 MUTATED                                       2
  AXIN2 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AXIN2 MUTATED                                                       10
  AXIN2 WILD-TYPE                                                    125
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AXIN2 MUTATED                                                                   2
  AXIN2 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AXIN2 MUTATED                                                  1
  AXIN2 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AXIN2 MUTATED                                                          0
  AXIN2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AXIN2 MUTATED                                                           0
  AXIN2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AXIN2 MUTATED                                          0
  AXIN2 WILD-TYPE                                        3
D252V8, multiclass
                                                                   clus
vv                                                                  AXIN2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  AXIN2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D252V9, binary
                 cls
clus                0   1
  AXIN2 MUTATED     0  15
  AXIN2 WILD-TYPE   5 269
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN2 MUTATED      0   15
  AXIN2 WILD-TYPE    5  269
     clus
vv    AXIN2 MUTATED AXIN2 WILD-TYPE
  NO              0               5
  YES            15             269
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AXIN2 MUTATED    12   0   1   1
  AXIN2 WILD-TYPE 215  10   9  23
D252V10, multiclass
    clus
vv   AXIN2 MUTATED AXIN2 WILD-TYPE
  R0            12             215
  R1             0              10
  R2             1               9
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D252V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AXIN2 MUTATED       2                         0    10
  AXIN2 WILD-TYPE    74                         4   158
D252V12, multiclass
                           clus
vv                          AXIN2 MUTATED AXIN2 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                10             158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(253) Variable = CYP27B1 MUTATION ANALYSIS
D253V1, survival
                   sevent
clus2                 0   1
  CYP27B1 MUTATED     4   1
  CYP27B1 WILD-TYPE 177  79
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
                5               256 
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
                1                79 
$`CYP27B1 MUTATED`
TCGA-BR-8059 TCGA-BR-8680 TCGA-CG-5728 TCGA-HU-A4GX TCGA-HU-A4H4 
       14.43        15.81        65.10        10.19        23.84 

$`CYP27B1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       19.36        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
            10.19              0.00 
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
            65.10            105.07 
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
           15.810            12.575 
[1] "10.2 - 65.1 (15.8)" "0.0 - 105.1 (12.6)"
[1] "hr=" "2.5"
D253V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CYP27B1 MUTATED         0        0        1        0         0         1
  CYP27B1 WILD-TYPE       1        9       26       26        31        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP27B1 MUTATED           1          0          0          1        1
  CYP27B1 WILD-TYPE         2         49         36         23       23
D253V3, multiclass
            clus
vv           CYP27B1 MUTATED CYP27B1 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 0                26
  STAGE IIA                0                31
  STAGE IIB                1                43
  STAGE III                1                 2
  STAGE IIIA               0                49
  STAGE IIIB               0                36
  STAGE IIIC               1                23
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CYP27B1 MUTATED     0   2   0   3
  CYP27B1 WILD-TYPE  11  70 122  72
D253V4, multiclass
    clus
vv   CYP27B1 MUTATED CYP27B1 WILD-TYPE
  T1               0                11
  T2               2                70
  T3               0               122
  T4               3                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  CYP27B1 MUTATED    1  1  3  0
  CYP27B1 WILD-TYPE 92 80 47 53
D253V5, multiclass
    clus
vv   CYP27B1 MUTATED CYP27B1 WILD-TYPE
  N0               1                92
  N1               1                80
  N2               3                47
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D253V6, binary
                   cls
clus                  0   1
  CYP27B1 MUTATED     4   1
  CYP27B1 WILD-TYPE 253  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP27B1 MUTATED      4    1
  CYP27B1 WILD-TYPE  253   17
   clus
vv  CYP27B1 MUTATED CYP27B1 WILD-TYPE
  0               4               253
  1               1                17
[1] 2 2
[1] FALSE
D253V7, binary
                   cls
clus                  0   1
  CYP27B1 MUTATED     3   2
  CYP27B1 WILD-TYPE 107 177
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP27B1 MUTATED      3    2
  CYP27B1 WILD-TYPE  107  177
        clus
vv       CYP27B1 MUTATED CYP27B1 WILD-TYPE
  FEMALE               3               107
  MALE                 2               177
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CYP27B1 MUTATED                                       1
  CYP27B1 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CYP27B1 MUTATED                                                        0
  CYP27B1 WILD-TYPE                                                    135
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CYP27B1 MUTATED                                                                   2
  CYP27B1 WILD-TYPE                                                                38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CYP27B1 MUTATED                                                  2
  CYP27B1 WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CYP27B1 MUTATED                                                          0
  CYP27B1 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CYP27B1 MUTATED                                                           0
  CYP27B1 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CYP27B1 MUTATED                                          0
  CYP27B1 WILD-TYPE                                        3
D253V8, multiclass
                                                                   clus
vv                                                                  CYP27B1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          0
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  CYP27B1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          135
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D253V9, binary
                   cls
clus                  0   1
  CYP27B1 MUTATED     0   5
  CYP27B1 WILD-TYPE   5 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP27B1 MUTATED      0    5
  CYP27B1 WILD-TYPE    5  279
     clus
vv    CYP27B1 MUTATED CYP27B1 WILD-TYPE
  NO                0                 5
  YES               5               279
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CYP27B1 MUTATED     5   0   0   0
  CYP27B1 WILD-TYPE 222  10  10  24
D253V10, multiclass
    clus
vv   CYP27B1 MUTATED CYP27B1 WILD-TYPE
  R0               5               222
  R1               0                10
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D253V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CYP27B1 MUTATED       3                         0     1
  CYP27B1 WILD-TYPE    73                         4   167
D253V12, multiclass
                           clus
vv                          CYP27B1 MUTATED CYP27B1 WILD-TYPE
  ASIAN                                   3                73
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   1               167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(254) Variable = C12ORF51 MUTATION ANALYSIS
D254V1, survival
                    sevent
clus2                  0   1
  C12ORF51 MUTATED    18   6
  C12ORF51 WILD-TYPE 163  74
  C12ORF51 MUTATED C12ORF51 WILD-TYPE 
                24                237 
  C12ORF51 MUTATED C12ORF51 WILD-TYPE 
                 6                 74 
$`C12ORF51 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8360 
        6.97        34.68        30.90        23.93        12.26         6.18 
TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-CD-A4MI 
        0.26        19.17        11.54        15.81        16.44         0.10 
TCGA-CG-4305 TCGA-CG-4437 TCGA-CG-5724 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-A4YV 
       15.95         8.05        12.03        65.10        21.07         5.92 
TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H3 
       11.41        11.84        24.20         0.10        10.19        19.36 

$`C12ORF51 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 
       31.20        32.94        12.82         9.21        24.76        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        20.55         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
        2.20        15.58         7.40        19.50        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8683 TCGA-BR-8686 
       13.45         6.28         7.53         0.49         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       12.20        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        7.99        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        6.02         0.99       105.07        28.96        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.51         6.25         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  C12ORF51 MUTATED C12ORF51 WILD-TYPE 
               0.1                0.0 
  C12ORF51 MUTATED C12ORF51 WILD-TYPE 
             65.10             105.07 
  C12ORF51 MUTATED C12ORF51 WILD-TYPE 
            12.145             12.660 
[1] "0.1 - 65.1 (12.1)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.4"
D254V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C12ORF51 MUTATED         1        1        4        2         2         5
  C12ORF51 WILD-TYPE       0        8       23       24        29        39
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C12ORF51 MUTATED           0          4          1          5        3
  C12ORF51 WILD-TYPE         3         45         35         19       21
D254V3, multiclass
            clus
vv           C12ORF51 MUTATED C12ORF51 WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                  1                  8
  STAGE IB                  4                 23
  STAGE II                  2                 24
  STAGE IIA                 2                 29
  STAGE IIB                 5                 39
  STAGE III                 0                  3
  STAGE IIIA                4                 45
  STAGE IIIB                1                 35
  STAGE IIIC                5                 19
  STAGE IV                  3                 21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C12ORF51 MUTATED     2   7   8  11
  C12ORF51 WILD-TYPE   9  65 114  64
D254V4, multiclass
    clus
vv   C12ORF51 MUTATED C12ORF51 WILD-TYPE
  T1                2                  9
  T2                7                 65
  T3                8                114
  T4               11                 64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  C12ORF51 MUTATED   11  8  6  4
  C12ORF51 WILD-TYPE 82 73 44 49
D254V5, multiclass
    clus
vv   C12ORF51 MUTATED C12ORF51 WILD-TYPE
  N0               11                 82
  N1                8                 73
  N2                6                 44
  N3                4                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D254V6, binary
                    cls
clus                   0   1
  C12ORF51 MUTATED    26   2
  C12ORF51 WILD-TYPE 231  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF51 MUTATED     26    2
  C12ORF51 WILD-TYPE  231   16
   clus
vv  C12ORF51 MUTATED C12ORF51 WILD-TYPE
  0               26                231
  1                2                 16
[1] 2 2
[1] FALSE
D254V7, binary
                    cls
clus                   0   1
  C12ORF51 MUTATED    15  15
  C12ORF51 WILD-TYPE  95 164
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF51 MUTATED     15   15
  C12ORF51 WILD-TYPE   95  164
        clus
vv       C12ORF51 MUTATED C12ORF51 WILD-TYPE
  FEMALE               15                 95
  MALE                 15                164
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C12ORF51 MUTATED                                       6
  C12ORF51 WILD-TYPE                                    44
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C12ORF51 MUTATED                                                       15
  C12ORF51 WILD-TYPE                                                    120
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C12ORF51 MUTATED                                                                   4
  C12ORF51 WILD-TYPE                                                                36
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C12ORF51 MUTATED                                                  4
  C12ORF51 WILD-TYPE                                               34
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C12ORF51 MUTATED                                                          1
  C12ORF51 WILD-TYPE                                                       15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C12ORF51 MUTATED                                                           0
  C12ORF51 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C12ORF51 MUTATED                                          0
  C12ORF51 WILD-TYPE                                        3
D254V8, multiclass
                                                                   clus
vv                                                                  C12ORF51 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          15
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  C12ORF51 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             44
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           120
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D254V9, binary
                    cls
clus                   0   1
  C12ORF51 MUTATED     0  30
  C12ORF51 WILD-TYPE   5 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF51 MUTATED      0   30
  C12ORF51 WILD-TYPE    5  254
     clus
vv    C12ORF51 MUTATED C12ORF51 WILD-TYPE
  NO                 0                  5
  YES               30                254
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C12ORF51 MUTATED    22   0   1   5
  C12ORF51 WILD-TYPE 205  10   9  19
D254V10, multiclass
    clus
vv   C12ORF51 MUTATED C12ORF51 WILD-TYPE
  R0               22                205
  R1                0                 10
  R2                1                  9
  RX                5                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D254V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C12ORF51 MUTATED       9                         1    14
  C12ORF51 WILD-TYPE    67                         3   154
D254V12, multiclass
                           clus
vv                          C12ORF51 MUTATED C12ORF51 WILD-TYPE
  ASIAN                                    9                 67
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                   14                154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(255) Variable = UBQLN2 MUTATION ANALYSIS
D255V1, survival
                  sevent
clus2                0   1
  UBQLN2 MUTATED     4   0
  UBQLN2 WILD-TYPE 177  80
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
               4              257 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
               0               80 
$`UBQLN2 MUTATED`
TCGA-BR-6802 TCGA-CD-8536 TCGA-CG-5723 TCGA-HU-A4G9 
       30.90         0.10       105.07        24.20 

$`UBQLN2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.13         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        11.84         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
             0.1              0.0 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
          105.07            79.07 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
           27.55            12.59 
[1] "0.1 - 105.1 (27.5)" "0.0 - 79.1 (12.6)" 
[1] "hr="     "2.9e+07"
D255V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UBQLN2 MUTATED         0        1        0        2         0         0
  UBQLN2 WILD-TYPE       1        8       27       24        31        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UBQLN2 MUTATED           0          2          0          0        0
  UBQLN2 WILD-TYPE         3         47         36         24       24
D255V3, multiclass
            clus
vv           UBQLN2 MUTATED UBQLN2 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                0               27
  STAGE II                2               24
  STAGE IIA               0               31
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  UBQLN2 MUTATED     1   1   2   1
  UBQLN2 WILD-TYPE  10  71 120  74
D255V4, multiclass
    clus
vv   UBQLN2 MUTATED UBQLN2 WILD-TYPE
  T1              1               10
  T2              1               71
  T3              2              120
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  UBQLN2 MUTATED    3  1  1  0
  UBQLN2 WILD-TYPE 90 80 49 53
D255V5, multiclass
    clus
vv   UBQLN2 MUTATED UBQLN2 WILD-TYPE
  N0              3               90
  N1              1               80
  N2              1               49
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D255V6, binary
                  cls
clus                 0   1
  UBQLN2 MUTATED     5   0
  UBQLN2 WILD-TYPE 252  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBQLN2 MUTATED      5    0
  UBQLN2 WILD-TYPE  252   18
   clus
vv  UBQLN2 MUTATED UBQLN2 WILD-TYPE
  0              5              252
  1              0               18
[1] 2 2
[1] FALSE
D255V7, binary
                  cls
clus                 0   1
  UBQLN2 MUTATED     2   3
  UBQLN2 WILD-TYPE 108 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBQLN2 MUTATED      2    3
  UBQLN2 WILD-TYPE  108  176
        clus
vv       UBQLN2 MUTATED UBQLN2 WILD-TYPE
  FEMALE              2              108
  MALE                3              176
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  UBQLN2 MUTATED                                       0
  UBQLN2 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  UBQLN2 MUTATED                                                        4
  UBQLN2 WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  UBQLN2 MUTATED                                                                   0
  UBQLN2 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  UBQLN2 MUTATED                                                  1
  UBQLN2 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  UBQLN2 MUTATED                                                          0
  UBQLN2 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  UBQLN2 MUTATED                                                           0
  UBQLN2 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  UBQLN2 MUTATED                                          0
  UBQLN2 WILD-TYPE                                        3
D255V8, multiclass
                                                                   clus
vv                                                                  UBQLN2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  UBQLN2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D255V9, binary
                  cls
clus                 0   1
  UBQLN2 MUTATED     0   5
  UBQLN2 WILD-TYPE   5 279
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBQLN2 MUTATED      0    5
  UBQLN2 WILD-TYPE    5  279
     clus
vv    UBQLN2 MUTATED UBQLN2 WILD-TYPE
  NO               0                5
  YES              5              279
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  UBQLN2 MUTATED     4   0   0   1
  UBQLN2 WILD-TYPE 223  10  10  23
D255V10, multiclass
    clus
vv   UBQLN2 MUTATED UBQLN2 WILD-TYPE
  R0              4              223
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D255V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UBQLN2 MUTATED       2                         0     2
  UBQLN2 WILD-TYPE    74                         4   166
D255V12, multiclass
                           clus
vv                          UBQLN2 MUTATED UBQLN2 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  2              166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(256) Variable = PHACTR2 MUTATION ANALYSIS
D256V1, survival
                   sevent
clus2                 0   1
  PHACTR2 MUTATED    10   2
  PHACTR2 WILD-TYPE 171  78
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
               12               249 
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
                2                78 
$`PHACTR2 MUTATED`
TCGA-BR-7707 TCGA-BR-8373 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-8682 
       23.93        14.79         1.12        13.45        15.81        16.44 
TCGA-BR-A4PE TCGA-CD-A4MJ TCGA-CG-4306 TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4H8 
       20.42        12.62         1.02        11.41         0.10         8.88 

$`PHACTR2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       19.17         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
        9.21        20.22        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        7.53         0.49        11.54         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        11.77        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
              0.1               0.0 
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
            23.93            105.07 
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
           13.035            12.590 
[1] "0.1 - 23.9 (13.0)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.5"
D256V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PHACTR2 MUTATED         0        0        4        0         1         2
  PHACTR2 WILD-TYPE       1        9       23       26        30        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PHACTR2 MUTATED           0          1          0          2        3
  PHACTR2 WILD-TYPE         3         48         36         22       21
D256V3, multiclass
            clus
vv           PHACTR2 MUTATED PHACTR2 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 4                23
  STAGE II                 0                26
  STAGE IIA                1                30
  STAGE IIB                2                42
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               0                36
  STAGE IIIC               2                22
  STAGE IV                 3                21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PHACTR2 MUTATED     1   3   2   7
  PHACTR2 WILD-TYPE  10  69 120  68
D256V4, multiclass
    clus
vv   PHACTR2 MUTATED PHACTR2 WILD-TYPE
  T1               1                10
  T2               3                69
  T3               2               120
  T4               7                68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  PHACTR2 MUTATED    6  2  4  1
  PHACTR2 WILD-TYPE 87 79 46 52
D256V5, multiclass
    clus
vv   PHACTR2 MUTATED PHACTR2 WILD-TYPE
  N0               6                87
  N1               2                79
  N2               4                46
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D256V6, binary
                   cls
clus                  0   1
  PHACTR2 MUTATED    11   2
  PHACTR2 WILD-TYPE 246  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR2 MUTATED     11    2
  PHACTR2 WILD-TYPE  246   16
   clus
vv  PHACTR2 MUTATED PHACTR2 WILD-TYPE
  0              11               246
  1               2                16
[1] 2 2
[1] FALSE
D256V7, binary
                   cls
clus                  0   1
  PHACTR2 MUTATED     6   7
  PHACTR2 WILD-TYPE 104 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR2 MUTATED      6    7
  PHACTR2 WILD-TYPE  104  172
        clus
vv       PHACTR2 MUTATED PHACTR2 WILD-TYPE
  FEMALE               6               104
  MALE                 7               172
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PHACTR2 MUTATED                                       1
  PHACTR2 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PHACTR2 MUTATED                                                        7
  PHACTR2 WILD-TYPE                                                    128
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PHACTR2 MUTATED                                                                   1
  PHACTR2 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PHACTR2 MUTATED                                                  3
  PHACTR2 WILD-TYPE                                               35
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PHACTR2 MUTATED                                                          1
  PHACTR2 WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PHACTR2 MUTATED                                                           0
  PHACTR2 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PHACTR2 MUTATED                                          0
  PHACTR2 WILD-TYPE                                        3
D256V8, multiclass
                                                                   clus
vv                                                                  PHACTR2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  PHACTR2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D256V9, binary
                   cls
clus                  0   1
  PHACTR2 MUTATED     0  13
  PHACTR2 WILD-TYPE   5 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR2 MUTATED      0   13
  PHACTR2 WILD-TYPE    5  271
     clus
vv    PHACTR2 MUTATED PHACTR2 WILD-TYPE
  NO                0                 5
  YES              13               271
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PHACTR2 MUTATED    10   0   1   1
  PHACTR2 WILD-TYPE 217  10   9  23
D256V10, multiclass
    clus
vv   PHACTR2 MUTATED PHACTR2 WILD-TYPE
  R0              10               217
  R1               0                10
  R2               1                 9
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D256V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHACTR2 MUTATED       6                         0     6
  PHACTR2 WILD-TYPE    70                         4   162
D256V12, multiclass
                           clus
vv                          PHACTR2 MUTATED PHACTR2 WILD-TYPE
  ASIAN                                   6                70
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   6               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(257) Variable = ADNP2 MUTATION ANALYSIS
D257V1, survival
                 sevent
clus2               0   1
  ADNP2 MUTATED    15   2
  ADNP2 WILD-TYPE 166  78
  ADNP2 MUTATED ADNP2 WILD-TYPE 
             17             244 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
              2              78 
$`ADNP2 MUTATED`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7703 
       26.70        11.70         6.97        34.68        32.94        24.76 
TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8487 TCGA-CD-8536 TCGA-CG-4305 TCGA-CG-5726 
       12.26         6.18         1.12         0.10        15.95        28.96 
TCGA-D7-A4YY TCGA-F1-A448 TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H0 
       13.78        21.27         6.51        10.19         2.10 

$`ADNP2 WILD-TYPE`
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.61         4.64         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       12.82         9.21        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       15.16        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 
        8.98         0.10         6.25         0.26        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  ADNP2 MUTATED ADNP2 WILD-TYPE 
            0.1             0.0 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
          34.68          105.07 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
          12.26           12.64 
[1] "0.1 - 34.7 (12.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "3.1"
D257V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ADNP2 MUTATED         0        2        1        2         5         2
  ADNP2 WILD-TYPE       1        7       26       24        26        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADNP2 MUTATED           0          2          2          2        0
  ADNP2 WILD-TYPE         3         47         34         22       24
D257V3, multiclass
            clus
vv           ADNP2 MUTATED ADNP2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               2               7
  STAGE IB               1              26
  STAGE II               2              24
  STAGE IIA              5              26
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             2              34
  STAGE IIIC             2              22
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ADNP2 MUTATED     2   2   9   5
  ADNP2 WILD-TYPE   9  70 113  70
D257V4, multiclass
    clus
vv   ADNP2 MUTATED ADNP2 WILD-TYPE
  T1             2               9
  T2             2              70
  T3             9             113
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ADNP2 MUTATED   12  2  1  3
  ADNP2 WILD-TYPE 81 79 49 50
D257V5, multiclass
    clus
vv   ADNP2 MUTATED ADNP2 WILD-TYPE
  N0            12              81
  N1             2              79
  N2             1              49
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D257V6, binary
                 cls
clus                0   1
  ADNP2 MUTATED    17   0
  ADNP2 WILD-TYPE 240  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED     17    0
  ADNP2 WILD-TYPE  240   18
   clus
vv  ADNP2 MUTATED ADNP2 WILD-TYPE
  0            17             240
  1             0              18
[1] 2 2
[1] FALSE
D257V7, binary
                 cls
clus                0   1
  ADNP2 MUTATED     8  10
  ADNP2 WILD-TYPE 102 169
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED      8   10
  ADNP2 WILD-TYPE  102  169
        clus
vv       ADNP2 MUTATED ADNP2 WILD-TYPE
  FEMALE             8             102
  MALE              10             169
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ADNP2 MUTATED                                       4
  ADNP2 WILD-TYPE                                    46
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ADNP2 MUTATED                                                        9
  ADNP2 WILD-TYPE                                                    126
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ADNP2 MUTATED                                                                   2
  ADNP2 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ADNP2 MUTATED                                                  1
  ADNP2 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ADNP2 MUTATED                                                          1
  ADNP2 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ADNP2 MUTATED                                                           1
  ADNP2 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ADNP2 MUTATED                                          0
  ADNP2 WILD-TYPE                                        3
D257V8, multiclass
                                                                   clus
vv                                                                  ADNP2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ADNP2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D257V9, binary
                 cls
clus                0   1
  ADNP2 MUTATED     0  18
  ADNP2 WILD-TYPE   5 266
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED      0   18
  ADNP2 WILD-TYPE    5  266
     clus
vv    ADNP2 MUTATED ADNP2 WILD-TYPE
  NO              0               5
  YES            18             266
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ADNP2 MUTATED    16   0   0   2
  ADNP2 WILD-TYPE 211  10  10  22
D257V10, multiclass
    clus
vv   ADNP2 MUTATED ADNP2 WILD-TYPE
  R0            16             211
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D257V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ADNP2 MUTATED       4                         0    12
  ADNP2 WILD-TYPE    72                         4   156
D257V12, multiclass
                           clus
vv                          ADNP2 MUTATED ADNP2 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                12             156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(258) Variable = VPRBP MUTATION ANALYSIS
D258V1, survival
                 sevent
clus2               0   1
  VPRBP MUTATED     8   2
  VPRBP WILD-TYPE 173  78
  VPRBP MUTATED VPRBP WILD-TYPE 
             10             251 
  VPRBP MUTATED VPRBP WILD-TYPE 
              2              78 
$`VPRBP MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6457 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL 
       26.70         6.97        13.68        13.45        15.81        11.57 
TCGA-CD-8536 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5721 
        0.10        15.95         1.02         6.02 

$`VPRBP WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       17.29        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
        0.16         0.10         0.10         0.13         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 
       12.62        20.02         3.02        27.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  VPRBP MUTATED VPRBP WILD-TYPE 
            0.1             0.0 
  VPRBP MUTATED VPRBP WILD-TYPE 
          26.70          105.07 
  VPRBP MUTATED VPRBP WILD-TYPE 
          12.51           12.62 
[1] "0.1 - 26.7 (12.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D258V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  VPRBP MUTATED         0        0        1        2         1         1
  VPRBP WILD-TYPE       1        9       26       24        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VPRBP MUTATED           0          1          1          1        3
  VPRBP WILD-TYPE         3         48         35         23       21
D258V3, multiclass
            clus
vv           VPRBP MUTATED VPRBP WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               2              24
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               3              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  VPRBP MUTATED     0   2   5   4
  VPRBP WILD-TYPE  11  70 117  71
D258V4, multiclass
    clus
vv   VPRBP MUTATED VPRBP WILD-TYPE
  T1             0              11
  T2             2              70
  T3             5             117
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  VPRBP MUTATED    4  4  2  2
  VPRBP WILD-TYPE 89 77 48 51
D258V5, multiclass
    clus
vv   VPRBP MUTATED VPRBP WILD-TYPE
  N0             4              89
  N1             4              77
  N2             2              48
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D258V6, binary
                 cls
clus                0   1
  VPRBP MUTATED     9   2
  VPRBP WILD-TYPE 248  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPRBP MUTATED      9    2
  VPRBP WILD-TYPE  248   16
   clus
vv  VPRBP MUTATED VPRBP WILD-TYPE
  0             9             248
  1             2              16
[1] 2 2
[1] FALSE
D258V7, binary
                 cls
clus                0   1
  VPRBP MUTATED     3   9
  VPRBP WILD-TYPE 107 170
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPRBP MUTATED      3    9
  VPRBP WILD-TYPE  107  170
        clus
vv       VPRBP MUTATED VPRBP WILD-TYPE
  FEMALE             3             107
  MALE               9             170
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  VPRBP MUTATED                                       1
  VPRBP WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  VPRBP MUTATED                                                        8
  VPRBP WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  VPRBP MUTATED                                                                   2
  VPRBP WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  VPRBP MUTATED                                                  1
  VPRBP WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  VPRBP MUTATED                                                          0
  VPRBP WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  VPRBP MUTATED                                                           0
  VPRBP WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  VPRBP MUTATED                                          0
  VPRBP WILD-TYPE                                        3
D258V8, multiclass
                                                                   clus
vv                                                                  VPRBP MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  VPRBP WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D258V9, binary
                 cls
clus                0   1
  VPRBP MUTATED     0  12
  VPRBP WILD-TYPE   5 272
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPRBP MUTATED      0   12
  VPRBP WILD-TYPE    5  272
     clus
vv    VPRBP MUTATED VPRBP WILD-TYPE
  NO              0               5
  YES            12             272
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  VPRBP MUTATED     9   0   1   2
  VPRBP WILD-TYPE 218  10   9  22
D258V10, multiclass
    clus
vv   VPRBP MUTATED VPRBP WILD-TYPE
  R0             9             218
  R1             0              10
  R2             1               9
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D258V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  VPRBP MUTATED       2                         0     6
  VPRBP WILD-TYPE    74                         4   162
D258V12, multiclass
                           clus
vv                          VPRBP MUTATED VPRBP WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(259) Variable = PCGF3 MUTATION ANALYSIS
D259V1, survival
                 sevent
clus2               0   1
  PCGF3 MUTATED     5   1
  PCGF3 WILD-TYPE 176  79
  PCGF3 MUTATED PCGF3 WILD-TYPE 
              6             255 
  PCGF3 MUTATED PCGF3 WILD-TYPE 
              1              79 
$`PCGF3 MUTATED`
TCGA-BR-7703 TCGA-BR-8382 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-D7-A4YY TCGA-HU-A4H8 
       24.76        15.85        11.57         6.58        13.78         8.88 

$`PCGF3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       19.17        14.79         0.26         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       16.44         5.92        15.16        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  PCGF3 MUTATED PCGF3 WILD-TYPE 
           6.58            0.00 
  PCGF3 MUTATED PCGF3 WILD-TYPE 
          24.76          105.07 
  PCGF3 MUTATED PCGF3 WILD-TYPE 
         12.675          12.620 
[1] "6.6 - 24.8 (12.7)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.6"
D259V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PCGF3 MUTATED         0        1        1        0         1         0
  PCGF3 WILD-TYPE       1        8       26       26        30        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCGF3 MUTATED           0          0          2          1        0
  PCGF3 WILD-TYPE         3         49         34         23       24
D259V3, multiclass
            clus
vv           PCGF3 MUTATED PCGF3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             2              34
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PCGF3 MUTATED     2   0   3   1
  PCGF3 WILD-TYPE   9  72 119  74
D259V4, multiclass
    clus
vv   PCGF3 MUTATED PCGF3 WILD-TYPE
  T1             2               9
  T2             0              72
  T3             3             119
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PCGF3 MUTATED    2  1  0  3
  PCGF3 WILD-TYPE 91 80 50 50
D259V5, multiclass
    clus
vv   PCGF3 MUTATED PCGF3 WILD-TYPE
  N0             2              91
  N1             1              80
  N2             0              50
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D259V6, binary
                 cls
clus                0   1
  PCGF3 MUTATED     6   0
  PCGF3 WILD-TYPE 251  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCGF3 MUTATED      6    0
  PCGF3 WILD-TYPE  251   18
   clus
vv  PCGF3 MUTATED PCGF3 WILD-TYPE
  0             6             251
  1             0              18
[1] 2 2
[1] FALSE
D259V7, binary
                 cls
clus                0   1
  PCGF3 MUTATED     2   4
  PCGF3 WILD-TYPE 108 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCGF3 MUTATED      2    4
  PCGF3 WILD-TYPE  108  175
        clus
vv       PCGF3 MUTATED PCGF3 WILD-TYPE
  FEMALE             2             108
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PCGF3 MUTATED                                       1
  PCGF3 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PCGF3 MUTATED                                                        3
  PCGF3 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PCGF3 MUTATED                                                                   0
  PCGF3 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PCGF3 MUTATED                                                  1
  PCGF3 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PCGF3 MUTATED                                                          0
  PCGF3 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PCGF3 MUTATED                                                           1
  PCGF3 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PCGF3 MUTATED                                          0
  PCGF3 WILD-TYPE                                        3
D259V8, multiclass
                                                                   clus
vv                                                                  PCGF3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  PCGF3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D259V9, binary
                 cls
clus                0   1
  PCGF3 MUTATED     0   6
  PCGF3 WILD-TYPE   5 278
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCGF3 MUTATED      0    6
  PCGF3 WILD-TYPE    5  278
     clus
vv    PCGF3 MUTATED PCGF3 WILD-TYPE
  NO              0               5
  YES             6             278
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PCGF3 MUTATED     5   0   0   0
  PCGF3 WILD-TYPE 222  10  10  24
D259V10, multiclass
    clus
vv   PCGF3 MUTATED PCGF3 WILD-TYPE
  R0             5             222
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D259V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PCGF3 MUTATED       2                         0     4
  PCGF3 WILD-TYPE    74                         4   164
D259V12, multiclass
                           clus
vv                          PCGF3 MUTATED PCGF3 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(260) Variable = C20ORF160 MUTATION ANALYSIS
D260V1, survival
                     sevent
clus2                   0   1
  C20ORF160 MUTATED     6   2
  C20ORF160 WILD-TYPE 175  78
  C20ORF160 MUTATED C20ORF160 WILD-TYPE 
                  8                 253 
  C20ORF160 MUTATED C20ORF160 WILD-TYPE 
                  2                  78 
$`C20ORF160 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8361 TCGA-CG-5733 TCGA-D7-8572 
       34.68        32.94        12.26        19.50        21.07        16.80 
TCGA-HJ-7597 TCGA-HU-A4G8 
       26.47        11.84 

$`C20ORF160 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        24.72        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       11.08         5.52         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  C20ORF160 MUTATED C20ORF160 WILD-TYPE 
              11.84                0.00 
  C20ORF160 MUTATED C20ORF160 WILD-TYPE 
              34.68              105.07 
  C20ORF160 MUTATED C20ORF160 WILD-TYPE 
             20.285              12.560 
[1] "11.8 - 34.7 (20.3)" "0.0 - 105.1 (12.6)"
[1] "hr=" "2.1"
D260V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C20ORF160 MUTATED         0        0        1        0         2         3
  C20ORF160 WILD-TYPE       1        9       26       26        29        41
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C20ORF160 MUTATED           0          1          0          1        0
  C20ORF160 WILD-TYPE         3         48         36         23       24
D260V3, multiclass
            clus
vv           C20ORF160 MUTATED C20ORF160 WILD-TYPE
  STAGE I                    0                   1
  STAGE IA                   0                   9
  STAGE IB                   1                  26
  STAGE II                   0                  26
  STAGE IIA                  2                  29
  STAGE IIB                  3                  41
  STAGE III                  0                   3
  STAGE IIIA                 1                  48
  STAGE IIIB                 0                  36
  STAGE IIIC                 1                  23
  STAGE IV                   0                  24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  C20ORF160 MUTATED     0   3   3   2
  C20ORF160 WILD-TYPE  11  69 119  73
D260V4, multiclass
    clus
vv   C20ORF160 MUTATED C20ORF160 WILD-TYPE
  T1                 0                  11
  T2                 3                  69
  T3                 3                 119
  T4                 2                  73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  N0 N1 N2 N3
  C20ORF160 MUTATED    4  1  3  0
  C20ORF160 WILD-TYPE 89 80 47 53
D260V5, multiclass
    clus
vv   C20ORF160 MUTATED C20ORF160 WILD-TYPE
  N0                 4                  89
  N1                 1                  80
  N2                 3                  47
  N3                 0                  53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D260V6, binary
                     cls
clus                    0   1
  C20ORF160 MUTATED     7   0
  C20ORF160 WILD-TYPE 250  18
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF160 MUTATED      7    0
  C20ORF160 WILD-TYPE  250   18
   clus
vv  C20ORF160 MUTATED C20ORF160 WILD-TYPE
  0                 7                 250
  1                 0                  18
[1] 2 2
[1] FALSE
D260V7, binary
                     cls
clus                    0   1
  C20ORF160 MUTATED     7   1
  C20ORF160 WILD-TYPE 103 178
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF160 MUTATED      7    1
  C20ORF160 WILD-TYPE  103  178
        clus
vv       C20ORF160 MUTATED C20ORF160 WILD-TYPE
  FEMALE                 7                 103
  MALE                   1                 178
[1] 2 2
[1] FALSE
                     vv
clus                  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C20ORF160 MUTATED                                       1
  C20ORF160 WILD-TYPE                                    49
                     vv
clus                  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C20ORF160 MUTATED                                                        5
  C20ORF160 WILD-TYPE                                                    130
                     vv
clus                  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C20ORF160 MUTATED                                                                   1
  C20ORF160 WILD-TYPE                                                                39
                     vv
clus                  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C20ORF160 MUTATED                                                  0
  C20ORF160 WILD-TYPE                                               38
                     vv
clus                  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C20ORF160 MUTATED                                                          0
  C20ORF160 WILD-TYPE                                                       16
                     vv
clus                  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C20ORF160 MUTATED                                                           0
  C20ORF160 WILD-TYPE                                                         6
                     vv
clus                  STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C20ORF160 MUTATED                                          1
  C20ORF160 WILD-TYPE                                        2
D260V8, multiclass
                                                                   clus
vv                                                                  C20ORF160 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          1
                                                                   clus
vv                                                                  C20ORF160 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                              49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                   38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                           16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                           6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                            2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D260V9, binary
                     cls
clus                    0   1
  C20ORF160 MUTATED     0   8
  C20ORF160 WILD-TYPE   5 276
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF160 MUTATED      0    8
  C20ORF160 WILD-TYPE    5  276
     clus
vv    C20ORF160 MUTATED C20ORF160 WILD-TYPE
  NO                  0                   5
  YES                 8                 276
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  C20ORF160 MUTATED     7   0   0   0
  C20ORF160 WILD-TYPE 220  10  10  24
D260V10, multiclass
    clus
vv   C20ORF160 MUTATED C20ORF160 WILD-TYPE
  R0                 7                 220
  R1                 0                  10
  R2                 0                  10
  RX                 0                  24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D260V11, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C20ORF160 MUTATED       1                         0     6
  C20ORF160 WILD-TYPE    75                         4   162
D260V12, multiclass
                           clus
vv                          C20ORF160 MUTATED C20ORF160 WILD-TYPE
  ASIAN                                     1                  75
  BLACK OR AFRICAN AMERICAN                 0                   4
  WHITE                                     6                 162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(261) Variable = EFHA1 MUTATION ANALYSIS
D261V1, survival
                 sevent
clus2               0   1
  EFHA1 MUTATED     7   1
  EFHA1 WILD-TYPE 174  79
  EFHA1 MUTATED EFHA1 WILD-TYPE 
              8             253 
  EFHA1 MUTATED EFHA1 WILD-TYPE 
              1              79 
$`EFHA1 MUTATED`
TCGA-BR-7707 TCGA-BR-8360 TCGA-CG-5721 TCGA-F1-A448 TCGA-HU-8604 TCGA-HU-A4GN 
       23.93         6.18         6.02        21.27        12.10        29.98 
TCGA-HU-A4GQ TCGA-HU-A4H4 
        0.10        23.84 

$`EFHA1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        0.62         7.99        16.24        14.47        72.23         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        11.41        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       25.81        11.77         8.98         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  EFHA1 MUTATED EFHA1 WILD-TYPE 
            0.1             0.0 
  EFHA1 MUTATED EFHA1 WILD-TYPE 
          29.98          105.07 
  EFHA1 MUTATED EFHA1 WILD-TYPE 
         16.685          12.620 
[1] "0.1 - 30.0 (16.7)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.8"
D261V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EFHA1 MUTATED         0        0        1        0         3         1
  EFHA1 WILD-TYPE       1        9       26       26        28        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EFHA1 MUTATED           0          0          1          1        1
  EFHA1 WILD-TYPE         3         49         35         23       23
D261V3, multiclass
            clus
vv           EFHA1 MUTATED EFHA1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              3              28
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EFHA1 MUTATED     0   3   3   2
  EFHA1 WILD-TYPE  11  69 119  73
D261V4, multiclass
    clus
vv   EFHA1 MUTATED EFHA1 WILD-TYPE
  T1             0              11
  T2             3              69
  T3             3             119
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  EFHA1 MUTATED    3  2  2  1
  EFHA1 WILD-TYPE 90 79 48 52
D261V5, multiclass
    clus
vv   EFHA1 MUTATED EFHA1 WILD-TYPE
  N0             3              90
  N1             2              79
  N2             2              48
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D261V6, binary
                 cls
clus                0   1
  EFHA1 MUTATED     9   0
  EFHA1 WILD-TYPE 248  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHA1 MUTATED      9    0
  EFHA1 WILD-TYPE  248   18
   clus
vv  EFHA1 MUTATED EFHA1 WILD-TYPE
  0             9             248
  1             0              18
[1] 2 2
[1] FALSE
D261V7, binary
                 cls
clus                0   1
  EFHA1 MUTATED     4   5
  EFHA1 WILD-TYPE 106 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHA1 MUTATED      4    5
  EFHA1 WILD-TYPE  106  174
        clus
vv       EFHA1 MUTATED EFHA1 WILD-TYPE
  FEMALE             4             106
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  EFHA1 MUTATED                                       0
  EFHA1 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EFHA1 MUTATED                                                        2
  EFHA1 WILD-TYPE                                                    133
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EFHA1 MUTATED                                                                   2
  EFHA1 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  EFHA1 MUTATED                                                  4
  EFHA1 WILD-TYPE                                               34
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  EFHA1 MUTATED                                                          1
  EFHA1 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  EFHA1 MUTATED                                                           0
  EFHA1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  EFHA1 MUTATED                                          0
  EFHA1 WILD-TYPE                                        3
D261V8, multiclass
                                                                   clus
vv                                                                  EFHA1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  EFHA1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D261V9, binary
                 cls
clus                0   1
  EFHA1 MUTATED     0   9
  EFHA1 WILD-TYPE   5 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHA1 MUTATED      0    9
  EFHA1 WILD-TYPE    5  275
     clus
vv    EFHA1 MUTATED EFHA1 WILD-TYPE
  NO              0               5
  YES             9             275
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EFHA1 MUTATED     8   0   0   1
  EFHA1 WILD-TYPE 219  10  10  23
D261V10, multiclass
    clus
vv   EFHA1 MUTATED EFHA1 WILD-TYPE
  R0             8             219
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D261V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EFHA1 MUTATED       4                         0     4
  EFHA1 WILD-TYPE    72                         4   164
D261V12, multiclass
                           clus
vv                          EFHA1 MUTATED EFHA1 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(262) Variable = ALPK2 MUTATION ANALYSIS
D262V1, survival
                 sevent
clus2               0   1
  ALPK2 MUTATED    11   5
  ALPK2 WILD-TYPE 170  75
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             16             245 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
              5              75 
$`ALPK2 MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8382 TCGA-BR-8487 
        6.97         6.61        34.68        23.93        15.85         1.12 
TCGA-BR-8591 TCGA-BR-A453 TCGA-CD-A4MG TCGA-CG-5721 TCGA-HJ-7597 TCGA-HU-8602 
       13.45         6.08         6.58         6.02        26.47        11.41 
TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GX TCGA-HU-A4H8 
       24.20        29.98        10.19         8.88 

$`ALPK2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       30.90         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 
       31.20        32.94        12.82         9.21        24.76        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       15.81         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56        13.87         7.53        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56        11.08         5.52         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        11.84         3.25        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
       12.95        19.36        23.84        12.30         9.67        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  ALPK2 MUTATED ALPK2 WILD-TYPE 
           1.12            0.00 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
          34.68          105.07 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
          10.80           12.66 
[1] "1.1 - 34.7 (10.8)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1"  
D262V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ALPK2 MUTATED         0        1        3        0         4         1
  ALPK2 WILD-TYPE       1        8       24       26        27        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ALPK2 MUTATED           1          1          0          3        2
  ALPK2 WILD-TYPE         2         48         36         21       22
D262V3, multiclass
            clus
vv           ALPK2 MUTATED ALPK2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               3              24
  STAGE II               0              26
  STAGE IIA              4              27
  STAGE IIB              1              43
  STAGE III              1               2
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             3              21
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ALPK2 MUTATED     3   4   4   6
  ALPK2 WILD-TYPE   8  68 118  69
D262V4, multiclass
    clus
vv   ALPK2 MUTATED ALPK2 WILD-TYPE
  T1             3               8
  T2             4              68
  T3             4             118
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ALPK2 MUTATED    7  6  1  3
  ALPK2 WILD-TYPE 86 75 49 50
D262V5, multiclass
    clus
vv   ALPK2 MUTATED ALPK2 WILD-TYPE
  N0             7              86
  N1             6              75
  N2             1              49
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D262V6, binary
                 cls
clus                0   1
  ALPK2 MUTATED    16   1
  ALPK2 WILD-TYPE 241  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     16    1
  ALPK2 WILD-TYPE  241   17
   clus
vv  ALPK2 MUTATED ALPK2 WILD-TYPE
  0            16             241
  1             1              17
[1] 2 2
[1] FALSE
D262V7, binary
                 cls
clus                0   1
  ALPK2 MUTATED    11   8
  ALPK2 WILD-TYPE  99 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     11    8
  ALPK2 WILD-TYPE   99  171
        clus
vv       ALPK2 MUTATED ALPK2 WILD-TYPE
  FEMALE            11              99
  MALE               8             171
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ALPK2 MUTATED                                       3
  ALPK2 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ALPK2 MUTATED                                                       10
  ALPK2 WILD-TYPE                                                    125
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ALPK2 MUTATED                                                                   1
  ALPK2 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ALPK2 MUTATED                                                  3
  ALPK2 WILD-TYPE                                               35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ALPK2 MUTATED                                                          0
  ALPK2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ALPK2 MUTATED                                                           0
  ALPK2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ALPK2 MUTATED                                          2
  ALPK2 WILD-TYPE                                        1
D262V8, multiclass
                                                                   clus
vv                                                                  ALPK2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      2
                                                                   clus
vv                                                                  ALPK2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D262V9, binary
                 cls
clus                0   1
  ALPK2 MUTATED     0  19
  ALPK2 WILD-TYPE   5 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED      0   19
  ALPK2 WILD-TYPE    5  265
     clus
vv    ALPK2 MUTATED ALPK2 WILD-TYPE
  NO              0               5
  YES            19             265
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ALPK2 MUTATED    13   0   0   5
  ALPK2 WILD-TYPE 214  10  10  19
D262V10, multiclass
    clus
vv   ALPK2 MUTATED ALPK2 WILD-TYPE
  R0            13             214
  R1             0              10
  R2             0              10
  RX             5              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D262V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ALPK2 MUTATED       7                         0    11
  ALPK2 WILD-TYPE    69                         4   157
D262V12, multiclass
                           clus
vv                          ALPK2 MUTATED ALPK2 WILD-TYPE
  ASIAN                                 7              69
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                11             157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(263) Variable = C16ORF7 MUTATION ANALYSIS
D263V1, survival
                   sevent
clus2                 0   1
  C16ORF7 MUTATED     7   4
  C16ORF7 WILD-TYPE 174  76
  C16ORF7 MUTATED C16ORF7 WILD-TYPE 
               11               250 
  C16ORF7 MUTATED C16ORF7 WILD-TYPE 
                4                76 
$`C16ORF7 MUTATED`
TCGA-BR-4280 TCGA-BR-7716 TCGA-BR-8078 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-4306 
        6.61        28.01        12.26        15.81        11.57         1.02 
TCGA-CG-5721 TCGA-CG-5726 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4GU 
        6.02        28.96        11.84         0.10         6.25 

$`C16ORF7 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        23.93        15.42        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        13.64         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 
        1.02         0.99         0.99       105.07        12.03        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  C16ORF7 MUTATED C16ORF7 WILD-TYPE 
              0.1               0.0 
  C16ORF7 MUTATED C16ORF7 WILD-TYPE 
            28.96            105.07 
  C16ORF7 MUTATED C16ORF7 WILD-TYPE 
           11.570            12.775 
[1] "0.1 - 29.0 (11.6)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.4"
D263V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C16ORF7 MUTATED         1        1        0        0         0         4
  C16ORF7 WILD-TYPE       0        8       27       26        31        40
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C16ORF7 MUTATED           1          0          1          1        4
  C16ORF7 WILD-TYPE         2         49         35         23       20
D263V3, multiclass
            clus
vv           C16ORF7 MUTATED C16ORF7 WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                 1                 8
  STAGE IB                 0                27
  STAGE II                 0                26
  STAGE IIA                0                31
  STAGE IIB                4                40
  STAGE III                1                 2
  STAGE IIIA               0                49
  STAGE IIIB               1                35
  STAGE IIIC               1                23
  STAGE IV                 4                20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C16ORF7 MUTATED     2   1   5   5
  C16ORF7 WILD-TYPE   9  71 117  70
D263V4, multiclass
    clus
vv   C16ORF7 MUTATED C16ORF7 WILD-TYPE
  T1               2                 9
  T2               1                71
  T3               5               117
  T4               5                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  C16ORF7 MUTATED    2  7  4  1
  C16ORF7 WILD-TYPE 91 74 46 52
D263V5, multiclass
    clus
vv   C16ORF7 MUTATED C16ORF7 WILD-TYPE
  N0               2                91
  N1               7                74
  N2               4                46
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D263V6, binary
                   cls
clus                  0   1
  C16ORF7 MUTATED    11   2
  C16ORF7 WILD-TYPE 246  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C16ORF7 MUTATED     11    2
  C16ORF7 WILD-TYPE  246   16
   clus
vv  C16ORF7 MUTATED C16ORF7 WILD-TYPE
  0              11               246
  1               2                16
[1] 2 2
[1] FALSE
D263V7, binary
                   cls
clus                  0   1
  C16ORF7 MUTATED     6   8
  C16ORF7 WILD-TYPE 104 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C16ORF7 MUTATED      6    8
  C16ORF7 WILD-TYPE  104  171
        clus
vv       C16ORF7 MUTATED C16ORF7 WILD-TYPE
  FEMALE               6               104
  MALE                 8               171
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C16ORF7 MUTATED                                       2
  C16ORF7 WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C16ORF7 MUTATED                                                        8
  C16ORF7 WILD-TYPE                                                    127
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C16ORF7 MUTATED                                                                   2
  C16ORF7 WILD-TYPE                                                                38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C16ORF7 MUTATED                                                  2
  C16ORF7 WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C16ORF7 MUTATED                                                          0
  C16ORF7 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C16ORF7 MUTATED                                                           0
  C16ORF7 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C16ORF7 MUTATED                                          0
  C16ORF7 WILD-TYPE                                        3
D263V8, multiclass
                                                                   clus
vv                                                                  C16ORF7 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  C16ORF7 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D263V9, binary
                   cls
clus                  0   1
  C16ORF7 MUTATED     0  14
  C16ORF7 WILD-TYPE   5 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C16ORF7 MUTATED      0   14
  C16ORF7 WILD-TYPE    5  270
     clus
vv    C16ORF7 MUTATED C16ORF7 WILD-TYPE
  NO                0                 5
  YES              14               270
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C16ORF7 MUTATED     9   0   1   3
  C16ORF7 WILD-TYPE 218  10   9  21
D263V10, multiclass
    clus
vv   C16ORF7 MUTATED C16ORF7 WILD-TYPE
  R0               9               218
  R1               0                10
  R2               1                 9
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D263V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C16ORF7 MUTATED       4                         1     6
  C16ORF7 WILD-TYPE    72                         3   162
D263V12, multiclass
                           clus
vv                          C16ORF7 MUTATED C16ORF7 WILD-TYPE
  ASIAN                                   4                72
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   6               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(264) Variable = HIVEP1 MUTATION ANALYSIS
D264V1, survival
                  sevent
clus2                0   1
  HIVEP1 MUTATED    16   4
  HIVEP1 WILD-TYPE 165  76
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
              20              241 
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
               4               76 
$`HIVEP1 MUTATED`
TCGA-BR-6802 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8370 TCGA-BR-8382 
       30.90        12.26        20.55         8.05         3.32        15.85 
TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8528 TCGA-CD-A4MG 
        1.12        13.45        15.81        11.57         0.10         6.58 
TCGA-CG-4437 TCGA-CG-5717 TCGA-CG-5721 TCGA-CG-5726 TCGA-EQ-A4SO TCGA-HU-A4GT 
        8.05         6.97         6.02        28.96        16.24         6.51 
TCGA-HU-A4H4 TCGA-HU-A4H8 
       23.84         8.88 

$`HIVEP1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 
       17.49        14.43         0.69         9.60        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
       14.04        11.80        19.17        14.79         0.26         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        9.34         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        22.98        30.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         0.10         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        19.36        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        9.67        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
             0.1              0.0 
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
           30.90           105.07 
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
          10.225           12.760 
[1] "0.1 - 30.9 (10.2)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.4"
D264V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HIVEP1 MUTATED         0        1        1        2         3         3
  HIVEP1 WILD-TYPE       1        8       26       24        28        41
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIVEP1 MUTATED           0          3          3          3        2
  HIVEP1 WILD-TYPE         3         46         33         21       22
D264V3, multiclass
            clus
vv           HIVEP1 MUTATED HIVEP1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                1               26
  STAGE II                2               24
  STAGE IIA               3               28
  STAGE IIB               3               41
  STAGE III               0                3
  STAGE IIIA              3               46
  STAGE IIIB              3               33
  STAGE IIIC              3               21
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HIVEP1 MUTATED     2   3   7  10
  HIVEP1 WILD-TYPE   9  69 115  65
D264V4, multiclass
    clus
vv   HIVEP1 MUTATED HIVEP1 WILD-TYPE
  T1              2                9
  T2              3               69
  T3              7              115
  T4             10               65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  HIVEP1 MUTATED    8  5  3  5
  HIVEP1 WILD-TYPE 85 76 47 48
D264V5, multiclass
    clus
vv   HIVEP1 MUTATED HIVEP1 WILD-TYPE
  N0              8               85
  N1              5               76
  N2              3               47
  N3              5               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D264V6, binary
                  cls
clus                 0   1
  HIVEP1 MUTATED    19   1
  HIVEP1 WILD-TYPE 238  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP1 MUTATED     19    1
  HIVEP1 WILD-TYPE  238   17
   clus
vv  HIVEP1 MUTATED HIVEP1 WILD-TYPE
  0             19              238
  1              1               17
[1] 2 2
[1] FALSE
D264V7, binary
                  cls
clus                 0   1
  HIVEP1 MUTATED    11  11
  HIVEP1 WILD-TYPE  99 168
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP1 MUTATED     11   11
  HIVEP1 WILD-TYPE   99  168
        clus
vv       HIVEP1 MUTATED HIVEP1 WILD-TYPE
  FEMALE             11               99
  MALE               11              168
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  HIVEP1 MUTATED                                       2
  HIVEP1 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HIVEP1 MUTATED                                                       12
  HIVEP1 WILD-TYPE                                                    123
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HIVEP1 MUTATED                                                                   4
  HIVEP1 WILD-TYPE                                                                36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  HIVEP1 MUTATED                                                  4
  HIVEP1 WILD-TYPE                                               34
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  HIVEP1 MUTATED                                                          0
  HIVEP1 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  HIVEP1 MUTATED                                                           0
  HIVEP1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  HIVEP1 MUTATED                                          0
  HIVEP1 WILD-TYPE                                        3
D264V8, multiclass
                                                                   clus
vv                                                                  HIVEP1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        12
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  HIVEP1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         123
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D264V9, binary
                  cls
clus                 0   1
  HIVEP1 MUTATED     0  22
  HIVEP1 WILD-TYPE   5 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP1 MUTATED      0   22
  HIVEP1 WILD-TYPE    5  262
     clus
vv    HIVEP1 MUTATED HIVEP1 WILD-TYPE
  NO               0                5
  YES             22              262
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  HIVEP1 MUTATED    19   0   0   2
  HIVEP1 WILD-TYPE 208  10  10  22
D264V10, multiclass
    clus
vv   HIVEP1 MUTATED HIVEP1 WILD-TYPE
  R0             19              208
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D264V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HIVEP1 MUTATED       6                         0    12
  HIVEP1 WILD-TYPE    70                         4   156
D264V12, multiclass
                           clus
vv                          HIVEP1 MUTATED HIVEP1 WILD-TYPE
  ASIAN                                  6               70
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                 12              156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(265) Variable = VEZF1 MUTATION ANALYSIS
D265V1, survival
                 sevent
clus2               0   1
  VEZF1 MUTATED     2   1
  VEZF1 WILD-TYPE 179  79
  VEZF1 MUTATED VEZF1 WILD-TYPE 
              3             258 
  VEZF1 MUTATED VEZF1 WILD-TYPE 
              1              79 
$`VEZF1 MUTATED`
TCGA-BR-8590 TCGA-BR-A4QL TCGA-CG-5721 
        9.34        11.57         6.02 

$`VEZF1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       15.81        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  VEZF1 MUTATED VEZF1 WILD-TYPE 
           6.02            0.00 
  VEZF1 MUTATED VEZF1 WILD-TYPE 
          11.57          105.07 
  VEZF1 MUTATED VEZF1 WILD-TYPE 
           9.34           12.71 
[1] "6.0 - 11.6 (9.3)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.9"
D265V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  VEZF1 MUTATED         0        0        0        0         0         0
  VEZF1 WILD-TYPE       1        9       27       26        31        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VEZF1 MUTATED           0          1          1          1        1
  VEZF1 WILD-TYPE         3         48         35         23       23
D265V3, multiclass
            clus
vv           VEZF1 MUTATED VEZF1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              0              31
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  VEZF1 MUTATED     0   0   2   3
  VEZF1 WILD-TYPE  11  72 120  72
D265V4, multiclass
    clus
vv   VEZF1 MUTATED VEZF1 WILD-TYPE
  T1             0              11
  T2             0              72
  T3             2             120
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  VEZF1 MUTATED    1  1  1  1
  VEZF1 WILD-TYPE 92 80 49 52
D265V5, multiclass
    clus
vv   VEZF1 MUTATED VEZF1 WILD-TYPE
  N0             1              92
  N1             1              80
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D265V6, binary
                 cls
clus                0   1
  VEZF1 MUTATED     4   0
  VEZF1 WILD-TYPE 253  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEZF1 MUTATED      4    0
  VEZF1 WILD-TYPE  253   18
   clus
vv  VEZF1 MUTATED VEZF1 WILD-TYPE
  0             4             253
  1             0              18
[1] 2 2
[1] FALSE
D265V7, binary
                 cls
clus                0   1
  VEZF1 MUTATED     3   2
  VEZF1 WILD-TYPE 107 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEZF1 MUTATED      3    2
  VEZF1 WILD-TYPE  107  177
        clus
vv       VEZF1 MUTATED VEZF1 WILD-TYPE
  FEMALE             3             107
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  VEZF1 MUTATED                                       0
  VEZF1 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  VEZF1 MUTATED                                                        4
  VEZF1 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  VEZF1 MUTATED                                                                   1
  VEZF1 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  VEZF1 MUTATED                                                  0
  VEZF1 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  VEZF1 MUTATED                                                          0
  VEZF1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  VEZF1 MUTATED                                                           0
  VEZF1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  VEZF1 MUTATED                                          0
  VEZF1 WILD-TYPE                                        3
D265V8, multiclass
                                                                   clus
vv                                                                  VEZF1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  VEZF1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D265V9, binary
                 cls
clus                0   1
  VEZF1 MUTATED     0   5
  VEZF1 WILD-TYPE   5 279
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEZF1 MUTATED      0    5
  VEZF1 WILD-TYPE    5  279
     clus
vv    VEZF1 MUTATED VEZF1 WILD-TYPE
  NO              0               5
  YES             5             279
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  VEZF1 MUTATED     3   0   0   2
  VEZF1 WILD-TYPE 224  10  10  22
D265V10, multiclass
    clus
vv   VEZF1 MUTATED VEZF1 WILD-TYPE
  R0             3             224
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D265V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  VEZF1 MUTATED       0                         0     4
  VEZF1 WILD-TYPE    76                         4   164
D265V12, multiclass
                           clus
vv                          VEZF1 MUTATED VEZF1 WILD-TYPE
  ASIAN                                 0              76
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(266) Variable = SBNO1 MUTATION ANALYSIS
D266V1, survival
                 sevent
clus2               0   1
  SBNO1 MUTATED    13   3
  SBNO1 WILD-TYPE 168  77
  SBNO1 MUTATED SBNO1 WILD-TYPE 
             16             245 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
              3              77 
$`SBNO1 MUTATED`
TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8382 TCGA-CD-5801 
       34.68        19.50         4.31        19.17        15.85        13.18 
TCGA-CD-A4MG TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-6518 TCGA-D7-6528 
        6.58         9.01         6.02        65.10        19.13        15.22 
TCGA-HU-8602 TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H3 
       11.41         6.25        10.19        19.36 

$`SBNO1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
       26.33        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        2.83         3.25        13.15         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       47.05        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        0.99       105.07        12.03        28.96        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         0.10         6.51         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       12.95        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  SBNO1 MUTATED SBNO1 WILD-TYPE 
           4.31            0.00 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
          65.10          105.07 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
          14.20           12.59 
[1] "4.3 - 65.1 (14.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.9"
D266V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SBNO1 MUTATED         0        0        3        1         2         2
  SBNO1 WILD-TYPE       1        9       24       25        29        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SBNO1 MUTATED           0          2          0          5        2
  SBNO1 WILD-TYPE         3         47         36         19       22
D266V3, multiclass
            clus
vv           SBNO1 MUTATED SBNO1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               3              24
  STAGE II               1              25
  STAGE IIA              2              29
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             0              36
  STAGE IIIC             5              19
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SBNO1 MUTATED     0   5   4   8
  SBNO1 WILD-TYPE  11  67 118  67
D266V4, multiclass
    clus
vv   SBNO1 MUTATED SBNO1 WILD-TYPE
  T1             0              11
  T2             5              67
  T3             4             118
  T4             8              67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  SBNO1 MUTATED    6  4  2  5
  SBNO1 WILD-TYPE 87 77 48 48
D266V5, multiclass
    clus
vv   SBNO1 MUTATED SBNO1 WILD-TYPE
  N0             6              87
  N1             4              77
  N2             2              48
  N3             5              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D266V6, binary
                 cls
clus                0   1
  SBNO1 MUTATED    16   1
  SBNO1 WILD-TYPE 241  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SBNO1 MUTATED     16    1
  SBNO1 WILD-TYPE  241   17
   clus
vv  SBNO1 MUTATED SBNO1 WILD-TYPE
  0            16             241
  1             1              17
[1] 2 2
[1] FALSE
D266V7, binary
                 cls
clus                0   1
  SBNO1 MUTATED    10   7
  SBNO1 WILD-TYPE 100 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SBNO1 MUTATED     10    7
  SBNO1 WILD-TYPE  100  172
        clus
vv       SBNO1 MUTATED SBNO1 WILD-TYPE
  FEMALE            10             100
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SBNO1 MUTATED                                       7
  SBNO1 WILD-TYPE                                    43
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SBNO1 MUTATED                                                        6
  SBNO1 WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SBNO1 MUTATED                                                                   2
  SBNO1 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SBNO1 MUTATED                                                  1
  SBNO1 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SBNO1 MUTATED                                                          1
  SBNO1 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SBNO1 MUTATED                                                           0
  SBNO1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SBNO1 MUTATED                                          0
  SBNO1 WILD-TYPE                                        3
D266V8, multiclass
                                                                   clus
vv                                                                  SBNO1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  SBNO1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          43
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D266V9, binary
                 cls
clus                0   1
  SBNO1 MUTATED     1  16
  SBNO1 WILD-TYPE   4 268
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SBNO1 MUTATED      1   16
  SBNO1 WILD-TYPE    4  268
     clus
vv    SBNO1 MUTATED SBNO1 WILD-TYPE
  NO              1               4
  YES            16             268
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SBNO1 MUTATED    14   1   1   0
  SBNO1 WILD-TYPE 213   9   9  24
D266V10, multiclass
    clus
vv   SBNO1 MUTATED SBNO1 WILD-TYPE
  R0            14             213
  R1             1               9
  R2             1               9
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D266V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SBNO1 MUTATED       6                         0     7
  SBNO1 WILD-TYPE    70                         4   161
D266V12, multiclass
                           clus
vv                          SBNO1 MUTATED SBNO1 WILD-TYPE
  ASIAN                                 6              70
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 7             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(267) Variable = WASF3 MUTATION ANALYSIS
D267V1, survival
                 sevent
clus2               0   1
  WASF3 MUTATED     8   1
  WASF3 WILD-TYPE 173  79
  WASF3 MUTATED WASF3 WILD-TYPE 
              9             252 
  WASF3 MUTATED WASF3 WILD-TYPE 
              1              79 
$`WASF3 MUTATED`
TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8682 TCGA-BR-A4CQ TCGA-CD-A4MG TCGA-CG-5728 
       34.68        23.93        16.44        22.26         6.58        65.10 
TCGA-D7-A4YY TCGA-HU-A4GU TCGA-HU-A4H0 
       13.78         6.25         2.10 

$`WASF3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        79.07         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       15.16        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        10.19         0.26 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  WASF3 MUTATED WASF3 WILD-TYPE 
            2.1             0.0 
  WASF3 MUTATED WASF3 WILD-TYPE 
          65.10          105.07 
  WASF3 MUTATED WASF3 WILD-TYPE 
         16.440          12.575 
[1] "2.1 - 65.1 (16.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "4"  
D267V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WASF3 MUTATED         1        0        3        0         2         2
  WASF3 WILD-TYPE       0        9       24       26        29        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WASF3 MUTATED           0          1          1          1        0
  WASF3 WILD-TYPE         3         48         35         23       24
D267V3, multiclass
            clus
vv           WASF3 MUTATED WASF3 WILD-TYPE
  STAGE I                1               0
  STAGE IA               0               9
  STAGE IB               3              24
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WASF3 MUTATED     1   3   4   3
  WASF3 WILD-TYPE  10  69 118  72
D267V4, multiclass
    clus
vv   WASF3 MUTATED WASF3 WILD-TYPE
  T1             1              10
  T2             3              69
  T3             4             118
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  WASF3 MUTATED    6  3  0  2
  WASF3 WILD-TYPE 87 78 50 51
D267V5, multiclass
    clus
vv   WASF3 MUTATED WASF3 WILD-TYPE
  N0             6              87
  N1             3              78
  N2             0              50
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D267V6, binary
                 cls
clus                0   1
  WASF3 MUTATED    10   0
  WASF3 WILD-TYPE 247  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASF3 MUTATED     10    0
  WASF3 WILD-TYPE  247   18
   clus
vv  WASF3 MUTATED WASF3 WILD-TYPE
  0            10             247
  1             0              18
[1] 2 2
[1] FALSE
D267V7, binary
                 cls
clus                0   1
  WASF3 MUTATED     3   8
  WASF3 WILD-TYPE 107 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASF3 MUTATED      3    8
  WASF3 WILD-TYPE  107  171
        clus
vv       WASF3 MUTATED WASF3 WILD-TYPE
  FEMALE             3             107
  MALE               8             171
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  WASF3 MUTATED                                       3
  WASF3 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WASF3 MUTATED                                                        5
  WASF3 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WASF3 MUTATED                                                                   2
  WASF3 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  WASF3 MUTATED                                                  0
  WASF3 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  WASF3 MUTATED                                                          1
  WASF3 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  WASF3 MUTATED                                                           0
  WASF3 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  WASF3 MUTATED                                          0
  WASF3 WILD-TYPE                                        3
D267V8, multiclass
                                                                   clus
vv                                                                  WASF3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  WASF3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D267V9, binary
                 cls
clus                0   1
  WASF3 MUTATED     0  11
  WASF3 WILD-TYPE   5 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASF3 MUTATED      0   11
  WASF3 WILD-TYPE    5  273
     clus
vv    WASF3 MUTATED WASF3 WILD-TYPE
  NO              0               5
  YES            11             273
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  WASF3 MUTATED    10   0   0   0
  WASF3 WILD-TYPE 217  10  10  24
D267V10, multiclass
    clus
vv   WASF3 MUTATED WASF3 WILD-TYPE
  R0            10             217
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D267V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WASF3 MUTATED       4                         1     4
  WASF3 WILD-TYPE    72                         3   164
D267V12, multiclass
                           clus
vv                          WASF3 MUTATED WASF3 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(268) Variable = RAB14 MUTATION ANALYSIS
D268V1, survival
                 sevent
clus2               0   1
  RAB14 MUTATED     4   3
  RAB14 WILD-TYPE 177  77
  RAB14 MUTATED RAB14 WILD-TYPE 
              7             254 
  RAB14 MUTATED RAB14 WILD-TYPE 
              3              77 
$`RAB14 MUTATED`
TCGA-BR-4184 TCGA-BR-8361 TCGA-BR-A4QL TCGA-CD-A4MH TCGA-CG-5726 TCGA-HU-A4GQ 
        6.97        19.50        11.57        12.20        28.96         0.10 
TCGA-HU-A4GT 
        6.51 

$`RAB14 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX 
       25.81        11.77        29.98         8.98         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  RAB14 MUTATED RAB14 WILD-TYPE 
            0.1             0.0 
  RAB14 MUTATED RAB14 WILD-TYPE 
          28.96          105.07 
  RAB14 MUTATED RAB14 WILD-TYPE 
          11.57           12.71 
[1] "0.1 - 29.0 (11.6)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.6"
D268V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RAB14 MUTATED         0        1        0        0         2         0
  RAB14 WILD-TYPE       1        8       27       26        29        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAB14 MUTATED           0          1          1          2        0
  RAB14 WILD-TYPE         3         48         35         22       24
D268V3, multiclass
            clus
vv           RAB14 MUTATED RAB14 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             2              22
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RAB14 MUTATED     1   0   4   2
  RAB14 WILD-TYPE  10  72 118  73
D268V4, multiclass
    clus
vv   RAB14 MUTATED RAB14 WILD-TYPE
  T1             1              10
  T2             0              72
  T3             4             118
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  RAB14 MUTATED    3  2  2  1
  RAB14 WILD-TYPE 90 79 48 52
D268V5, multiclass
    clus
vv   RAB14 MUTATED RAB14 WILD-TYPE
  N0             3              90
  N1             2              79
  N2             2              48
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D268V6, binary
                 cls
clus                0   1
  RAB14 MUTATED     7   0
  RAB14 WILD-TYPE 250  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB14 MUTATED      7    0
  RAB14 WILD-TYPE  250   18
   clus
vv  RAB14 MUTATED RAB14 WILD-TYPE
  0             7             250
  1             0              18
[1] 2 2
[1] FALSE
D268V7, binary
                 cls
clus                0   1
  RAB14 MUTATED     5   3
  RAB14 WILD-TYPE 105 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB14 MUTATED      5    3
  RAB14 WILD-TYPE  105  176
        clus
vv       RAB14 MUTATED RAB14 WILD-TYPE
  FEMALE             5             105
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RAB14 MUTATED                                       0
  RAB14 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RAB14 MUTATED                                                        5
  RAB14 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RAB14 MUTATED                                                                   1
  RAB14 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RAB14 MUTATED                                                  2
  RAB14 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RAB14 MUTATED                                                          0
  RAB14 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RAB14 MUTATED                                                           0
  RAB14 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RAB14 MUTATED                                          0
  RAB14 WILD-TYPE                                        3
D268V8, multiclass
                                                                   clus
vv                                                                  RAB14 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  RAB14 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D268V9, binary
                 cls
clus                0   1
  RAB14 MUTATED     0   8
  RAB14 WILD-TYPE   5 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB14 MUTATED      0    8
  RAB14 WILD-TYPE    5  276
     clus
vv    RAB14 MUTATED RAB14 WILD-TYPE
  NO              0               5
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RAB14 MUTATED     5   0   0   2
  RAB14 WILD-TYPE 222  10  10  22
D268V10, multiclass
    clus
vv   RAB14 MUTATED RAB14 WILD-TYPE
  R0             5             222
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D268V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RAB14 MUTATED       3                         0     4
  RAB14 WILD-TYPE    73                         4   164
D268V12, multiclass
                           clus
vv                          RAB14 MUTATED RAB14 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(269) Variable = ZNF124 MUTATION ANALYSIS
D269V1, survival
                  sevent
clus2                0   1
  ZNF124 MUTATED     5   2
  ZNF124 WILD-TYPE 176  78
  ZNF124 MUTATED ZNF124 WILD-TYPE 
               7              254 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
               2               78 
$`ZNF124 MUTATED`
TCGA-BR-4184 TCGA-BR-7707 TCGA-BR-8591 TCGA-CD-8528 TCGA-CG-5721 TCGA-CG-5726 
        6.97        23.93        13.45         0.10         6.02        28.96 
TCGA-HU-A4GX 
       10.19 

$`ZNF124 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.07         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  ZNF124 MUTATED ZNF124 WILD-TYPE 
             0.1              0.0 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
           28.96           105.07 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
           10.19            12.64 
[1] "0.1 - 29.0 (10.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1"  
D269V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF124 MUTATED         0        1        2        0         0         0
  ZNF124 WILD-TYPE       1        8       25       26        31        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF124 MUTATED           0          2          0          2        1
  ZNF124 WILD-TYPE         3         47         36         22       23
D269V3, multiclass
            clus
vv           ZNF124 MUTATED ZNF124 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                2               25
  STAGE II                0               26
  STAGE IIA               0               31
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              0               36
  STAGE IIIC              2               22
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF124 MUTATED     1   2   1   4
  ZNF124 WILD-TYPE  10  70 121  71
D269V4, multiclass
    clus
vv   ZNF124 MUTATED ZNF124 WILD-TYPE
  T1              1               10
  T2              2               70
  T3              1              121
  T4              4               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZNF124 MUTATED    4  3  1  1
  ZNF124 WILD-TYPE 89 78 49 52
D269V5, multiclass
    clus
vv   ZNF124 MUTATED ZNF124 WILD-TYPE
  N0              4               89
  N1              3               78
  N2              1               49
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D269V6, binary
                  cls
clus                 0   1
  ZNF124 MUTATED     8   0
  ZNF124 WILD-TYPE 249  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF124 MUTATED      8    0
  ZNF124 WILD-TYPE  249   18
   clus
vv  ZNF124 MUTATED ZNF124 WILD-TYPE
  0              8              249
  1              0               18
[1] 2 2
[1] FALSE
D269V7, binary
                  cls
clus                 0   1
  ZNF124 MUTATED     4   5
  ZNF124 WILD-TYPE 106 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF124 MUTATED      4    5
  ZNF124 WILD-TYPE  106  174
        clus
vv       ZNF124 MUTATED ZNF124 WILD-TYPE
  FEMALE              4              106
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZNF124 MUTATED                                       1
  ZNF124 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF124 MUTATED                                                        5
  ZNF124 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF124 MUTATED                                                                   3
  ZNF124 WILD-TYPE                                                                37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZNF124 MUTATED                                                  0
  ZNF124 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZNF124 MUTATED                                                          0
  ZNF124 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZNF124 MUTATED                                                           0
  ZNF124 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZNF124 MUTATED                                          0
  ZNF124 WILD-TYPE                                        3
D269V8, multiclass
                                                                   clus
vv                                                                  ZNF124 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ZNF124 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D269V9, binary
                  cls
clus                 0   1
  ZNF124 MUTATED     0   9
  ZNF124 WILD-TYPE   5 275
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF124 MUTATED      0    9
  ZNF124 WILD-TYPE    5  275
     clus
vv    ZNF124 MUTATED ZNF124 WILD-TYPE
  NO               0                5
  YES              9              275
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF124 MUTATED     7   0   0   2
  ZNF124 WILD-TYPE 220  10  10  22
D269V10, multiclass
    clus
vv   ZNF124 MUTATED ZNF124 WILD-TYPE
  R0              7              220
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D269V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF124 MUTATED       2                         0     4
  ZNF124 WILD-TYPE    74                         4   164
D269V12, multiclass
                           clus
vv                          ZNF124 MUTATED ZNF124 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(270) Variable = RB1CC1 MUTATION ANALYSIS
D270V1, survival
                  sevent
clus2                0   1
  RB1CC1 MUTATED     8   1
  RB1CC1 WILD-TYPE 173  79
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
               9              252 
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
               1               79 
$`RB1CC1 MUTATED`
TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CG-4305 TCGA-CG-5723 
       19.50        19.17        13.45        11.57        15.95       105.07 
TCGA-D7-A4YV TCGA-HU-A4H3 TCGA-HU-A4H8 
        5.92        19.36         8.88 

$`RB1CC1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
            5.92             0.00 
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
          105.07            79.07 
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
          15.950           12.575 
[1] "5.9 - 105.1 (15.9)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "4.4"
D270V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RB1CC1 MUTATED         0        0        1        2         0         1
  RB1CC1 WILD-TYPE       1        9       26       24        31        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RB1CC1 MUTATED           0          0          1          4        0
  RB1CC1 WILD-TYPE         3         49         35         20       24
D270V3, multiclass
            clus
vv           RB1CC1 MUTATED RB1CC1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                2               24
  STAGE IIA               0               31
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              1               35
  STAGE IIIC              4               20
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RB1CC1 MUTATED     1   2   2   4
  RB1CC1 WILD-TYPE  10  70 120  71
D270V4, multiclass
    clus
vv   RB1CC1 MUTATED RB1CC1 WILD-TYPE
  T1              1               10
  T2              2               70
  T3              2              120
  T4              4               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  RB1CC1 MUTATED    0  5  1  4
  RB1CC1 WILD-TYPE 93 76 49 49
D270V5, multiclass
    clus
vv   RB1CC1 MUTATED RB1CC1 WILD-TYPE
  N0              0               93
  N1              5               76
  N2              1               49
  N3              4               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D270V6, binary
                  cls
clus                 0   1
  RB1CC1 MUTATED    10   0
  RB1CC1 WILD-TYPE 247  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RB1CC1 MUTATED     10    0
  RB1CC1 WILD-TYPE  247   18
   clus
vv  RB1CC1 MUTATED RB1CC1 WILD-TYPE
  0             10              247
  1              0               18
[1] 2 2
[1] FALSE
D270V7, binary
                  cls
clus                 0   1
  RB1CC1 MUTATED     5   5
  RB1CC1 WILD-TYPE 105 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RB1CC1 MUTATED      5    5
  RB1CC1 WILD-TYPE  105  174
        clus
vv       RB1CC1 MUTATED RB1CC1 WILD-TYPE
  FEMALE              5              105
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RB1CC1 MUTATED                                       1
  RB1CC1 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RB1CC1 MUTATED                                                        7
  RB1CC1 WILD-TYPE                                                    128
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RB1CC1 MUTATED                                                                   0
  RB1CC1 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RB1CC1 MUTATED                                                  2
  RB1CC1 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RB1CC1 MUTATED                                                          0
  RB1CC1 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RB1CC1 MUTATED                                                           0
  RB1CC1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RB1CC1 MUTATED                                          0
  RB1CC1 WILD-TYPE                                        3
D270V8, multiclass
                                                                   clus
vv                                                                  RB1CC1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  RB1CC1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D270V9, binary
                  cls
clus                 0   1
  RB1CC1 MUTATED     0  10
  RB1CC1 WILD-TYPE   5 274
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RB1CC1 MUTATED      0   10
  RB1CC1 WILD-TYPE    5  274
     clus
vv    RB1CC1 MUTATED RB1CC1 WILD-TYPE
  NO               0                5
  YES             10              274
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RB1CC1 MUTATED     9   0   0   1
  RB1CC1 WILD-TYPE 218  10  10  23
D270V10, multiclass
    clus
vv   RB1CC1 MUTATED RB1CC1 WILD-TYPE
  R0              9              218
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D270V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RB1CC1 MUTATED       2                         0     6
  RB1CC1 WILD-TYPE    74                         4   162
D270V12, multiclass
                           clus
vv                          RB1CC1 MUTATED RB1CC1 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(271) Variable = HIVEP3 MUTATION ANALYSIS
D271V1, survival
                  sevent
clus2                0   1
  HIVEP3 MUTATED    20   6
  HIVEP3 WILD-TYPE 161  74
  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
              26              235 
  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
               6               74 
$`HIVEP3 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7851 TCGA-BR-8361 TCGA-BR-8363 
       26.70        34.68        32.94        12.43        19.50         0.26 
TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8680 TCGA-CD-5800 TCGA-CD-A4MG 
        4.31         1.12        15.81        15.81        13.15         6.58 
TCGA-CG-4306 TCGA-CG-4449 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5730 TCGA-D7-6822 
        1.02        19.07         6.02       105.07         4.01        12.33 
TCGA-D7-A4YV TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4H0 TCGA-HU-A4H2 
        5.92        24.20        29.98         0.10         2.10        12.95 
TCGA-HU-A4H8 TCGA-IN-7808 
        8.88         3.45 

$`HIVEP3 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       15.42        28.01        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 
       16.31         2.20        15.58         7.40         6.18        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
       25.18         9.21        20.22        12.79         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       47.05        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 
        0.99        12.03        28.96        79.07        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       11.84         3.25        22.75        25.81        11.77         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51         6.25        10.19         0.26        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
       12.30         9.67        27.42        21.21        18.81         3.39 
TCGA-IP-7968 
        2.53 

  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
             0.1              0.0 
  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
          105.07            79.07 
  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
           12.38            12.66 
[1] "0.1 - 105.1 (12.4)" "0.0 - 79.1 (12.7)" 
[1] "hr=" "1.5"
D271V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HIVEP3 MUTATED         0        1        4        3         5         3
  HIVEP3 WILD-TYPE       1        8       23       23        26        41
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIVEP3 MUTATED           1          0          2          3        4
  HIVEP3 WILD-TYPE         2         49         34         21       20
D271V3, multiclass
            clus
vv           HIVEP3 MUTATED HIVEP3 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                4               23
  STAGE II                3               23
  STAGE IIA               5               26
  STAGE IIB               3               41
  STAGE III               1                2
  STAGE IIIA              0               49
  STAGE IIIB              2               34
  STAGE IIIC              3               21
  STAGE IV                4               20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HIVEP3 MUTATED     2   7  10   8
  HIVEP3 WILD-TYPE   9  65 112  67
D271V4, multiclass
    clus
vv   HIVEP3 MUTATED HIVEP3 WILD-TYPE
  T1              2                9
  T2              7               65
  T3             10              112
  T4              8               67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  HIVEP3 MUTATED   11  8  4  3
  HIVEP3 WILD-TYPE 82 73 46 50
D271V5, multiclass
    clus
vv   HIVEP3 MUTATED HIVEP3 WILD-TYPE
  N0             11               82
  N1              8               73
  N2              4               46
  N3              3               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D271V6, binary
                  cls
clus                 0   1
  HIVEP3 MUTATED    22   4
  HIVEP3 WILD-TYPE 235  14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP3 MUTATED     22    4
  HIVEP3 WILD-TYPE  235   14
   clus
vv  HIVEP3 MUTATED HIVEP3 WILD-TYPE
  0             22              235
  1              4               14
[1] 2 2
[1] FALSE
D271V7, binary
                  cls
clus                 0   1
  HIVEP3 MUTATED    13  14
  HIVEP3 WILD-TYPE  97 165
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP3 MUTATED     13   14
  HIVEP3 WILD-TYPE   97  165
        clus
vv       HIVEP3 MUTATED HIVEP3 WILD-TYPE
  FEMALE             13               97
  MALE               14              165
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  HIVEP3 MUTATED                                       4
  HIVEP3 WILD-TYPE                                    46
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HIVEP3 MUTATED                                                       10
  HIVEP3 WILD-TYPE                                                    125
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HIVEP3 MUTATED                                                                   3
  HIVEP3 WILD-TYPE                                                                37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  HIVEP3 MUTATED                                                  8
  HIVEP3 WILD-TYPE                                               30
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  HIVEP3 MUTATED                                                          1
  HIVEP3 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  HIVEP3 MUTATED                                                           1
  HIVEP3 WILD-TYPE                                                         5
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  HIVEP3 MUTATED                                          0
  HIVEP3 WILD-TYPE                                        3
D271V8, multiclass
                                                                   clus
vv                                                                  HIVEP3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  HIVEP3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                30
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D271V9, binary
                  cls
clus                 0   1
  HIVEP3 MUTATED     0  27
  HIVEP3 WILD-TYPE   5 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP3 MUTATED      0   27
  HIVEP3 WILD-TYPE    5  257
     clus
vv    HIVEP3 MUTATED HIVEP3 WILD-TYPE
  NO               0                5
  YES             27              257
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  HIVEP3 MUTATED    22   0   2   1
  HIVEP3 WILD-TYPE 205  10   8  23
D271V10, multiclass
    clus
vv   HIVEP3 MUTATED HIVEP3 WILD-TYPE
  R0             22              205
  R1              0               10
  R2              2                8
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D271V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HIVEP3 MUTATED       9                         0    13
  HIVEP3 WILD-TYPE    67                         4   155
D271V12, multiclass
                           clus
vv                          HIVEP3 MUTATED HIVEP3 WILD-TYPE
  ASIAN                                  9               67
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                 13              155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(272) Variable = OTX2 MUTATION ANALYSIS
D272V1, survival
                sevent
clus2              0   1
  OTX2 MUTATED     5   1
  OTX2 WILD-TYPE 176  79
  OTX2 MUTATED OTX2 WILD-TYPE 
             6            255 
  OTX2 MUTATED OTX2 WILD-TYPE 
             1             79 
$`OTX2 MUTATED`
TCGA-BR-6452 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-5723 TCGA-HU-A4GN TCGA-HU-A4H8 
       34.68        11.57         6.58       105.07        29.98         8.88 

$`OTX2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       22.75        25.81        11.77         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  OTX2 MUTATED OTX2 WILD-TYPE 
          6.58           0.00 
  OTX2 MUTATED OTX2 WILD-TYPE 
        105.07          79.07 
  OTX2 MUTATED OTX2 WILD-TYPE 
        20.775         12.620 
[1] "6.6 - 105.1 (20.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "4.2"
D272V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OTX2 MUTATED         0        0        1        1         3         0
  OTX2 WILD-TYPE       1        9       26       25        28        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OTX2 MUTATED           0          1          1          0        1
  OTX2 WILD-TYPE         3         48         35         24       23
D272V3, multiclass
            clus
vv           OTX2 MUTATED OTX2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              1             25
  STAGE IIA             3             28
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  OTX2 MUTATED     1   2   3   2
  OTX2 WILD-TYPE  10  70 119  73
D272V4, multiclass
    clus
vv   OTX2 MUTATED OTX2 WILD-TYPE
  T1            1             10
  T2            2             70
  T3            3            119
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  OTX2 MUTATED    3  3  1  1
  OTX2 WILD-TYPE 90 78 49 52
D272V5, multiclass
    clus
vv   OTX2 MUTATED OTX2 WILD-TYPE
  N0            3             90
  N1            3             78
  N2            1             49
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D272V6, binary
                cls
clus               0   1
  OTX2 MUTATED     9   0
  OTX2 WILD-TYPE 248  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX2 MUTATED      9    0
  OTX2 WILD-TYPE  248   18
   clus
vv  OTX2 MUTATED OTX2 WILD-TYPE
  0            9            248
  1            0             18
[1] 2 2
[1] FALSE
D272V7, binary
                cls
clus               0   1
  OTX2 MUTATED     5   4
  OTX2 WILD-TYPE 105 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX2 MUTATED      5    4
  OTX2 WILD-TYPE  105  175
        clus
vv       OTX2 MUTATED OTX2 WILD-TYPE
  FEMALE            5            105
  MALE              4            175
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  OTX2 MUTATED                                       1
  OTX2 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OTX2 MUTATED                                                        6
  OTX2 WILD-TYPE                                                    129
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OTX2 MUTATED                                                                   0
  OTX2 WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  OTX2 MUTATED                                                  2
  OTX2 WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  OTX2 MUTATED                                                          0
  OTX2 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  OTX2 MUTATED                                                           0
  OTX2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  OTX2 MUTATED                                          0
  OTX2 WILD-TYPE                                        3
D272V8, multiclass
                                                                   clus
vv                                                                  OTX2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  OTX2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D272V9, binary
                cls
clus               0   1
  OTX2 MUTATED     0   9
  OTX2 WILD-TYPE   5 275
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX2 MUTATED      0    9
  OTX2 WILD-TYPE    5  275
     clus
vv    OTX2 MUTATED OTX2 WILD-TYPE
  NO             0              5
  YES            9            275
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  OTX2 MUTATED     5   0   0   3
  OTX2 WILD-TYPE 222  10  10  21
D272V10, multiclass
    clus
vv   OTX2 MUTATED OTX2 WILD-TYPE
  R0            5            222
  R1            0             10
  R2            0             10
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D272V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OTX2 MUTATED       3                         0     5
  OTX2 WILD-TYPE    73                         4   163
D272V12, multiclass
                           clus
vv                          OTX2 MUTATED OTX2 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                5            163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(273) Variable = CRYGD MUTATION ANALYSIS
D273V1, survival
                 sevent
clus2               0   1
  CRYGD MUTATED     9   1
  CRYGD WILD-TYPE 172  79
  CRYGD MUTATED CRYGD WILD-TYPE 
             10             251 
  CRYGD MUTATED CRYGD WILD-TYPE 
              1              79 
$`CRYGD MUTATED`
TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8382 TCGA-CD-8528 TCGA-CD-A4MI TCGA-CG-5721 
       12.26         6.18        15.85         0.10         0.10         6.02 
TCGA-D7-A4YU TCGA-HU-A4GQ TCGA-HU-A4H3 TCGA-HU-A4H8 
       16.44         0.10        19.36         8.88 

$`CRYGD WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.07         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
        2.10        12.95        23.84        12.30         9.67        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  CRYGD MUTATED CRYGD WILD-TYPE 
            0.1             0.0 
  CRYGD MUTATED CRYGD WILD-TYPE 
          19.36          105.07 
  CRYGD MUTATED CRYGD WILD-TYPE 
           7.53           12.76 
[1] "0.1 - 19.4 (7.5)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.8"
D273V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CRYGD MUTATED         0        0        1        0         1         1
  CRYGD WILD-TYPE       1        9       26       26        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CRYGD MUTATED           0          2          2          3        1
  CRYGD WILD-TYPE         3         47         34         21       23
D273V3, multiclass
            clus
vv           CRYGD MUTATED CRYGD WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             2              34
  STAGE IIIC             3              21
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CRYGD MUTATED     2   0   3   7
  CRYGD WILD-TYPE   9  72 119  68
D273V4, multiclass
    clus
vv   CRYGD MUTATED CRYGD WILD-TYPE
  T1             2               9
  T2             0              72
  T3             3             119
  T4             7              68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CRYGD MUTATED    4  3  1  3
  CRYGD WILD-TYPE 89 78 49 50
D273V5, multiclass
    clus
vv   CRYGD MUTATED CRYGD WILD-TYPE
  N0             4              89
  N1             3              78
  N2             1              49
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D273V6, binary
                 cls
clus                0   1
  CRYGD MUTATED    12   0
  CRYGD WILD-TYPE 245  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRYGD MUTATED     12    0
  CRYGD WILD-TYPE  245   18
   clus
vv  CRYGD MUTATED CRYGD WILD-TYPE
  0            12             245
  1             0              18
[1] 2 2
[1] FALSE
D273V7, binary
                 cls
clus                0   1
  CRYGD MUTATED     6   6
  CRYGD WILD-TYPE 104 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRYGD MUTATED      6    6
  CRYGD WILD-TYPE  104  173
        clus
vv       CRYGD MUTATED CRYGD WILD-TYPE
  FEMALE             6             104
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CRYGD MUTATED                                       1
  CRYGD WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CRYGD MUTATED                                                        6
  CRYGD WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CRYGD MUTATED                                                                   2
  CRYGD WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CRYGD MUTATED                                                  3
  CRYGD WILD-TYPE                                               35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CRYGD MUTATED                                                          0
  CRYGD WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CRYGD MUTATED                                                           0
  CRYGD WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CRYGD MUTATED                                          0
  CRYGD WILD-TYPE                                        3
D273V8, multiclass
                                                                   clus
vv                                                                  CRYGD MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  CRYGD WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D273V9, binary
                 cls
clus                0   1
  CRYGD MUTATED     0  12
  CRYGD WILD-TYPE   5 272
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRYGD MUTATED      0   12
  CRYGD WILD-TYPE    5  272
     clus
vv    CRYGD MUTATED CRYGD WILD-TYPE
  NO              0               5
  YES            12             272
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CRYGD MUTATED     9   0   0   2
  CRYGD WILD-TYPE 218  10  10  22
D273V10, multiclass
    clus
vv   CRYGD MUTATED CRYGD WILD-TYPE
  R0             9             218
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D273V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CRYGD MUTATED       5                         0     6
  CRYGD WILD-TYPE    71                         4   162
D273V12, multiclass
                           clus
vv                          CRYGD MUTATED CRYGD WILD-TYPE
  ASIAN                                 5              71
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(274) Variable = MSL3 MUTATION ANALYSIS
D274V1, survival
                sevent
clus2              0   1
  MSL3 MUTATED     7   3
  MSL3 WILD-TYPE 174  77
  MSL3 MUTATED MSL3 WILD-TYPE 
            10            251 
  MSL3 MUTATED MSL3 WILD-TYPE 
             3             77 
$`MSL3 MUTATED`
TCGA-BR-7717 TCGA-BR-8081 TCGA-BR-8487 TCGA-BR-A44T TCGA-CD-5801 TCGA-CG-5721 
       18.15        20.55         1.12        12.56        13.18         6.02 
TCGA-D7-6522 TCGA-D7-A4YY TCGA-F1-6874 TCGA-HJ-7597 
       18.61        13.78        14.47        26.47 

$`MSL3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 
        9.21        24.76        23.93        15.42        28.01        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       17.49        14.43         0.69        12.26         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 
        9.86        15.68         8.22        10.68        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.15         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.84        18.54        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 
       14.76         0.62         7.99        16.24        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 
        5.03        13.58         0.56        11.08         5.52         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  MSL3 MUTATED MSL3 WILD-TYPE 
          1.12           0.00 
  MSL3 MUTATED MSL3 WILD-TYPE 
         26.47         105.07 
  MSL3 MUTATED MSL3 WILD-TYPE 
        14.125         12.430 
[1] "1.1 - 26.5 (14.1)"  "0.0 - 105.1 (12.4)"
[1] "hr=" "1.1"
D274V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MSL3 MUTATED         0        0        3        0         2         1
  MSL3 WILD-TYPE       1        9       24       26        29        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MSL3 MUTATED           0          1          1          0        2
  MSL3 WILD-TYPE         3         48         35         24       22
D274V3, multiclass
            clus
vv           MSL3 MUTATED MSL3 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              3             24
  STAGE II              0             26
  STAGE IIA             2             29
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            0             24
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MSL3 MUTATED     0   3   4   3
  MSL3 WILD-TYPE  11  69 118  72
D274V4, multiclass
    clus
vv   MSL3 MUTATED MSL3 WILD-TYPE
  T1            0             11
  T2            3             69
  T3            4            118
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  MSL3 MUTATED    6  3  0  1
  MSL3 WILD-TYPE 87 78 50 52
D274V5, multiclass
    clus
vv   MSL3 MUTATED MSL3 WILD-TYPE
  N0            6             87
  N1            3             78
  N2            0             50
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D274V6, binary
                cls
clus               0   1
  MSL3 MUTATED     9   0
  MSL3 WILD-TYPE 248  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSL3 MUTATED      9    0
  MSL3 WILD-TYPE  248   18
   clus
vv  MSL3 MUTATED MSL3 WILD-TYPE
  0            9            248
  1            0             18
[1] 2 2
[1] FALSE
D274V7, binary
                cls
clus               0   1
  MSL3 MUTATED     4   6
  MSL3 WILD-TYPE 106 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSL3 MUTATED      4    6
  MSL3 WILD-TYPE  106  173
        clus
vv       MSL3 MUTATED MSL3 WILD-TYPE
  FEMALE            4            106
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MSL3 MUTATED                                       2
  MSL3 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MSL3 MUTATED                                                        5
  MSL3 WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MSL3 MUTATED                                                                   2
  MSL3 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MSL3 MUTATED                                                  0
  MSL3 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MSL3 MUTATED                                                          0
  MSL3 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MSL3 MUTATED                                                           0
  MSL3 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MSL3 MUTATED                                          1
  MSL3 WILD-TYPE                                        2
D274V8, multiclass
                                                                   clus
vv                                                                  MSL3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  MSL3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D274V9, binary
                cls
clus               0   1
  MSL3 MUTATED     0  10
  MSL3 WILD-TYPE   5 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSL3 MUTATED      0   10
  MSL3 WILD-TYPE    5  274
     clus
vv    MSL3 MUTATED MSL3 WILD-TYPE
  NO             0              5
  YES           10            274
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MSL3 MUTATED    10   0   0   0
  MSL3 WILD-TYPE 217  10  10  24
D274V10, multiclass
    clus
vv   MSL3 MUTATED MSL3 WILD-TYPE
  R0           10            217
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D274V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MSL3 MUTATED       1                         0     8
  MSL3 WILD-TYPE    75                         4   160
D274V12, multiclass
                           clus
vv                          MSL3 MUTATED MSL3 WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                8            160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(275) Variable = GPR160 MUTATION ANALYSIS
D275V1, survival
                  sevent
clus2                0   1
  GPR160 MUTATED     5   1
  GPR160 WILD-TYPE 176  79
  GPR160 MUTATED GPR160 WILD-TYPE 
               6              255 
  GPR160 MUTATED GPR160 WILD-TYPE 
               1               79 
$`GPR160 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8297 TCGA-BR-8680 TCGA-CG-5728 TCGA-HU-A4GX 
        6.97        34.68         7.40        15.81        65.10        10.19 

$`GPR160 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 
       12.95         2.66        16.31         2.20        15.58         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        28.96        79.07         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  GPR160 MUTATED GPR160 WILD-TYPE 
            6.97             0.00 
  GPR160 MUTATED GPR160 WILD-TYPE 
           65.10           105.07 
  GPR160 MUTATED GPR160 WILD-TYPE 
           13.00            12.62 
[1] "7.0 - 65.1 (13.0)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.9"
D275V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPR160 MUTATED         0        0        1        0         1         0
  GPR160 WILD-TYPE       1        9       26       26        30        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR160 MUTATED           0          1          0          2        1
  GPR160 WILD-TYPE         3         48         36         22       23
D275V3, multiclass
            clus
vv           GPR160 MUTATED GPR160 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              2               22
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR160 MUTATED     1   1   2   3
  GPR160 WILD-TYPE  10  71 120  72
D275V4, multiclass
    clus
vv   GPR160 MUTATED GPR160 WILD-TYPE
  T1              1               10
  T2              1               71
  T3              2              120
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  GPR160 MUTATED    2  1  2  1
  GPR160 WILD-TYPE 91 80 48 52
D275V5, multiclass
    clus
vv   GPR160 MUTATED GPR160 WILD-TYPE
  N0              2               91
  N1              1               80
  N2              2               48
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D275V6, binary
                  cls
clus                 0   1
  GPR160 MUTATED     6   1
  GPR160 WILD-TYPE 251  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR160 MUTATED      6    1
  GPR160 WILD-TYPE  251   17
   clus
vv  GPR160 MUTATED GPR160 WILD-TYPE
  0              6              251
  1              1               17
[1] 2 2
[1] FALSE
D275V7, binary
                  cls
clus                 0   1
  GPR160 MUTATED     5   3
  GPR160 WILD-TYPE 105 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR160 MUTATED      5    3
  GPR160 WILD-TYPE  105  176
        clus
vv       GPR160 MUTATED GPR160 WILD-TYPE
  FEMALE              5              105
  MALE                3              176
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GPR160 MUTATED                                       2
  GPR160 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPR160 MUTATED                                                        4
  GPR160 WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPR160 MUTATED                                                                   1
  GPR160 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GPR160 MUTATED                                                  1
  GPR160 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GPR160 MUTATED                                                          0
  GPR160 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GPR160 MUTATED                                                           0
  GPR160 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GPR160 MUTATED                                          0
  GPR160 WILD-TYPE                                        3
D275V8, multiclass
                                                                   clus
vv                                                                  GPR160 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  GPR160 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D275V9, binary
                  cls
clus                 0   1
  GPR160 MUTATED     0   8
  GPR160 WILD-TYPE   5 276
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR160 MUTATED      0    8
  GPR160 WILD-TYPE    5  276
     clus
vv    GPR160 MUTATED GPR160 WILD-TYPE
  NO               0                5
  YES              8              276
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GPR160 MUTATED     5   0   0   3
  GPR160 WILD-TYPE 222  10  10  21
D275V10, multiclass
    clus
vv   GPR160 MUTATED GPR160 WILD-TYPE
  R0              5              222
  R1              0               10
  R2              0               10
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D275V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPR160 MUTATED       2                         0     5
  GPR160 WILD-TYPE    74                         4   163
D275V12, multiclass
                           clus
vv                          GPR160 MUTATED GPR160 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  5              163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(276) Variable = KIN MUTATION ANALYSIS
D276V1, survival
               sevent
clus2             0   1
  KIN MUTATED     8   2
  KIN WILD-TYPE 173  78
  KIN MUTATED KIN WILD-TYPE 
           10           251 
  KIN MUTATED KIN WILD-TYPE 
            2            78 
$`KIN MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-8680 
       26.70        34.68        32.94        12.26         1.12        15.81 
TCGA-D7-A4YV TCGA-HJ-7597 TCGA-HU-A4GN TCGA-HU-A4GX 
        5.92        26.47        29.98        10.19 

$`KIN WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.52         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       24.20         3.25        22.75        25.81        11.77         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  KIN MUTATED KIN WILD-TYPE 
         1.12          0.00 
  KIN MUTATED KIN WILD-TYPE 
        34.68        105.07 
  KIN MUTATED KIN WILD-TYPE 
        21.14         12.59 
[1] "1.1 - 34.7 (21.1)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.5"
D276V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIN MUTATED         0        0        1        0         4         3
  KIN WILD-TYPE       1        9       26       26        27        41
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIN MUTATED           0          0          0          1        1
  KIN WILD-TYPE         3         49         36         23       23
D276V3, multiclass
            clus
vv           KIN MUTATED KIN WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             9
  STAGE IB             1            26
  STAGE II             0            26
  STAGE IIA            4            27
  STAGE IIB            3            41
  STAGE III            0             3
  STAGE IIIA           0            49
  STAGE IIIB           0            36
  STAGE IIIC           1            23
  STAGE IV             1            23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  KIN MUTATED     1   2   4   4
  KIN WILD-TYPE  10  70 118  71
D276V4, multiclass
    clus
vv   KIN MUTATED KIN WILD-TYPE
  T1           1            10
  T2           2            70
  T3           4           118
  T4           4            71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  KIN MUTATED    6  2  2  0
  KIN WILD-TYPE 87 79 48 53
D276V5, multiclass
    clus
vv   KIN MUTATED KIN WILD-TYPE
  N0           6            87
  N1           2            79
  N2           2            48
  N3           0            53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D276V6, binary
               cls
clus              0   1
  KIN MUTATED     9   1
  KIN WILD-TYPE 248  17
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIN MUTATED      9    1
  KIN WILD-TYPE  248   17
   clus
vv  KIN MUTATED KIN WILD-TYPE
  0           9           248
  1           1            17
[1] 2 2
[1] FALSE
D276V7, binary
               cls
clus              0   1
  KIN MUTATED     9   2
  KIN WILD-TYPE 101 177
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIN MUTATED      9    2
  KIN WILD-TYPE  101  177
        clus
vv       KIN MUTATED KIN WILD-TYPE
  FEMALE           9           101
  MALE             2           177
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KIN MUTATED                                       2
  KIN WILD-TYPE                                    48
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIN MUTATED                                                        5
  KIN WILD-TYPE                                                    130
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIN MUTATED                                                                   0
  KIN WILD-TYPE                                                                40
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KIN MUTATED                                                  3
  KIN WILD-TYPE                                               35
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KIN MUTATED                                                          0
  KIN WILD-TYPE                                                       16
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KIN MUTATED                                                           0
  KIN WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KIN MUTATED                                          1
  KIN WILD-TYPE                                        2
D276V8, multiclass
                                                                   clus
vv                                                                  KIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    1
                                                                   clus
vv                                                                  KIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D276V9, binary
               cls
clus              0   1
  KIN MUTATED     0  11
  KIN WILD-TYPE   5 273
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIN MUTATED      0   11
  KIN WILD-TYPE    5  273
     clus
vv    KIN MUTATED KIN WILD-TYPE
  NO            0             5
  YES          11           273
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  KIN MUTATED    10   0   0   1
  KIN WILD-TYPE 217  10  10  23
D276V10, multiclass
    clus
vv   KIN MUTATED KIN WILD-TYPE
  R0          10           217
  R1           0            10
  R2           0            10
  RX           1            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D276V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIN MUTATED       3                         0     8
  KIN WILD-TYPE    73                         4   160
D276V12, multiclass
                           clus
vv                          KIN MUTATED KIN WILD-TYPE
  ASIAN                               3            73
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                               8           160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(277) Variable = SRCIN1 MUTATION ANALYSIS
D277V1, survival
                  sevent
clus2                0   1
  SRCIN1 MUTATED     6   5
  SRCIN1 WILD-TYPE 175  75
  SRCIN1 MUTATED SRCIN1 WILD-TYPE 
              11              250 
  SRCIN1 MUTATED SRCIN1 WILD-TYPE 
               5               75 
$`SRCIN1 MUTATED`
TCGA-BR-4280 TCGA-BR-7707 TCGA-BR-8363 TCGA-BR-8487 TCGA-CD-8529 TCGA-CD-A4MG 
        6.61        23.93         0.26         1.12         0.13         6.58 
TCGA-CG-4437 TCGA-CG-4469 TCGA-D7-6815 TCGA-HU-A4GH TCGA-HU-A4GQ 
        8.05         7.07        15.98        11.77         0.10 

$`SRCIN1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        19.50        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.10         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
        3.25        22.75        25.81        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  SRCIN1 MUTATED SRCIN1 WILD-TYPE 
             0.1              0.0 
  SRCIN1 MUTATED SRCIN1 WILD-TYPE 
           23.93           105.07 
  SRCIN1 MUTATED SRCIN1 WILD-TYPE 
            6.61            12.79 
[1] "0.1 - 23.9 (6.6)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "3.2"
D277V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SRCIN1 MUTATED         1        1        3        1         2         1
  SRCIN1 WILD-TYPE       0        8       24       25        29        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SRCIN1 MUTATED           1          0          0          1        2
  SRCIN1 WILD-TYPE         2         49         36         23       22
D277V3, multiclass
            clus
vv           SRCIN1 MUTATED SRCIN1 WILD-TYPE
  STAGE I                 1                0
  STAGE IA                1                8
  STAGE IB                3               24
  STAGE II                1               25
  STAGE IIA               2               29
  STAGE IIB               1               43
  STAGE III               1                2
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SRCIN1 MUTATED     2   6   3   2
  SRCIN1 WILD-TYPE   9  66 119  73
D277V4, multiclass
    clus
vv   SRCIN1 MUTATED SRCIN1 WILD-TYPE
  T1              2                9
  T2              6               66
  T3              3              119
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  SRCIN1 MUTATED    7  3  2  1
  SRCIN1 WILD-TYPE 86 78 48 52
D277V5, multiclass
    clus
vv   SRCIN1 MUTATED SRCIN1 WILD-TYPE
  N0              7               86
  N1              3               78
  N2              2               48
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D277V6, binary
                  cls
clus                 0   1
  SRCIN1 MUTATED    11   1
  SRCIN1 WILD-TYPE 246  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRCIN1 MUTATED     11    1
  SRCIN1 WILD-TYPE  246   17
   clus
vv  SRCIN1 MUTATED SRCIN1 WILD-TYPE
  0             11              246
  1              1               17
[1] 2 2
[1] FALSE
D277V7, binary
                  cls
clus                 0   1
  SRCIN1 MUTATED     5   8
  SRCIN1 WILD-TYPE 105 171
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRCIN1 MUTATED      5    8
  SRCIN1 WILD-TYPE  105  171
        clus
vv       SRCIN1 MUTATED SRCIN1 WILD-TYPE
  FEMALE              5              105
  MALE                8              171
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SRCIN1 MUTATED                                       1
  SRCIN1 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SRCIN1 MUTATED                                                        5
  SRCIN1 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SRCIN1 MUTATED                                                                   3
  SRCIN1 WILD-TYPE                                                                37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SRCIN1 MUTATED                                                  3
  SRCIN1 WILD-TYPE                                               35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SRCIN1 MUTATED                                                          1
  SRCIN1 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SRCIN1 MUTATED                                                           0
  SRCIN1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SRCIN1 MUTATED                                          0
  SRCIN1 WILD-TYPE                                        3
D277V8, multiclass
                                                                   clus
vv                                                                  SRCIN1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  SRCIN1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D277V9, binary
                  cls
clus                 0   1
  SRCIN1 MUTATED     0  13
  SRCIN1 WILD-TYPE   5 271
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRCIN1 MUTATED      0   13
  SRCIN1 WILD-TYPE    5  271
     clus
vv    SRCIN1 MUTATED SRCIN1 WILD-TYPE
  NO               0                5
  YES             13              271
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SRCIN1 MUTATED    10   1   0   1
  SRCIN1 WILD-TYPE 217   9  10  23
D277V10, multiclass
    clus
vv   SRCIN1 MUTATED SRCIN1 WILD-TYPE
  R0             10              217
  R1              1                9
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D277V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SRCIN1 MUTATED       4                         1     5
  SRCIN1 WILD-TYPE    72                         3   163
D277V12, multiclass
                           clus
vv                          SRCIN1 MUTATED SRCIN1 WILD-TYPE
  ASIAN                                  4               72
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  5              163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(278) Variable = KDELR3 MUTATION ANALYSIS
D278V1, survival
                  sevent
clus2                0   1
  KDELR3 MUTATED     2   1
  KDELR3 WILD-TYPE 179  79
  KDELR3 MUTATED KDELR3 WILD-TYPE 
               3              258 
  KDELR3 MUTATED KDELR3 WILD-TYPE 
               1               79 
$`KDELR3 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8295 
       26.70        34.68         2.20 

$`KDELR3 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       12.95         2.66        16.31        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  KDELR3 MUTATED KDELR3 WILD-TYPE 
             2.2              0.0 
  KDELR3 MUTATED KDELR3 WILD-TYPE 
           34.68           105.07 
  KDELR3 MUTATED KDELR3 WILD-TYPE 
          26.700           12.605 
[1] "2.2 - 34.7 (26.7)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.6"
D278V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KDELR3 MUTATED         0        0        0        0         1         2
  KDELR3 WILD-TYPE       1        9       27       26        30        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KDELR3 MUTATED           0          0          0          0        0
  KDELR3 WILD-TYPE         3         49         36         24       24
D278V3, multiclass
            clus
vv           KDELR3 MUTATED KDELR3 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KDELR3 MUTATED     0   0   1   2
  KDELR3 WILD-TYPE  11  72 121  73
D278V4, multiclass
    clus
vv   KDELR3 MUTATED KDELR3 WILD-TYPE
  T1              0               11
  T2              0               72
  T3              1              121
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  KDELR3 MUTATED    3  0  0  0
  KDELR3 WILD-TYPE 90 81 50 53
D278V5, multiclass
    clus
vv   KDELR3 MUTATED KDELR3 WILD-TYPE
  N0              3               90
  N1              0               81
  N2              0               50
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D278V6, binary
                  cls
clus                 0   1
  KDELR3 MUTATED     3   0
  KDELR3 WILD-TYPE 254  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KDELR3 MUTATED      3    0
  KDELR3 WILD-TYPE  254   18
   clus
vv  KDELR3 MUTATED KDELR3 WILD-TYPE
  0              3              254
  1              0               18
[1] 2 2
[1] FALSE
D278V7, binary
                  cls
clus                 0   1
  KDELR3 MUTATED     3   0
  KDELR3 WILD-TYPE 107 179
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KDELR3 MUTATED      3    0
  KDELR3 WILD-TYPE  107  179
        clus
vv       KDELR3 MUTATED KDELR3 WILD-TYPE
  FEMALE              3              107
  MALE                0              179
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KDELR3 MUTATED                                       1
  KDELR3 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KDELR3 MUTATED                                                        2
  KDELR3 WILD-TYPE                                                    133
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KDELR3 MUTATED                                                                   0
  KDELR3 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KDELR3 MUTATED                                                  0
  KDELR3 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KDELR3 MUTATED                                                          0
  KDELR3 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KDELR3 MUTATED                                                           0
  KDELR3 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KDELR3 MUTATED                                          0
  KDELR3 WILD-TYPE                                        3
D278V8, multiclass
                                                                   clus
vv                                                                  KDELR3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  KDELR3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D278V9, binary
                  cls
clus                 0   1
  KDELR3 MUTATED     0   3
  KDELR3 WILD-TYPE   5 281
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KDELR3 MUTATED      0    3
  KDELR3 WILD-TYPE    5  281
     clus
vv    KDELR3 MUTATED KDELR3 WILD-TYPE
  NO               0                5
  YES              3              281
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  KDELR3 MUTATED     3   0   0   0
  KDELR3 WILD-TYPE 224  10  10  24
D278V10, multiclass
    clus
vv   KDELR3 MUTATED KDELR3 WILD-TYPE
  R0              3              224
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D278V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KDELR3 MUTATED       0                         0     3
  KDELR3 WILD-TYPE    76                         4   165
D278V12, multiclass
                           clus
vv                          KDELR3 MUTATED KDELR3 WILD-TYPE
  ASIAN                                  0               76
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  3              165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(279) Variable = FBXO48 MUTATION ANALYSIS
D279V1, survival
                  sevent
clus2                0   1
  FBXO48 MUTATED     2   1
  FBXO48 WILD-TYPE 179  79
  FBXO48 MUTATED FBXO48 WILD-TYPE 
               3              258 
  FBXO48 MUTATED FBXO48 WILD-TYPE 
               1               79 
$`FBXO48 MUTATED`
TCGA-CG-5726 TCGA-F1-6874 TCGA-FP-A4BE 
       28.96        14.47        11.08 

$`FBXO48 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
       13.78        14.76         0.62         7.99        16.24        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 
       59.54         5.03        13.58         0.56         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  FBXO48 MUTATED FBXO48 WILD-TYPE 
           11.08             0.00 
  FBXO48 MUTATED FBXO48 WILD-TYPE 
           28.96           105.07 
  FBXO48 MUTATED FBXO48 WILD-TYPE 
          14.470           12.605 
[1] "11.1 - 29.0 (14.5)" "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D279V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FBXO48 MUTATED         0        1        2        0         1         0
  FBXO48 WILD-TYPE       1        8       25       26        30        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO48 MUTATED           0          0          0          0        0
  FBXO48 WILD-TYPE         3         49         36         24       24
D279V3, multiclass
            clus
vv           FBXO48 MUTATED FBXO48 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                2               25
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FBXO48 MUTATED     1   2   1   0
  FBXO48 WILD-TYPE  10  70 121  75
D279V4, multiclass
    clus
vv   FBXO48 MUTATED FBXO48 WILD-TYPE
  T1              1               10
  T2              2               70
  T3              1              121
  T4              0               75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  FBXO48 MUTATED    4  0  0  0
  FBXO48 WILD-TYPE 89 81 50 53
D279V5, multiclass
    clus
vv   FBXO48 MUTATED FBXO48 WILD-TYPE
  N0              4               89
  N1              0               81
  N2              0               50
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D279V6, binary
                  cls
clus                 0   1
  FBXO48 MUTATED     4   0
  FBXO48 WILD-TYPE 253  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO48 MUTATED      4    0
  FBXO48 WILD-TYPE  253   18
   clus
vv  FBXO48 MUTATED FBXO48 WILD-TYPE
  0              4              253
  1              0               18
[1] 2 2
[1] FALSE
D279V7, binary
                  cls
clus                 0   1
  FBXO48 MUTATED     0   4
  FBXO48 WILD-TYPE 110 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO48 MUTATED      0    4
  FBXO48 WILD-TYPE  110  175
        clus
vv       FBXO48 MUTATED FBXO48 WILD-TYPE
  FEMALE              0              110
  MALE                4              175
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FBXO48 MUTATED                                       0
  FBXO48 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FBXO48 MUTATED                                                        1
  FBXO48 WILD-TYPE                                                    134
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FBXO48 MUTATED                                                                   3
  FBXO48 WILD-TYPE                                                                37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FBXO48 MUTATED                                                  0
  FBXO48 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FBXO48 MUTATED                                                          0
  FBXO48 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FBXO48 MUTATED                                                           0
  FBXO48 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FBXO48 MUTATED                                          0
  FBXO48 WILD-TYPE                                        3
D279V8, multiclass
                                                                   clus
vv                                                                  FBXO48 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         1
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  FBXO48 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D279V9, binary
                  cls
clus                 0   1
  FBXO48 MUTATED     0   4
  FBXO48 WILD-TYPE   5 280
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO48 MUTATED      0    4
  FBXO48 WILD-TYPE    5  280
     clus
vv    FBXO48 MUTATED FBXO48 WILD-TYPE
  NO               0                5
  YES              4              280
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FBXO48 MUTATED     4   0   0   0
  FBXO48 WILD-TYPE 223  10  10  24
D279V10, multiclass
    clus
vv   FBXO48 MUTATED FBXO48 WILD-TYPE
  R0              4              223
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D279V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FBXO48 MUTATED       0                         1     1
  FBXO48 WILD-TYPE    76                         3   167
D279V12, multiclass
[1] "Remove cluster labels:" "FBXO48 MUTATED"        
clus
  FBXO48 MUTATED FBXO48 WILD-TYPE 
               2              246 
      TCGA-B7-5816       TCGA-B7-5818       TCGA-BR-4183       TCGA-BR-4184 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-4187       TCGA-BR-4188       TCGA-BR-4191       TCGA-BR-4201 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-4253       TCGA-BR-4255       TCGA-BR-4256       TCGA-BR-4257 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-4267       TCGA-BR-4279       TCGA-BR-4280       TCGA-BR-4292 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-4294       TCGA-BR-4357       TCGA-BR-4361       TCGA-BR-4362 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-4363       TCGA-BR-4366       TCGA-BR-4368       TCGA-BR-4369 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-4370       TCGA-BR-4371       TCGA-BR-6452       TCGA-BR-6453 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-6454       TCGA-BR-6455       TCGA-BR-6456       TCGA-BR-6457 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-6458       TCGA-BR-6563       TCGA-BR-6564       TCGA-BR-6565 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-6566       TCGA-BR-6705       TCGA-BR-6706       TCGA-BR-6707 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-6710       TCGA-BR-6801       TCGA-BR-6802       TCGA-BR-6803 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-6852       TCGA-BR-7196       TCGA-BR-7197       TCGA-BR-7703 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-7707       TCGA-BR-7715       TCGA-BR-7716       TCGA-BR-7717 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-7722       TCGA-BR-7723       TCGA-BR-7851       TCGA-BR-7901 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-7957       TCGA-BR-7958       TCGA-BR-7959       TCGA-BR-8058 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-8059       TCGA-BR-8077       TCGA-BR-8078       TCGA-BR-8080 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-8081       TCGA-BR-8284       TCGA-BR-8286       TCGA-BR-8289 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-8291       TCGA-BR-8295       TCGA-BR-8296       TCGA-BR-8297 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-8360       TCGA-BR-8361       TCGA-BR-8363       TCGA-BR-8364 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-8365       TCGA-BR-8366       TCGA-BR-8367       TCGA-BR-8368 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-8369       TCGA-BR-8370       TCGA-BR-8371       TCGA-BR-8372 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-8373       TCGA-BR-8380       TCGA-BR-8381       TCGA-BR-8382 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-8384       TCGA-BR-8483       TCGA-BR-8484       TCGA-BR-8485 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-8486       TCGA-BR-8487       TCGA-BR-8588       TCGA-BR-8589 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-8590       TCGA-BR-8591       TCGA-BR-8592       TCGA-BR-8676 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-8677       TCGA-BR-8678       TCGA-BR-8679       TCGA-BR-8680 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-8682       TCGA-BR-8683       TCGA-BR-8686       TCGA-BR-8687 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-8690       TCGA-BR-A44T       TCGA-BR-A44U       TCGA-BR-A452 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-A453       TCGA-BR-A4CQ       TCGA-BR-A4CR       TCGA-BR-A4CS 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-A4IU       TCGA-BR-A4IV       TCGA-BR-A4IY       TCGA-BR-A4IZ 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-A4J1       TCGA-BR-A4J2       TCGA-BR-A4J4       TCGA-BR-A4J6 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-A4J7       TCGA-BR-A4J8       TCGA-BR-A4PD       TCGA-BR-A4PE 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-BR-A4PF       TCGA-BR-A4QI       TCGA-BR-A4QL       TCGA-BR-A4QM 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-CD-5798       TCGA-CD-5799       TCGA-CD-5800       TCGA-CD-5801 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-CD-5802       TCGA-CD-5803       TCGA-CD-5804       TCGA-CD-5813 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-CD-8524       TCGA-CD-8525       TCGA-CD-8526       TCGA-CD-8527 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-CD-8528       TCGA-CD-8529       TCGA-CD-8530       TCGA-CD-8531 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-CD-8532       TCGA-CD-8534       TCGA-CD-8535       TCGA-CD-8536 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-CD-A486       TCGA-CD-A487       TCGA-CD-A489       TCGA-CD-A48A 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-CD-A48C       TCGA-CD-A4MG       TCGA-CD-A4MH       TCGA-CD-A4MI 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-CD-A4MJ       TCGA-D7-5577       TCGA-D7-5578       TCGA-D7-5579 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-D7-6518       TCGA-D7-6519       TCGA-D7-6520       TCGA-D7-6521 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-D7-6522       TCGA-D7-6524       TCGA-D7-6525       TCGA-D7-6526 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-D7-6527       TCGA-D7-6528       TCGA-D7-6815       TCGA-D7-6817 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-D7-6818       TCGA-D7-6820       TCGA-D7-6822       TCGA-D7-8570 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-D7-8572       TCGA-D7-8573       TCGA-D7-8574       TCGA-D7-8575 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-D7-8576       TCGA-D7-8578       TCGA-D7-8579       TCGA-D7-A4YT 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-D7-A4YU       TCGA-D7-A4YV       TCGA-D7-A4YX       TCGA-D7-A4YY 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-D7-A4Z0       TCGA-EQ-5647       TCGA-EQ-8122       TCGA-EQ-A4SO 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-F1-6177       TCGA-F1-6875       TCGA-F1-A448       TCGA-FP-7735 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-FP-7829       TCGA-FP-7916       TCGA-FP-7998       TCGA-FP-8099 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-FP-8209       TCGA-FP-8210       TCGA-FP-8211       TCGA-FP-8631 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-FP-A4BF       TCGA-HJ-7597       TCGA-HU-8243       TCGA-HU-8245 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-HU-8249       TCGA-HU-8602       TCGA-HU-8604       TCGA-HU-8608 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-HU-8610       TCGA-HU-A4G2       TCGA-HU-A4G3       TCGA-HU-A4G6 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-HU-A4G8       TCGA-HU-A4G9       TCGA-HU-A4GC       TCGA-HU-A4GD 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-HU-A4GF       TCGA-HU-A4GH       TCGA-HU-A4GN       TCGA-HU-A4GP 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-HU-A4GQ       TCGA-HU-A4GT       TCGA-HU-A4GU       TCGA-HU-A4GX 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-HU-A4GY       TCGA-HU-A4H0       TCGA-HU-A4H2       TCGA-HU-A4H3 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-HU-A4H4       TCGA-HU-A4H5       TCGA-HU-A4H6       TCGA-HU-A4H8 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-HU-A4HD       TCGA-IN-7806       TCGA-IN-7808       TCGA-IN-8462 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 
      TCGA-IN-8663       TCGA-IP-7968 
"FBXO48 WILD-TYPE" "FBXO48 WILD-TYPE" 

Clustering(280) Variable = TBC1D22B MUTATION ANALYSIS
D280V1, survival
                    sevent
clus2                  0   1
  TBC1D22B MUTATED     5   1
  TBC1D22B WILD-TYPE 176  79
  TBC1D22B MUTATED TBC1D22B WILD-TYPE 
                 6                255 
  TBC1D22B MUTATED TBC1D22B WILD-TYPE 
                 1                 79 
$`TBC1D22B MUTATED`
TCGA-BR-6566 TCGA-BR-8078 TCGA-BR-8487 TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4GU 
       32.78        12.26         1.12        11.41         0.10         6.25 

$`TBC1D22B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        11.77        29.98         8.98         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  TBC1D22B MUTATED TBC1D22B WILD-TYPE 
               0.1                0.0 
  TBC1D22B MUTATED TBC1D22B WILD-TYPE 
             32.78             105.07 
  TBC1D22B MUTATED TBC1D22B WILD-TYPE 
              8.83              12.76 
[1] "0.1 - 32.8 (8.8)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.5"
D280V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TBC1D22B MUTATED         0        0        0        0         2         3
  TBC1D22B WILD-TYPE       1        9       27       26        29        41
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBC1D22B MUTATED           0          0          0          1        0
  TBC1D22B WILD-TYPE         3         49         36         23       24
D280V3, multiclass
            clus
vv           TBC1D22B MUTATED TBC1D22B WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  0                 27
  STAGE II                  0                 26
  STAGE IIA                 2                 29
  STAGE IIB                 3                 41
  STAGE III                 0                  3
  STAGE IIIA                0                 49
  STAGE IIIB                0                 36
  STAGE IIIC                1                 23
  STAGE IV                  0                 24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  TBC1D22B MUTATED     0   0   4   3
  TBC1D22B WILD-TYPE  11  72 118  72
D280V4, multiclass
    clus
vv   TBC1D22B MUTATED TBC1D22B WILD-TYPE
  T1                0                 11
  T2                0                 72
  T3                4                118
  T4                3                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  TBC1D22B MUTATED    4  1  1  0
  TBC1D22B WILD-TYPE 89 80 49 53
D280V5, multiclass
    clus
vv   TBC1D22B MUTATED TBC1D22B WILD-TYPE
  N0                4                 89
  N1                1                 80
  N2                1                 49
  N3                0                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D280V6, binary
                    cls
clus                   0   1
  TBC1D22B MUTATED     6   0
  TBC1D22B WILD-TYPE 251  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D22B MUTATED      6    0
  TBC1D22B WILD-TYPE  251   18
   clus
vv  TBC1D22B MUTATED TBC1D22B WILD-TYPE
  0                6                251
  1                0                 18
[1] 2 2
[1] FALSE
D280V7, binary
                    cls
clus                   0   1
  TBC1D22B MUTATED     5   2
  TBC1D22B WILD-TYPE 105 177
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D22B MUTATED      5    2
  TBC1D22B WILD-TYPE  105  177
        clus
vv       TBC1D22B MUTATED TBC1D22B WILD-TYPE
  FEMALE                5                105
  MALE                  2                177
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TBC1D22B MUTATED                                       2
  TBC1D22B WILD-TYPE                                    48
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TBC1D22B MUTATED                                                        4
  TBC1D22B WILD-TYPE                                                    131
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TBC1D22B MUTATED                                                                   0
  TBC1D22B WILD-TYPE                                                                40
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TBC1D22B MUTATED                                                  1
  TBC1D22B WILD-TYPE                                               37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TBC1D22B MUTATED                                                          0
  TBC1D22B WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TBC1D22B MUTATED                                                           0
  TBC1D22B WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TBC1D22B MUTATED                                          0
  TBC1D22B WILD-TYPE                                        3
D280V8, multiclass
                                                                   clus
vv                                                                  TBC1D22B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  TBC1D22B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D280V9, binary
                    cls
clus                   0   1
  TBC1D22B MUTATED     0   7
  TBC1D22B WILD-TYPE   5 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D22B MUTATED      0    7
  TBC1D22B WILD-TYPE    5  277
     clus
vv    TBC1D22B MUTATED TBC1D22B WILD-TYPE
  NO                 0                  5
  YES                7                277
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  TBC1D22B MUTATED     6   0   0   1
  TBC1D22B WILD-TYPE 221  10  10  23
D280V10, multiclass
    clus
vv   TBC1D22B MUTATED TBC1D22B WILD-TYPE
  R0                6                221
  R1                0                 10
  R2                0                 10
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D280V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TBC1D22B MUTATED       3                         0     4
  TBC1D22B WILD-TYPE    73                         4   164
D280V12, multiclass
                           clus
vv                          TBC1D22B MUTATED TBC1D22B WILD-TYPE
  ASIAN                                    3                 73
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    4                164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(281) Variable = CDH16 MUTATION ANALYSIS
D281V1, survival
                 sevent
clus2               0   1
  CDH16 MUTATED    10   3
  CDH16 WILD-TYPE 171  77
  CDH16 MUTATED CDH16 WILD-TYPE 
             13             248 
  CDH16 MUTATED CDH16 WILD-TYPE 
              3              77 
$`CDH16 MUTATED`
TCGA-BR-4201 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-8360 TCGA-BR-8368 TCGA-BR-8372 
       30.90        32.78        32.94         6.18         4.31        19.17 
TCGA-BR-8680 TCGA-CG-4306 TCGA-D7-6815 TCGA-FP-7998 TCGA-HJ-7597 TCGA-HU-A4G9 
       15.81         1.02        15.98        22.29        26.47        24.20 
TCGA-HU-A4H3 
       19.36 

$`CDH16 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        2.66        16.31         2.20        15.58         7.40        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        3.48        19.53        14.07        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56        11.08         5.52         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        11.84         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  CDH16 MUTATED CDH16 WILD-TYPE 
           1.02            0.00 
  CDH16 MUTATED CDH16 WILD-TYPE 
          32.94          105.07 
  CDH16 MUTATED CDH16 WILD-TYPE 
          19.36           12.43 
[1] "1.0 - 32.9 (19.4)"  "0.0 - 105.1 (12.4)"
[1] "hr=" "2.1"
D281V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDH16 MUTATED         0        1        2        0         3         1
  CDH16 WILD-TYPE       1        8       25       26        28        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDH16 MUTATED           0          0          0          3        2
  CDH16 WILD-TYPE         3         49         36         21       22
D281V3, multiclass
            clus
vv           CDH16 MUTATED CDH16 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              3              28
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             3              21
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDH16 MUTATED     1   4   4   4
  CDH16 WILD-TYPE  10  68 118  71
D281V4, multiclass
    clus
vv   CDH16 MUTATED CDH16 WILD-TYPE
  T1             1              10
  T2             4              68
  T3             4             118
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CDH16 MUTATED    6  0  3  3
  CDH16 WILD-TYPE 87 81 47 50
D281V5, multiclass
    clus
vv   CDH16 MUTATED CDH16 WILD-TYPE
  N0             6              87
  N1             0              81
  N2             3              47
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D281V6, binary
                 cls
clus                0   1
  CDH16 MUTATED     9   2
  CDH16 WILD-TYPE 248  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH16 MUTATED      9    2
  CDH16 WILD-TYPE  248   16
   clus
vv  CDH16 MUTATED CDH16 WILD-TYPE
  0             9             248
  1             2              16
[1] 2 2
[1] FALSE
D281V7, binary
                 cls
clus                0   1
  CDH16 MUTATED     8   5
  CDH16 WILD-TYPE 102 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH16 MUTATED      8    5
  CDH16 WILD-TYPE  102  174
        clus
vv       CDH16 MUTATED CDH16 WILD-TYPE
  FEMALE             8             102
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CDH16 MUTATED                                       2
  CDH16 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CDH16 MUTATED                                                        6
  CDH16 WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CDH16 MUTATED                                                                   1
  CDH16 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CDH16 MUTATED                                                  3
  CDH16 WILD-TYPE                                               35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CDH16 MUTATED                                                          0
  CDH16 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CDH16 MUTATED                                                           0
  CDH16 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CDH16 MUTATED                                          1
  CDH16 WILD-TYPE                                        2
D281V8, multiclass
                                                                   clus
vv                                                                  CDH16 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  CDH16 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D281V9, binary
                 cls
clus                0   1
  CDH16 MUTATED     0  13
  CDH16 WILD-TYPE   5 271
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH16 MUTATED      0   13
  CDH16 WILD-TYPE    5  271
     clus
vv    CDH16 MUTATED CDH16 WILD-TYPE
  NO              0               5
  YES            13             271
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDH16 MUTATED    11   0   1   1
  CDH16 WILD-TYPE 216  10   9  23
D281V10, multiclass
    clus
vv   CDH16 MUTATED CDH16 WILD-TYPE
  R0            11             216
  R1             0              10
  R2             1               9
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D281V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDH16 MUTATED       3                         0     9
  CDH16 WILD-TYPE    73                         4   159
D281V12, multiclass
                           clus
vv                          CDH16 MUTATED CDH16 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 9             159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(282) Variable = GLT8D1 MUTATION ANALYSIS
D282V1, survival
                  sevent
clus2                0   1
  GLT8D1 MUTATED     3   3
  GLT8D1 WILD-TYPE 178  77
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               6              255 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               3               77 
$`GLT8D1 MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-7703 TCGA-BR-8363 TCGA-CG-5726 TCGA-HU-A4GN 
       26.70        30.90        24.76         0.26        28.96        29.98 

$`GLT8D1 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 
       30.90        31.20        32.94        12.82         9.21        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       19.50        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
            0.26             0.00 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
           30.90           105.07 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
           27.83            12.56 
[1] "0.3 - 30.9 (27.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D282V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GLT8D1 MUTATED         0        2        1        0         1         1
  GLT8D1 WILD-TYPE       1        7       26       26        30        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLT8D1 MUTATED           0          0          0          0        0
  GLT8D1 WILD-TYPE         3         49         36         24       24
D282V3, multiclass
            clus
vv           GLT8D1 MUTATED GLT8D1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                2                7
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GLT8D1 MUTATED     3   3   1   1
  GLT8D1 WILD-TYPE   8  69 121  74
D282V4, multiclass
    clus
vv   GLT8D1 MUTATED GLT8D1 WILD-TYPE
  T1              3                8
  T2              3               69
  T3              1              121
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  GLT8D1 MUTATED    4  1  0  0
  GLT8D1 WILD-TYPE 89 80 50 53
D282V5, multiclass
    clus
vv   GLT8D1 MUTATED GLT8D1 WILD-TYPE
  N0              4               89
  N1              1               80
  N2              0               50
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D282V6, binary
                  cls
clus                 0   1
  GLT8D1 MUTATED     7   0
  GLT8D1 WILD-TYPE 250  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT8D1 MUTATED      7    0
  GLT8D1 WILD-TYPE  250   18
   clus
vv  GLT8D1 MUTATED GLT8D1 WILD-TYPE
  0              7              250
  1              0               18
[1] 2 2
[1] FALSE
D282V7, binary
                  cls
clus                 0   1
  GLT8D1 MUTATED     5   3
  GLT8D1 WILD-TYPE 105 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT8D1 MUTATED      5    3
  GLT8D1 WILD-TYPE  105  176
        clus
vv       GLT8D1 MUTATED GLT8D1 WILD-TYPE
  FEMALE              5              105
  MALE                3              176
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GLT8D1 MUTATED                                       1
  GLT8D1 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GLT8D1 MUTATED                                                        4
  GLT8D1 WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GLT8D1 MUTATED                                                                   1
  GLT8D1 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GLT8D1 MUTATED                                                  1
  GLT8D1 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GLT8D1 MUTATED                                                          0
  GLT8D1 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GLT8D1 MUTATED                                                           1
  GLT8D1 WILD-TYPE                                                         5
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GLT8D1 MUTATED                                          0
  GLT8D1 WILD-TYPE                                        3
D282V8, multiclass
                                                                   clus
vv                                                                  GLT8D1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  GLT8D1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D282V9, binary
                  cls
clus                 0   1
  GLT8D1 MUTATED     0   8
  GLT8D1 WILD-TYPE   5 276
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT8D1 MUTATED      0    8
  GLT8D1 WILD-TYPE    5  276
     clus
vv    GLT8D1 MUTATED GLT8D1 WILD-TYPE
  NO               0                5
  YES              8              276
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GLT8D1 MUTATED     5   0   0   3
  GLT8D1 WILD-TYPE 222  10  10  21
D282V10, multiclass
    clus
vv   GLT8D1 MUTATED GLT8D1 WILD-TYPE
  R0              5              222
  R1              0               10
  R2              0               10
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D282V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GLT8D1 MUTATED       1                         0     6
  GLT8D1 WILD-TYPE    75                         4   162
D282V12, multiclass
                           clus
vv                          GLT8D1 MUTATED GLT8D1 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(283) Variable = TAS2R42 MUTATION ANALYSIS
D283V1, survival
                   sevent
clus2                 0   1
  TAS2R42 MUTATED     3   1
  TAS2R42 WILD-TYPE 178  79
  TAS2R42 MUTATED TAS2R42 WILD-TYPE 
                4               257 
  TAS2R42 MUTATED TAS2R42 WILD-TYPE 
                1                79 
$`TAS2R42 MUTATED`
TCGA-BR-8081 TCGA-BR-8363 TCGA-HU-A4GD TCGA-HU-A4H2 
       20.55         0.26        22.75        12.95 

$`TAS2R42 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        19.50        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  TAS2R42 MUTATED TAS2R42 WILD-TYPE 
             0.26              0.00 
  TAS2R42 MUTATED TAS2R42 WILD-TYPE 
            22.75            105.07 
  TAS2R42 MUTATED TAS2R42 WILD-TYPE 
            16.75             12.59 
[1] "0.3 - 22.8 (16.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D283V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TAS2R42 MUTATED         0        0        1        0         0         2
  TAS2R42 WILD-TYPE       1        9       26       26        31        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TAS2R42 MUTATED           0          0          1          0        0
  TAS2R42 WILD-TYPE         3         49         35         24       24
D283V3, multiclass
            clus
vv           TAS2R42 MUTATED TAS2R42 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 0                26
  STAGE IIA                0                31
  STAGE IIB                2                42
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               1                35
  STAGE IIIC               0                24
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TAS2R42 MUTATED     0   1   2   1
  TAS2R42 WILD-TYPE  11  71 120  74
D283V4, multiclass
    clus
vv   TAS2R42 MUTATED TAS2R42 WILD-TYPE
  T1               0                11
  T2               1                71
  T3               2               120
  T4               1                74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  TAS2R42 MUTATED    2  1  0  1
  TAS2R42 WILD-TYPE 91 80 50 52
D283V5, multiclass
    clus
vv   TAS2R42 MUTATED TAS2R42 WILD-TYPE
  N0               2                91
  N1               1                80
  N2               0                50
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D283V6, binary
                   cls
clus                  0   1
  TAS2R42 MUTATED     4   0
  TAS2R42 WILD-TYPE 253  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R42 MUTATED      4    0
  TAS2R42 WILD-TYPE  253   18
   clus
vv  TAS2R42 MUTATED TAS2R42 WILD-TYPE
  0               4               253
  1               0                18
[1] 2 2
[1] FALSE
D283V7, binary
                   cls
clus                  0   1
  TAS2R42 MUTATED     3   1
  TAS2R42 WILD-TYPE 107 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R42 MUTATED      3    1
  TAS2R42 WILD-TYPE  107  178
        clus
vv       TAS2R42 MUTATED TAS2R42 WILD-TYPE
  FEMALE               3               107
  MALE                 1               178
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TAS2R42 MUTATED                                       0
  TAS2R42 WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TAS2R42 MUTATED                                                        2
  TAS2R42 WILD-TYPE                                                    133
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TAS2R42 MUTATED                                                                   0
  TAS2R42 WILD-TYPE                                                                40
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TAS2R42 MUTATED                                                  2
  TAS2R42 WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TAS2R42 MUTATED                                                          0
  TAS2R42 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TAS2R42 MUTATED                                                           0
  TAS2R42 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TAS2R42 MUTATED                                          0
  TAS2R42 WILD-TYPE                                        3
D283V8, multiclass
                                                                   clus
vv                                                                  TAS2R42 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  TAS2R42 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D283V9, binary
                   cls
clus                  0   1
  TAS2R42 MUTATED     0   4
  TAS2R42 WILD-TYPE   5 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R42 MUTATED      0    4
  TAS2R42 WILD-TYPE    5  280
     clus
vv    TAS2R42 MUTATED TAS2R42 WILD-TYPE
  NO                0                 5
  YES               4               280
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TAS2R42 MUTATED     4   0   0   0
  TAS2R42 WILD-TYPE 223  10  10  24
D283V10, multiclass
    clus
vv   TAS2R42 MUTATED TAS2R42 WILD-TYPE
  R0               4               223
  R1               0                10
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D283V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TAS2R42 MUTATED       2                         0     2
  TAS2R42 WILD-TYPE    74                         4   166
D283V12, multiclass
                           clus
vv                          TAS2R42 MUTATED TAS2R42 WILD-TYPE
  ASIAN                                   2                74
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   2               166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(284) Variable = POP1 MUTATION ANALYSIS
D284V1, survival
                sevent
clus2              0   1
  POP1 MUTATED    10   6
  POP1 WILD-TYPE 171  74
  POP1 MUTATED POP1 WILD-TYPE 
            16            245 
  POP1 MUTATED POP1 WILD-TYPE 
             6             74 
$`POP1 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-8059 
       26.70         6.97        18.35        32.94         9.21        14.43 
TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-4300 
       20.55        19.50        19.17        15.81         6.58        20.02 
TCGA-CG-5721 TCGA-FP-A4BE TCGA-HU-A4GN TCGA-IN-7808 
        6.02        11.08        29.98         3.45 

$`POP1 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 
       11.70         6.61         4.64         7.43        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       31.20        12.82        24.76        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       12.76        18.71        17.49         0.69        12.26         9.60 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20         0.10        12.62         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       24.20         3.25        22.75        25.81        11.77         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21        18.81         3.39         2.53 

  POP1 MUTATED POP1 WILD-TYPE 
          3.45           0.00 
  POP1 MUTATED POP1 WILD-TYPE 
         32.94         105.07 
  POP1 MUTATED POP1 WILD-TYPE 
         17.08          12.56 
[1] "3.5 - 32.9 (17.1)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1"  
D284V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  POP1 MUTATED         0        0        1        1         4         2
  POP1 WILD-TYPE       1        9       26       25        27        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  POP1 MUTATED           2          1          1          2        2
  POP1 WILD-TYPE         1         48         35         22       22
D284V3, multiclass
            clus
vv           POP1 MUTATED POP1 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              1             25
  STAGE IIA             4             27
  STAGE IIB             2             42
  STAGE III             2              1
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            2             22
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  POP1 MUTATED     0   2   8   7
  POP1 WILD-TYPE  11  70 114  68
D284V4, multiclass
    clus
vv   POP1 MUTATED POP1 WILD-TYPE
  T1            0             11
  T2            2             70
  T3            8            114
  T4            7             68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  POP1 MUTATED    7  5  3  2
  POP1 WILD-TYPE 86 76 47 51
D284V5, multiclass
    clus
vv   POP1 MUTATED POP1 WILD-TYPE
  N0            7             86
  N1            5             76
  N2            3             47
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D284V6, binary
                cls
clus               0   1
  POP1 MUTATED    15   2
  POP1 WILD-TYPE 242  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  POP1 MUTATED     15    2
  POP1 WILD-TYPE  242   16
   clus
vv  POP1 MUTATED POP1 WILD-TYPE
  0           15            242
  1            2             16
[1] 2 2
[1] FALSE
D284V7, binary
                cls
clus               0   1
  POP1 MUTATED     5  14
  POP1 WILD-TYPE 105 165
[1] "tbl2"
                cls
clus             [,1] [,2]
  POP1 MUTATED      5   14
  POP1 WILD-TYPE  105  165
        clus
vv       POP1 MUTATED POP1 WILD-TYPE
  FEMALE            5            105
  MALE             14            165
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  POP1 MUTATED                                       3
  POP1 WILD-TYPE                                    47
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  POP1 MUTATED                                                       11
  POP1 WILD-TYPE                                                    124
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  POP1 MUTATED                                                                   3
  POP1 WILD-TYPE                                                                37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  POP1 MUTATED                                                  2
  POP1 WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  POP1 MUTATED                                                          0
  POP1 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  POP1 MUTATED                                                           0
  POP1 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  POP1 MUTATED                                          0
  POP1 WILD-TYPE                                        3
D284V8, multiclass
                                                                   clus
vv                                                                  POP1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  POP1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D284V9, binary
                cls
clus               0   1
  POP1 MUTATED     0  19
  POP1 WILD-TYPE   5 265
[1] "tbl2"
                cls
clus             [,1] [,2]
  POP1 MUTATED      0   19
  POP1 WILD-TYPE    5  265
     clus
vv    POP1 MUTATED POP1 WILD-TYPE
  NO             0              5
  YES           19            265
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  POP1 MUTATED    13   0   0   4
  POP1 WILD-TYPE 214  10  10  20
D284V10, multiclass
    clus
vv   POP1 MUTATED POP1 WILD-TYPE
  R0           13            214
  R1            0             10
  R2            0             10
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D284V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  POP1 MUTATED       3                         1    12
  POP1 WILD-TYPE    73                         3   156
D284V12, multiclass
                           clus
vv                          POP1 MUTATED POP1 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                               12            156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(285) Variable = PIGO MUTATION ANALYSIS
D285V1, survival
                sevent
clus2              0   1
  PIGO MUTATED     8   1
  PIGO WILD-TYPE 173  79
  PIGO MUTATED PIGO WILD-TYPE 
             9            252 
  PIGO MUTATED PIGO WILD-TYPE 
             1             79 
$`PIGO MUTATED`
TCGA-BR-6452 TCGA-BR-8366 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8536 
       34.68         0.95         1.12        15.81        11.57         0.10 
TCGA-CD-A4MI TCGA-CG-5733 TCGA-HU-A4H3 
        0.10        21.07        19.36 

$`PIGO WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        13.64         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 
        0.13         0.16         0.10         0.10         0.13         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10         4.01        69.04         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  PIGO MUTATED PIGO WILD-TYPE 
           0.1            0.0 
  PIGO MUTATED PIGO WILD-TYPE 
         34.68         105.07 
  PIGO MUTATED PIGO WILD-TYPE 
         11.57          12.64 
[1] "0.1 - 34.7 (11.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.5"
D285V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIGO MUTATED         0        0        0        2         3         0
  PIGO WILD-TYPE       1        9       27       24        28        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIGO MUTATED           0          1          2          1        1
  PIGO WILD-TYPE         3         48         34         23       23
D285V3, multiclass
            clus
vv           PIGO MUTATED PIGO WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              2             24
  STAGE IIA             3             28
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            2             34
  STAGE IIIC            1             23
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PIGO MUTATED     0   2   6   2
  PIGO WILD-TYPE  11  70 116  73
D285V4, multiclass
    clus
vv   PIGO MUTATED PIGO WILD-TYPE
  T1            0             11
  T2            2             70
  T3            6            116
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  PIGO MUTATED    4  2  2  2
  PIGO WILD-TYPE 89 79 48 51
D285V5, multiclass
    clus
vv   PIGO MUTATED PIGO WILD-TYPE
  N0            4             89
  N1            2             79
  N2            2             48
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D285V6, binary
                cls
clus               0   1
  PIGO MUTATED     9   1
  PIGO WILD-TYPE 248  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGO MUTATED      9    1
  PIGO WILD-TYPE  248   17
   clus
vv  PIGO MUTATED PIGO WILD-TYPE
  0            9            248
  1            1             17
[1] 2 2
[1] FALSE
D285V7, binary
                cls
clus               0   1
  PIGO MUTATED     6   4
  PIGO WILD-TYPE 104 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGO MUTATED      6    4
  PIGO WILD-TYPE  104  175
        clus
vv       PIGO MUTATED PIGO WILD-TYPE
  FEMALE            6            104
  MALE              4            175
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PIGO MUTATED                                       1
  PIGO WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIGO MUTATED                                                        6
  PIGO WILD-TYPE                                                    129
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIGO MUTATED                                                                   1
  PIGO WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PIGO MUTATED                                                  1
  PIGO WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PIGO MUTATED                                                          1
  PIGO WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PIGO MUTATED                                                           0
  PIGO WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PIGO MUTATED                                          0
  PIGO WILD-TYPE                                        3
D285V8, multiclass
                                                                   clus
vv                                                                  PIGO MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  PIGO WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D285V9, binary
                cls
clus               0   1
  PIGO MUTATED     1   9
  PIGO WILD-TYPE   4 275
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGO MUTATED      1    9
  PIGO WILD-TYPE    4  275
     clus
vv    PIGO MUTATED PIGO WILD-TYPE
  NO             1              4
  YES            9            275
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PIGO MUTATED     9   0   0   0
  PIGO WILD-TYPE 218  10  10  24
D285V10, multiclass
    clus
vv   PIGO MUTATED PIGO WILD-TYPE
  R0            9            218
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D285V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIGO MUTATED       4                         0     4
  PIGO WILD-TYPE    72                         4   164
D285V12, multiclass
                           clus
vv                          PIGO MUTATED PIGO WILD-TYPE
  ASIAN                                4             72
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                4            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(286) Variable = NEXN MUTATION ANALYSIS
D286V1, survival
                sevent
clus2              0   1
  NEXN MUTATED     5   2
  NEXN WILD-TYPE 176  78
  NEXN MUTATED NEXN WILD-TYPE 
             7            254 
  NEXN MUTATED NEXN WILD-TYPE 
             2             78 
$`NEXN MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-7707 TCGA-BR-8680 TCGA-CD-5802 TCGA-CG-5723 
        6.97        30.90        23.93        15.81         0.30       105.07 
TCGA-HU-A4G8 
       11.84 

$`NEXN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 
        5.13         2.83         3.25        13.15        13.18         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  NEXN MUTATED NEXN WILD-TYPE 
           0.3            0.0 
  NEXN MUTATED NEXN WILD-TYPE 
        105.07          79.07 
  NEXN MUTATED NEXN WILD-TYPE 
        15.810         12.605 
[1] "0.3 - 105.1 (15.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "2"  
D286V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NEXN MUTATED         0        0        1        3         0         1
  NEXN WILD-TYPE       1        9       26       23        31        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NEXN MUTATED           0          1          0          0        1
  NEXN WILD-TYPE         3         48         36         24       23
D286V3, multiclass
            clus
vv           NEXN MUTATED NEXN WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              3             23
  STAGE IIA             0             31
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NEXN MUTATED     0   4   3   1
  NEXN WILD-TYPE  11  68 119  74
D286V4, multiclass
    clus
vv   NEXN MUTATED NEXN WILD-TYPE
  T1            0             11
  T2            4             68
  T3            3            119
  T4            1             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  NEXN MUTATED    2  4  1  0
  NEXN WILD-TYPE 91 77 49 53
D286V5, multiclass
    clus
vv   NEXN MUTATED NEXN WILD-TYPE
  N0            2             91
  N1            4             77
  N2            1             49
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D286V6, binary
                cls
clus               0   1
  NEXN MUTATED     6   1
  NEXN WILD-TYPE 251  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEXN MUTATED      6    1
  NEXN WILD-TYPE  251   17
   clus
vv  NEXN MUTATED NEXN WILD-TYPE
  0            6            251
  1            1             17
[1] 2 2
[1] FALSE
D286V7, binary
                cls
clus               0   1
  NEXN MUTATED     3   5
  NEXN WILD-TYPE 107 174
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEXN MUTATED      3    5
  NEXN WILD-TYPE  107  174
        clus
vv       NEXN MUTATED NEXN WILD-TYPE
  FEMALE            3            107
  MALE              5            174
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NEXN MUTATED                                       1
  NEXN WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NEXN MUTATED                                                        5
  NEXN WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NEXN MUTATED                                                                   0
  NEXN WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NEXN MUTATED                                                  1
  NEXN WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NEXN MUTATED                                                          1
  NEXN WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NEXN MUTATED                                                           0
  NEXN WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NEXN MUTATED                                          0
  NEXN WILD-TYPE                                        3
D286V8, multiclass
                                                                   clus
vv                                                                  NEXN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  NEXN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D286V9, binary
                cls
clus               0   1
  NEXN MUTATED     1   7
  NEXN WILD-TYPE   4 277
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEXN MUTATED      1    7
  NEXN WILD-TYPE    4  277
     clus
vv    NEXN MUTATED NEXN WILD-TYPE
  NO             1              4
  YES            7            277
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NEXN MUTATED     4   0   0   2
  NEXN WILD-TYPE 223  10  10  22
D286V10, multiclass
    clus
vv   NEXN MUTATED NEXN WILD-TYPE
  R0            4            223
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D286V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NEXN MUTATED       3                         0     3
  NEXN WILD-TYPE    73                         4   165
D286V12, multiclass
                           clus
vv                          NEXN MUTATED NEXN WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                3            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(287) Variable = CLDN6 MUTATION ANALYSIS
D287V1, survival
                 sevent
clus2               0   1
  CLDN6 MUTATED     5   1
  CLDN6 WILD-TYPE 176  79
  CLDN6 MUTATED CLDN6 WILD-TYPE 
              6             255 
  CLDN6 MUTATED CLDN6 WILD-TYPE 
              1              79 
$`CLDN6 MUTATED`
TCGA-BR-7707 TCGA-BR-8368 TCGA-BR-8680 TCGA-BR-A4QL TCGA-D7-A4YV TCGA-HU-A4GT 
       23.93         4.31        15.81        11.57         5.92         6.51 

$`CLDN6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       16.44        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         0.10         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  CLDN6 MUTATED CLDN6 WILD-TYPE 
           4.31            0.00 
  CLDN6 MUTATED CLDN6 WILD-TYPE 
          23.93          105.07 
  CLDN6 MUTATED CLDN6 WILD-TYPE 
           9.04           12.66 
[1] "4.3 - 23.9 (9.0)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.3"
D287V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CLDN6 MUTATED         0        0        2        0         1         1
  CLDN6 WILD-TYPE       1        9       25       26        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLDN6 MUTATED           0          1          1          0        1
  CLDN6 WILD-TYPE         3         48         35         24       23
D287V3, multiclass
            clus
vv           CLDN6 MUTATED CLDN6 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CLDN6 MUTATED     0   2   3   2
  CLDN6 WILD-TYPE  11  70 119  73
D287V4, multiclass
    clus
vv   CLDN6 MUTATED CLDN6 WILD-TYPE
  T1             0              11
  T2             2              70
  T3             3             119
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CLDN6 MUTATED    4  1  1  1
  CLDN6 WILD-TYPE 89 80 49 52
D287V5, multiclass
    clus
vv   CLDN6 MUTATED CLDN6 WILD-TYPE
  N0             4              89
  N1             1              80
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D287V6, binary
                 cls
clus                0   1
  CLDN6 MUTATED     6   1
  CLDN6 WILD-TYPE 251  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN6 MUTATED      6    1
  CLDN6 WILD-TYPE  251   17
   clus
vv  CLDN6 MUTATED CLDN6 WILD-TYPE
  0             6             251
  1             1              17
[1] 2 2
[1] FALSE
D287V7, binary
                 cls
clus                0   1
  CLDN6 MUTATED     6   1
  CLDN6 WILD-TYPE 104 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN6 MUTATED      6    1
  CLDN6 WILD-TYPE  104  178
        clus
vv       CLDN6 MUTATED CLDN6 WILD-TYPE
  FEMALE             6             104
  MALE               1             178
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CLDN6 MUTATED                                       0
  CLDN6 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CLDN6 MUTATED                                                        4
  CLDN6 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CLDN6 MUTATED                                                                   0
  CLDN6 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CLDN6 MUTATED                                                  3
  CLDN6 WILD-TYPE                                               35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CLDN6 MUTATED                                                          0
  CLDN6 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CLDN6 MUTATED                                                           0
  CLDN6 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CLDN6 MUTATED                                          0
  CLDN6 WILD-TYPE                                        3
D287V8, multiclass
                                                                   clus
vv                                                                  CLDN6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  CLDN6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D287V9, binary
                 cls
clus                0   1
  CLDN6 MUTATED     0   7
  CLDN6 WILD-TYPE   5 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN6 MUTATED      0    7
  CLDN6 WILD-TYPE    5  277
     clus
vv    CLDN6 MUTATED CLDN6 WILD-TYPE
  NO              0               5
  YES             7             277
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CLDN6 MUTATED     6   0   0   1
  CLDN6 WILD-TYPE 221  10  10  23
D287V10, multiclass
    clus
vv   CLDN6 MUTATED CLDN6 WILD-TYPE
  R0             6             221
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D287V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CLDN6 MUTATED       2                         0     5
  CLDN6 WILD-TYPE    74                         4   163
D287V12, multiclass
                           clus
vv                          CLDN6 MUTATED CLDN6 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(288) Variable = MTIF2 MUTATION ANALYSIS
D288V1, survival
                 sevent
clus2               0   1
  MTIF2 MUTATED    10   3
  MTIF2 WILD-TYPE 171  77
  MTIF2 MUTATED MTIF2 WILD-TYPE 
             13             248 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
              3              77 
$`MTIF2 MUTATED`
TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-A4J4 
        6.97        32.94        24.76         1.12        15.81         0.53 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5728 TCGA-HU-A4G8 
        6.58         0.10         1.02         6.02        65.10        11.84 
TCGA-HU-A4GT 
        6.51 

$`MTIF2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 
       21.11        30.90        31.20        12.82         9.21        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.72        14.17         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ 
        9.34        11.31        12.43        11.61        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        28.96        79.07         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         0.10         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  MTIF2 MUTATED MTIF2 WILD-TYPE 
            0.1             0.0 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
          65.10          105.07 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
          6.580          12.775 
[1] "0.1 - 65.1 (6.6)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.2"
D288V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MTIF2 MUTATED         0        1        1        1         4         1
  MTIF2 WILD-TYPE       1        8       26       25        27        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MTIF2 MUTATED           0          2          3          0        2
  MTIF2 WILD-TYPE         3         47         33         24       22
D288V3, multiclass
            clus
vv           MTIF2 MUTATED MTIF2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              4              27
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             3              33
  STAGE IIIC             0              24
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MTIF2 MUTATED     1   2   8   4
  MTIF2 WILD-TYPE  10  70 114  71
D288V4, multiclass
    clus
vv   MTIF2 MUTATED MTIF2 WILD-TYPE
  T1             1              10
  T2             2              70
  T3             8             114
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  MTIF2 MUTATED    7  6  2  0
  MTIF2 WILD-TYPE 86 75 48 53
D288V5, multiclass
    clus
vv   MTIF2 MUTATED MTIF2 WILD-TYPE
  N0             7              86
  N1             6              75
  N2             2              48
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D288V6, binary
                 cls
clus                0   1
  MTIF2 MUTATED    13   1
  MTIF2 WILD-TYPE 244  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF2 MUTATED     13    1
  MTIF2 WILD-TYPE  244   17
   clus
vv  MTIF2 MUTATED MTIF2 WILD-TYPE
  0            13             244
  1             1              17
[1] 2 2
[1] FALSE
D288V7, binary
                 cls
clus                0   1
  MTIF2 MUTATED     6   9
  MTIF2 WILD-TYPE 104 170
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF2 MUTATED      6    9
  MTIF2 WILD-TYPE  104  170
        clus
vv       MTIF2 MUTATED MTIF2 WILD-TYPE
  FEMALE             6             104
  MALE               9             170
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MTIF2 MUTATED                                       2
  MTIF2 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MTIF2 MUTATED                                                        8
  MTIF2 WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MTIF2 MUTATED                                                                   2
  MTIF2 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MTIF2 MUTATED                                                  1
  MTIF2 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MTIF2 MUTATED                                                          1
  MTIF2 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MTIF2 MUTATED                                                           1
  MTIF2 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MTIF2 MUTATED                                          0
  MTIF2 WILD-TYPE                                        3
D288V8, multiclass
                                                                   clus
vv                                                                  MTIF2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  MTIF2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D288V9, binary
                 cls
clus                0   1
  MTIF2 MUTATED     1  14
  MTIF2 WILD-TYPE   4 270
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF2 MUTATED      1   14
  MTIF2 WILD-TYPE    4  270
     clus
vv    MTIF2 MUTATED MTIF2 WILD-TYPE
  NO              1               4
  YES            14             270
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MTIF2 MUTATED     9   0   1   2
  MTIF2 WILD-TYPE 218  10   9  22
D288V10, multiclass
    clus
vv   MTIF2 MUTATED MTIF2 WILD-TYPE
  R0             9             218
  R1             0              10
  R2             1               9
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D288V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MTIF2 MUTATED       5                         0     6
  MTIF2 WILD-TYPE    71                         4   162
D288V12, multiclass
                           clus
vv                          MTIF2 MUTATED MTIF2 WILD-TYPE
  ASIAN                                 5              71
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(289) Variable = HAUS6 MUTATION ANALYSIS
D289V1, survival
                 sevent
clus2               0   1
  HAUS6 MUTATED     6   3
  HAUS6 WILD-TYPE 175  77
  HAUS6 MUTATED HAUS6 WILD-TYPE 
              9             252 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
              3              77 
$`HAUS6 MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8680 TCGA-BR-A4QL 
        6.97         6.61        34.68        32.78        15.81        11.57 
TCGA-CD-8536 TCGA-CG-5721 TCGA-CG-5726 
        0.10         6.02        28.96 

$`HAUS6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       30.90         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       13.68        19.33        39.12        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
        0.16         0.10         0.10         0.13         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 
        0.99         0.99       105.07        12.03        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  HAUS6 MUTATED HAUS6 WILD-TYPE 
            0.1             0.0 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
          34.68          105.07 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
          11.57           12.64 
[1] "0.1 - 34.7 (11.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D289V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HAUS6 MUTATED         0        1        0        2         2         0
  HAUS6 WILD-TYPE       1        8       27       24        29        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HAUS6 MUTATED           1          2          1          0        2
  HAUS6 WILD-TYPE         2         47         35         24       22
D289V3, multiclass
            clus
vv           HAUS6 MUTATED HAUS6 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               2              24
  STAGE IIA              2              29
  STAGE IIB              0              44
  STAGE III              1               2
  STAGE IIIA             2              47
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HAUS6 MUTATED     1   2   6   2
  HAUS6 WILD-TYPE  10  70 116  73
D289V4, multiclass
    clus
vv   HAUS6 MUTATED HAUS6 WILD-TYPE
  T1             1              10
  T2             2              70
  T3             6             116
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  HAUS6 MUTATED    4  5  1  1
  HAUS6 WILD-TYPE 89 76 49 52
D289V5, multiclass
    clus
vv   HAUS6 MUTATED HAUS6 WILD-TYPE
  N0             4              89
  N1             5              76
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D289V6, binary
                 cls
clus                0   1
  HAUS6 MUTATED     9   1
  HAUS6 WILD-TYPE 248  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED      9    1
  HAUS6 WILD-TYPE  248   17
   clus
vv  HAUS6 MUTATED HAUS6 WILD-TYPE
  0             9             248
  1             1              17
[1] 2 2
[1] FALSE
D289V7, binary
                 cls
clus                0   1
  HAUS6 MUTATED     4   7
  HAUS6 WILD-TYPE 106 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED      4    7
  HAUS6 WILD-TYPE  106  172
        clus
vv       HAUS6 MUTATED HAUS6 WILD-TYPE
  FEMALE             4             106
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  HAUS6 MUTATED                                       0
  HAUS6 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HAUS6 MUTATED                                                        7
  HAUS6 WILD-TYPE                                                    128
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HAUS6 MUTATED                                                                   2
  HAUS6 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  HAUS6 MUTATED                                                  1
  HAUS6 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  HAUS6 MUTATED                                                          1
  HAUS6 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  HAUS6 MUTATED                                                           0
  HAUS6 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  HAUS6 MUTATED                                          0
  HAUS6 WILD-TYPE                                        3
D289V8, multiclass
                                                                   clus
vv                                                                  HAUS6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  HAUS6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D289V9, binary
                 cls
clus                0   1
  HAUS6 MUTATED     2   9
  HAUS6 WILD-TYPE   3 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED      2    9
  HAUS6 WILD-TYPE    3  275
     clus
vv    HAUS6 MUTATED HAUS6 WILD-TYPE
  NO              2               3
  YES             9             275
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HAUS6 MUTATED     8   1   0   2
  HAUS6 WILD-TYPE 219   9  10  22
D289V10, multiclass
    clus
vv   HAUS6 MUTATED HAUS6 WILD-TYPE
  R0             8             219
  R1             1               9
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D289V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HAUS6 MUTATED       2                         0     5
  HAUS6 WILD-TYPE    74                         4   163
D289V12, multiclass
                           clus
vv                          HAUS6 MUTATED HAUS6 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(290) Variable = PLEKHO1 MUTATION ANALYSIS
D290V1, survival
                   sevent
clus2                 0   1
  PLEKHO1 MUTATED     3   1
  PLEKHO1 WILD-TYPE 178  79
  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE 
                4               257 
  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE 
                1                79 
$`PLEKHO1 MUTATED`
TCGA-BR-8363 TCGA-BR-8589 TCGA-BR-8680 TCGA-CG-5723 
        0.26        15.81        15.81       105.07 

$`PLEKHO1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40         6.18        19.50        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 
       25.18         9.21        20.22         1.12        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE 
             0.26              0.00 
  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE 
           105.07             79.07 
  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE 
            15.81             12.59 
[1] "0.3 - 105.1 (15.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "2.6"
D290V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLEKHO1 MUTATED         1        0        1        1         0         0
  PLEKHO1 WILD-TYPE       0        9       26       25        31        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHO1 MUTATED           0          0          1          0        1
  PLEKHO1 WILD-TYPE         3         49         35         24       23
D290V3, multiclass
            clus
vv           PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 1                25
  STAGE IIA                0                31
  STAGE IIB                0                44
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               1                35
  STAGE IIIC               0                24
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHO1 MUTATED     2   2   0   2
  PLEKHO1 WILD-TYPE   9  70 122  73
D290V4, multiclass
    clus
vv   PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  T1               2                 9
  T2               2                70
  T3               0               122
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  PLEKHO1 MUTATED    1  3  1  0
  PLEKHO1 WILD-TYPE 92 78 49 53
D290V5, multiclass
    clus
vv   PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  N0               1                92
  N1               3                78
  N2               1                49
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D290V6, binary
                   cls
clus                  0   1
  PLEKHO1 MUTATED     5   1
  PLEKHO1 WILD-TYPE 252  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHO1 MUTATED      5    1
  PLEKHO1 WILD-TYPE  252   17
   clus
vv  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  0               5               252
  1               1                17
[1] 2 2
[1] FALSE
D290V7, binary
                   cls
clus                  0   1
  PLEKHO1 MUTATED     3   4
  PLEKHO1 WILD-TYPE 107 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHO1 MUTATED      3    4
  PLEKHO1 WILD-TYPE  107  175
        clus
vv       PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  FEMALE               3               107
  MALE                 4               175
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PLEKHO1 MUTATED                                       0
  PLEKHO1 WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLEKHO1 MUTATED                                                        6
  PLEKHO1 WILD-TYPE                                                    129
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLEKHO1 MUTATED                                                                   0
  PLEKHO1 WILD-TYPE                                                                40
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PLEKHO1 MUTATED                                                  1
  PLEKHO1 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PLEKHO1 MUTATED                                                          0
  PLEKHO1 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PLEKHO1 MUTATED                                                           0
  PLEKHO1 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PLEKHO1 MUTATED                                          0
  PLEKHO1 WILD-TYPE                                        3
D290V8, multiclass
                                                                   clus
vv                                                                  PLEKHO1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  PLEKHO1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D290V9, binary
                   cls
clus                  0   1
  PLEKHO1 MUTATED     0   7
  PLEKHO1 WILD-TYPE   5 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHO1 MUTATED      0    7
  PLEKHO1 WILD-TYPE    5  277
     clus
vv    PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  NO                0                 5
  YES               7               277
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PLEKHO1 MUTATED     5   0   0   2
  PLEKHO1 WILD-TYPE 222  10  10  22
D290V10, multiclass
    clus
vv   PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  R0               5               222
  R1               0                10
  R2               0                10
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D290V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLEKHO1 MUTATED       1                         1     4
  PLEKHO1 WILD-TYPE    75                         3   164
D290V12, multiclass
                           clus
vv                          PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  ASIAN                                   1                75
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   4               164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(291) Variable = ASPN MUTATION ANALYSIS
D291V1, survival
                sevent
clus2              0   1
  ASPN MUTATED     4   2
  ASPN WILD-TYPE 177  78
  ASPN MUTATED ASPN WILD-TYPE 
             6            255 
  ASPN MUTATED ASPN WILD-TYPE 
             2             78 
$`ASPN MUTATED`
TCGA-BR-7703 TCGA-BR-8081 TCGA-BR-8372 TCGA-BR-8680 TCGA-CG-4306 TCGA-CG-5726 
       24.76        20.55        19.17        15.81         1.02        28.96 

$`ASPN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       17.49        14.43         0.69        12.26         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  ASPN MUTATED ASPN WILD-TYPE 
          1.02           0.00 
  ASPN MUTATED ASPN WILD-TYPE 
         28.96         105.07 
  ASPN MUTATED ASPN WILD-TYPE 
         19.86          12.56 
[1] "1.0 - 29.0 (19.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D291V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ASPN MUTATED         0        2        0        0         0         1
  ASPN WILD-TYPE       1        7       27       26        31        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ASPN MUTATED           0          0          0          1        2
  ASPN WILD-TYPE         3         49         36         23       22
D291V3, multiclass
            clus
vv           ASPN MUTATED ASPN WILD-TYPE
  STAGE I               0              1
  STAGE IA              2              7
  STAGE IB              0             27
  STAGE II              0             26
  STAGE IIA             0             31
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            1             23
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ASPN MUTATED     2   0   1   3
  ASPN WILD-TYPE   9  72 121  72
D291V4, multiclass
    clus
vv   ASPN MUTATED ASPN WILD-TYPE
  T1            2              9
  T2            0             72
  T3            1            121
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  ASPN MUTATED    3  0  2  1
  ASPN WILD-TYPE 90 81 48 52
D291V5, multiclass
    clus
vv   ASPN MUTATED ASPN WILD-TYPE
  N0            3             90
  N1            0             81
  N2            2             48
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D291V6, binary
                cls
clus               0   1
  ASPN MUTATED     4   2
  ASPN WILD-TYPE 253  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPN MUTATED      4    2
  ASPN WILD-TYPE  253   16
   clus
vv  ASPN MUTATED ASPN WILD-TYPE
  0            4            253
  1            2             16
[1] 2 2
[1] FALSE
D291V7, binary
                cls
clus               0   1
  ASPN MUTATED     1   5
  ASPN WILD-TYPE 109 174
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPN MUTATED      1    5
  ASPN WILD-TYPE  109  174
        clus
vv       ASPN MUTATED ASPN WILD-TYPE
  FEMALE            1            109
  MALE              5            174
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ASPN MUTATED                                       0
  ASPN WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ASPN MUTATED                                                        3
  ASPN WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ASPN MUTATED                                                                   1
  ASPN WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ASPN MUTATED                                                  1
  ASPN WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ASPN MUTATED                                                          0
  ASPN WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ASPN MUTATED                                                           1
  ASPN WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ASPN MUTATED                                          0
  ASPN WILD-TYPE                                        3
D291V8, multiclass
                                                                   clus
vv                                                                  ASPN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  ASPN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D291V9, binary
                cls
clus               0   1
  ASPN MUTATED     0   6
  ASPN WILD-TYPE   5 278
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPN MUTATED      0    6
  ASPN WILD-TYPE    5  278
     clus
vv    ASPN MUTATED ASPN WILD-TYPE
  NO             0              5
  YES            6            278
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ASPN MUTATED     5   0   1   0
  ASPN WILD-TYPE 222  10   9  24
D291V10, multiclass
    clus
vv   ASPN MUTATED ASPN WILD-TYPE
  R0            5            222
  R1            0             10
  R2            1              9
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D291V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ASPN MUTATED       1                         0     3
  ASPN WILD-TYPE    75                         4   165
D291V12, multiclass
                           clus
vv                          ASPN MUTATED ASPN WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                3            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(292) Variable = HTR1E MUTATION ANALYSIS
D292V1, survival
                 sevent
clus2               0   1
  HTR1E MUTATED     5   3
  HTR1E WILD-TYPE 176  77
  HTR1E MUTATED HTR1E WILD-TYPE 
              8             253 
  HTR1E MUTATED HTR1E WILD-TYPE 
              3              77 
$`HTR1E MUTATED`
TCGA-BR-4184 TCGA-BR-8360 TCGA-BR-8680 TCGA-CD-8527 TCGA-CG-5733 TCGA-HU-A4GX 
        6.97         6.18        15.81         0.07        21.07        10.19 
TCGA-HU-A4H3 TCGA-IN-8663 
       19.36         3.39 

$`HTR1E WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.25         0.26         2.10        12.95        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IP-7968 
        2.53 

  HTR1E MUTATED HTR1E WILD-TYPE 
           0.07            0.00 
  HTR1E MUTATED HTR1E WILD-TYPE 
          21.07          105.07 
  HTR1E MUTATED HTR1E WILD-TYPE 
           8.58           12.66 
[1] "0.1 - 21.1 (8.6)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.7"
D292V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HTR1E MUTATED         0        0        0        2         1         1
  HTR1E WILD-TYPE       1        9       27       24        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HTR1E MUTATED           0          2          0          2        1
  HTR1E WILD-TYPE         3         47         36         22       23
D292V3, multiclass
            clus
vv           HTR1E MUTATED HTR1E WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               2              24
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             0              36
  STAGE IIIC             2              22
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HTR1E MUTATED     0   4   2   3
  HTR1E WILD-TYPE  11  68 120  72
D292V4, multiclass
    clus
vv   HTR1E MUTATED HTR1E WILD-TYPE
  T1             0              11
  T2             4              68
  T3             2             120
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  HTR1E MUTATED    1  3  4  1
  HTR1E WILD-TYPE 92 78 46 52
D292V5, multiclass
    clus
vv   HTR1E MUTATED HTR1E WILD-TYPE
  N0             1              92
  N1             3              78
  N2             4              46
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D292V6, binary
                 cls
clus                0   1
  HTR1E MUTATED     7   1
  HTR1E WILD-TYPE 250  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR1E MUTATED      7    1
  HTR1E WILD-TYPE  250   17
   clus
vv  HTR1E MUTATED HTR1E WILD-TYPE
  0             7             250
  1             1              17
[1] 2 2
[1] FALSE
D292V7, binary
                 cls
clus                0   1
  HTR1E MUTATED     4   5
  HTR1E WILD-TYPE 106 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR1E MUTATED      4    5
  HTR1E WILD-TYPE  106  174
        clus
vv       HTR1E MUTATED HTR1E WILD-TYPE
  FEMALE             4             106
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  HTR1E MUTATED                                       2
  HTR1E WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HTR1E MUTATED                                                        2
  HTR1E WILD-TYPE                                                    133
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HTR1E MUTATED                                                                   3
  HTR1E WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  HTR1E MUTATED                                                  1
  HTR1E WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  HTR1E MUTATED                                                          1
  HTR1E WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  HTR1E MUTATED                                                           0
  HTR1E WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  HTR1E MUTATED                                          0
  HTR1E WILD-TYPE                                        3
D292V8, multiclass
                                                                   clus
vv                                                                  HTR1E MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  HTR1E WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D292V9, binary
                 cls
clus                0   1
  HTR1E MUTATED     1   8
  HTR1E WILD-TYPE   4 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR1E MUTATED      1    8
  HTR1E WILD-TYPE    4  276
     clus
vv    HTR1E MUTATED HTR1E WILD-TYPE
  NO              1               4
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HTR1E MUTATED     8   0   0   1
  HTR1E WILD-TYPE 219  10  10  23
D292V10, multiclass
    clus
vv   HTR1E MUTATED HTR1E WILD-TYPE
  R0             8             219
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D292V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HTR1E MUTATED       4                         0     3
  HTR1E WILD-TYPE    72                         4   165
D292V12, multiclass
                           clus
vv                          HTR1E MUTATED HTR1E WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(293) Variable = KLC2 MUTATION ANALYSIS
D293V1, survival
                sevent
clus2              0   1
  KLC2 MUTATED     6   4
  KLC2 WILD-TYPE 175  76
  KLC2 MUTATED KLC2 WILD-TYPE 
            10            251 
  KLC2 MUTATED KLC2 WILD-TYPE 
             4             76 
$`KLC2 MUTATED`
TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8081 TCGA-BR-8487 TCGA-CG-5733 
        6.97        32.94        23.93        20.55         1.12        21.07 
TCGA-EQ-5647 TCGA-FP-8211 TCGA-HJ-7597 TCGA-HU-A4GX 
        0.62        13.58        26.47        10.19 

$`KLC2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69        12.26         9.60         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       15.16        13.78        14.76         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       17.06        59.54         5.03         0.56        11.08         5.52 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  KLC2 MUTATED KLC2 WILD-TYPE 
          0.62           0.00 
  KLC2 MUTATED KLC2 WILD-TYPE 
         32.94         105.07 
  KLC2 MUTATED KLC2 WILD-TYPE 
        17.065         12.590 
[1] "0.6 - 32.9 (17.1)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D293V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KLC2 MUTATED         0        0        2        0         2         2
  KLC2 WILD-TYPE       1        9       25       26        29        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KLC2 MUTATED           0          2          0          1        1
  KLC2 WILD-TYPE         3         47         36         23       23
D293V3, multiclass
            clus
vv           KLC2 MUTATED KLC2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              0             26
  STAGE IIA             2             29
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            0             36
  STAGE IIIC            1             23
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KLC2 MUTATED     0   4   4   3
  KLC2 WILD-TYPE  11  68 118  72
D293V4, multiclass
    clus
vv   KLC2 MUTATED KLC2 WILD-TYPE
  T1            0             11
  T2            4             68
  T3            4            118
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  KLC2 MUTATED    5  2  2  1
  KLC2 WILD-TYPE 88 79 48 52
D293V5, multiclass
    clus
vv   KLC2 MUTATED KLC2 WILD-TYPE
  N0            5             88
  N1            2             79
  N2            2             48
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D293V6, binary
                cls
clus               0   1
  KLC2 MUTATED     7   1
  KLC2 WILD-TYPE 250  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC2 MUTATED      7    1
  KLC2 WILD-TYPE  250   17
   clus
vv  KLC2 MUTATED KLC2 WILD-TYPE
  0            7            250
  1            1             17
[1] 2 2
[1] FALSE
D293V7, binary
                cls
clus               0   1
  KLC2 MUTATED     9   2
  KLC2 WILD-TYPE 101 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC2 MUTATED      9    2
  KLC2 WILD-TYPE  101  177
        clus
vv       KLC2 MUTATED KLC2 WILD-TYPE
  FEMALE            9            101
  MALE              2            177
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KLC2 MUTATED                                       1
  KLC2 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KLC2 MUTATED                                                        8
  KLC2 WILD-TYPE                                                    127
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KLC2 MUTATED                                                                   1
  KLC2 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KLC2 MUTATED                                                  0
  KLC2 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KLC2 MUTATED                                                          0
  KLC2 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KLC2 MUTATED                                                           0
  KLC2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KLC2 MUTATED                                          1
  KLC2 WILD-TYPE                                        2
D293V8, multiclass
                                                                   clus
vv                                                                  KLC2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  KLC2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D293V9, binary
                cls
clus               0   1
  KLC2 MUTATED     0  11
  KLC2 WILD-TYPE   5 273
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC2 MUTATED      0   11
  KLC2 WILD-TYPE    5  273
     clus
vv    KLC2 MUTATED KLC2 WILD-TYPE
  NO             0              5
  YES           11            273
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  KLC2 MUTATED     7   1   1   2
  KLC2 WILD-TYPE 220   9   9  22
D293V10, multiclass
    clus
vv   KLC2 MUTATED KLC2 WILD-TYPE
  R0            7            220
  R1            1              9
  R2            1              9
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D293V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KLC2 MUTATED       1                         0     9
  KLC2 WILD-TYPE    75                         4   159
D293V12, multiclass
                           clus
vv                          KLC2 MUTATED KLC2 WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                9            159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(294) Variable = BMPR1B MUTATION ANALYSIS
D294V1, survival
                  sevent
clus2                0   1
  BMPR1B MUTATED     4   1
  BMPR1B WILD-TYPE 177  79
  BMPR1B MUTATED BMPR1B WILD-TYPE 
               5              256 
  BMPR1B MUTATED BMPR1B WILD-TYPE 
               1               79 
$`BMPR1B MUTATED`
TCGA-BR-7958 TCGA-BR-8078 TCGA-CG-4465 TCGA-HU-A4G9 TCGA-HU-A4H3 
       12.76        12.26         9.01        24.20        19.36 

$`BMPR1B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 
       15.32        28.73        12.43         3.45         9.07        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       19.07        12.03         0.00        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        11.84         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  BMPR1B MUTATED BMPR1B WILD-TYPE 
            9.01             0.00 
  BMPR1B MUTATED BMPR1B WILD-TYPE 
           24.20           105.07 
  BMPR1B MUTATED BMPR1B WILD-TYPE 
          12.760           12.605 
[1] "9.0 - 24.2 (12.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.6"
D294V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BMPR1B MUTATED         1        1        0        0         0         1
  BMPR1B WILD-TYPE       0        8       27       26        31        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BMPR1B MUTATED           0          0          1          1        2
  BMPR1B WILD-TYPE         3         49         35         23       22
D294V3, multiclass
            clus
vv           BMPR1B MUTATED BMPR1B WILD-TYPE
  STAGE I                 1                0
  STAGE IA                1                8
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               0               31
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              1               35
  STAGE IIIC              1               23
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BMPR1B MUTATED     2   0   0   5
  BMPR1B WILD-TYPE   9  72 122  70
D294V4, multiclass
    clus
vv   BMPR1B MUTATED BMPR1B WILD-TYPE
  T1              2                9
  T2              0               72
  T3              0              122
  T4              5               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  BMPR1B MUTATED    3  1  1  2
  BMPR1B WILD-TYPE 90 80 49 51
D294V5, multiclass
    clus
vv   BMPR1B MUTATED BMPR1B WILD-TYPE
  N0              3               90
  N1              1               80
  N2              1               49
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D294V6, binary
                  cls
clus                 0   1
  BMPR1B MUTATED     5   1
  BMPR1B WILD-TYPE 252  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BMPR1B MUTATED      5    1
  BMPR1B WILD-TYPE  252   17
   clus
vv  BMPR1B MUTATED BMPR1B WILD-TYPE
  0              5              252
  1              1               17
[1] 2 2
[1] FALSE
D294V7, binary
                  cls
clus                 0   1
  BMPR1B MUTATED     5   2
  BMPR1B WILD-TYPE 105 177
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BMPR1B MUTATED      5    2
  BMPR1B WILD-TYPE  105  177
        clus
vv       BMPR1B MUTATED BMPR1B WILD-TYPE
  FEMALE              5              105
  MALE                2              177
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  BMPR1B MUTATED                                       2
  BMPR1B WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BMPR1B MUTATED                                                        4
  BMPR1B WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BMPR1B MUTATED                                                                   0
  BMPR1B WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  BMPR1B MUTATED                                                  1
  BMPR1B WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  BMPR1B MUTATED                                                          0
  BMPR1B WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  BMPR1B MUTATED                                                           0
  BMPR1B WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  BMPR1B MUTATED                                          0
  BMPR1B WILD-TYPE                                        3
D294V8, multiclass
                                                                   clus
vv                                                                  BMPR1B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  BMPR1B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D294V9, binary
                  cls
clus                 0   1
  BMPR1B MUTATED     0   7
  BMPR1B WILD-TYPE   5 277
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BMPR1B MUTATED      0    7
  BMPR1B WILD-TYPE    5  277
     clus
vv    BMPR1B MUTATED BMPR1B WILD-TYPE
  NO               0                5
  YES              7              277
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  BMPR1B MUTATED     5   0   1   1
  BMPR1B WILD-TYPE 222  10   9  23
D294V10, multiclass
    clus
vv   BMPR1B MUTATED BMPR1B WILD-TYPE
  R0              5              222
  R1              0               10
  R2              1                9
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D294V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BMPR1B MUTATED       2                         1     3
  BMPR1B WILD-TYPE    74                         3   165
D294V12, multiclass
                           clus
vv                          BMPR1B MUTATED BMPR1B WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  3              165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(295) Variable = PAPD4 MUTATION ANALYSIS
D295V1, survival
                 sevent
clus2               0   1
  PAPD4 MUTATED     6   2
  PAPD4 WILD-TYPE 175  78
  PAPD4 MUTATED PAPD4 WILD-TYPE 
              8             253 
  PAPD4 MUTATED PAPD4 WILD-TYPE 
              2              78 
$`PAPD4 MUTATED`
TCGA-BR-7851 TCGA-BR-8372 TCGA-BR-8680 TCGA-CG-4305 TCGA-CG-5726 TCGA-HU-A4GQ 
       12.43        19.17        15.81        15.95        28.96         0.10 
TCGA-HU-A4GX TCGA-HU-A4H3 
       10.19        19.36 

$`PAPD4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         6.51         6.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  PAPD4 MUTATED PAPD4 WILD-TYPE 
            0.1             0.0 
  PAPD4 MUTATED PAPD4 WILD-TYPE 
          28.96          105.07 
  PAPD4 MUTATED PAPD4 WILD-TYPE 
          15.88           12.59 
[1] "0.1 - 29.0 (15.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D295V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PAPD4 MUTATED         0        1        0        1         0         1
  PAPD4 WILD-TYPE       1        8       27       25        31        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PAPD4 MUTATED           0          0          0          4        1
  PAPD4 WILD-TYPE         3         49         36         20       23
D295V3, multiclass
            clus
vv           PAPD4 MUTATED PAPD4 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              0              31
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             4              20
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PAPD4 MUTATED     1   1   0   6
  PAPD4 WILD-TYPE  10  71 122  69
D295V4, multiclass
    clus
vv   PAPD4 MUTATED PAPD4 WILD-TYPE
  T1             1              10
  T2             1              71
  T3             0             122
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PAPD4 MUTATED    2  1  3  2
  PAPD4 WILD-TYPE 91 80 47 51
D295V5, multiclass
    clus
vv   PAPD4 MUTATED PAPD4 WILD-TYPE
  N0             2              91
  N1             1              80
  N2             3              47
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D295V6, binary
                 cls
clus                0   1
  PAPD4 MUTATED     7   1
  PAPD4 WILD-TYPE 250  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAPD4 MUTATED      7    1
  PAPD4 WILD-TYPE  250   17
   clus
vv  PAPD4 MUTATED PAPD4 WILD-TYPE
  0             7             250
  1             1              17
[1] 2 2
[1] FALSE
D295V7, binary
                 cls
clus                0   1
  PAPD4 MUTATED     2   6
  PAPD4 WILD-TYPE 108 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAPD4 MUTATED      2    6
  PAPD4 WILD-TYPE  108  173
        clus
vv       PAPD4 MUTATED PAPD4 WILD-TYPE
  FEMALE             2             108
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PAPD4 MUTATED                                       2
  PAPD4 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PAPD4 MUTATED                                                        2
  PAPD4 WILD-TYPE                                                    133
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PAPD4 MUTATED                                                                   2
  PAPD4 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PAPD4 MUTATED                                                  2
  PAPD4 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PAPD4 MUTATED                                                          0
  PAPD4 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PAPD4 MUTATED                                                           0
  PAPD4 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PAPD4 MUTATED                                          0
  PAPD4 WILD-TYPE                                        3
D295V8, multiclass
                                                                   clus
vv                                                                  PAPD4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  PAPD4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D295V9, binary
                 cls
clus                0   1
  PAPD4 MUTATED     0   8
  PAPD4 WILD-TYPE   5 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAPD4 MUTATED      0    8
  PAPD4 WILD-TYPE    5  276
     clus
vv    PAPD4 MUTATED PAPD4 WILD-TYPE
  NO              0               5
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PAPD4 MUTATED     8   0   0   0
  PAPD4 WILD-TYPE 219  10  10  24
D295V10, multiclass
    clus
vv   PAPD4 MUTATED PAPD4 WILD-TYPE
  R0             8             219
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D295V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PAPD4 MUTATED       4                         0     2
  PAPD4 WILD-TYPE    72                         4   166
D295V12, multiclass
                           clus
vv                          PAPD4 MUTATED PAPD4 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 2             166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(296) Variable = KIAA1009 MUTATION ANALYSIS
D296V1, survival
                    sevent
clus2                  0   1
  KIAA1009 MUTATED    11   4
  KIAA1009 WILD-TYPE 170  76
  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
                15                246 
  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
                 4                 76 
$`KIAA1009 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6565 TCGA-BR-8078 TCGA-BR-8289 TCGA-BR-8382 
       30.90        34.68         9.17        12.26         2.66        15.85 
TCGA-CD-A4MG TCGA-CG-5723 TCGA-F1-A448 TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GT 
        6.58       105.07        21.27        11.77        29.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H3 
        6.25        10.19        19.36 

$`KIAA1009 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       18.35         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       17.29        13.68        19.33        39.12        26.10        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8291 
        0.69         9.60        20.55         8.05        12.95        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
        3.32        11.80        19.17        14.79         0.26         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         6.02         0.99        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GY 
        3.25        22.75        25.81         8.98         0.10         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
              2.66               0.00 
  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
            105.07              79.07 
  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
             12.26              12.64 
[1] "2.7 - 105.1 (12.3)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.8"
D296V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1009 MUTATED         0        1        0        1         4         3
  KIAA1009 WILD-TYPE       1        8       27       25        27        41
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1009 MUTATED           0          0          1          3        1
  KIAA1009 WILD-TYPE         3         49         35         21       23
D296V3, multiclass
            clus
vv           KIAA1009 MUTATED KIAA1009 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  1                  8
  STAGE IB                  0                 27
  STAGE II                  1                 25
  STAGE IIA                 4                 27
  STAGE IIB                 3                 41
  STAGE III                 0                  3
  STAGE IIIA                0                 49
  STAGE IIIB                1                 35
  STAGE IIIC                3                 21
  STAGE IV                  1                 23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1009 MUTATED     1   3   5   6
  KIAA1009 WILD-TYPE  10  69 117  69
D296V4, multiclass
    clus
vv   KIAA1009 MUTATED KIAA1009 WILD-TYPE
  T1                1                 10
  T2                3                 69
  T3                5                117
  T4                6                 69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  KIAA1009 MUTATED    6  3  1  4
  KIAA1009 WILD-TYPE 87 78 49 49
D296V5, multiclass
    clus
vv   KIAA1009 MUTATED KIAA1009 WILD-TYPE
  N0                6                 87
  N1                3                 78
  N2                1                 49
  N3                4                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D296V6, binary
                    cls
clus                   0   1
  KIAA1009 MUTATED    14   1
  KIAA1009 WILD-TYPE 243  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1009 MUTATED     14    1
  KIAA1009 WILD-TYPE  243   17
   clus
vv  KIAA1009 MUTATED KIAA1009 WILD-TYPE
  0               14                243
  1                1                 17
[1] 2 2
[1] FALSE
D296V7, binary
                    cls
clus                   0   1
  KIAA1009 MUTATED     7   8
  KIAA1009 WILD-TYPE 103 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1009 MUTATED      7    8
  KIAA1009 WILD-TYPE  103  171
        clus
vv       KIAA1009 MUTATED KIAA1009 WILD-TYPE
  FEMALE                7                103
  MALE                  8                171
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KIAA1009 MUTATED                                       4
  KIAA1009 WILD-TYPE                                    46
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA1009 MUTATED                                                        6
  KIAA1009 WILD-TYPE                                                    129
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA1009 MUTATED                                                                   1
  KIAA1009 WILD-TYPE                                                                39
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KIAA1009 MUTATED                                                  3
  KIAA1009 WILD-TYPE                                               35
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KIAA1009 MUTATED                                                          1
  KIAA1009 WILD-TYPE                                                       15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KIAA1009 MUTATED                                                           0
  KIAA1009 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KIAA1009 MUTATED                                          0
  KIAA1009 WILD-TYPE                                        3
D296V8, multiclass
                                                                   clus
vv                                                                  KIAA1009 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  KIAA1009 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D296V9, binary
                    cls
clus                   0   1
  KIAA1009 MUTATED     0  15
  KIAA1009 WILD-TYPE   5 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1009 MUTATED      0   15
  KIAA1009 WILD-TYPE    5  269
     clus
vv    KIAA1009 MUTATED KIAA1009 WILD-TYPE
  NO                 0                  5
  YES               15                269
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA1009 MUTATED    13   0   0   1
  KIAA1009 WILD-TYPE 214  10  10  23
D296V10, multiclass
    clus
vv   KIAA1009 MUTATED KIAA1009 WILD-TYPE
  R0               13                214
  R1                0                 10
  R2                0                 10
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D296V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA1009 MUTATED       7                         0     7
  KIAA1009 WILD-TYPE    69                         4   161
D296V12, multiclass
                           clus
vv                          KIAA1009 MUTATED KIAA1009 WILD-TYPE
  ASIAN                                    7                 69
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    7                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(297) Variable = C5ORF42 MUTATION ANALYSIS
D297V1, survival
                   sevent
clus2                 0   1
  C5ORF42 MUTATED    20   4
  C5ORF42 WILD-TYPE 161  76
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
               24               237 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
                4                76 
$`C5ORF42 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6563 TCGA-BR-8078 TCGA-BR-8372 TCGA-BR-8373 
        6.97        34.68        39.12        12.26        19.17        14.79 
TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8680 TCGA-CD-8536 TCGA-CD-A4MG 
       15.85         1.12        15.81        15.81         0.10         6.58 
TCGA-CG-4477 TCGA-CG-5728 TCGA-D7-6525 TCGA-D7-A4Z0 TCGA-F1-A448 TCGA-FP-A4BE 
       30.97        65.10        13.35        14.76        21.27        11.08 
TCGA-HU-A4GH TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H3 
       11.77         0.10         6.51         6.25        10.19        19.36 

$`C5ORF42 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       17.29        13.68        19.33        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       14.04         3.32        11.80         0.26         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
       25.18         9.21        20.22        12.79         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        22.98         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-EQ-5647 
       14.27        16.44         5.92        15.16        13.78         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        7.99        16.24        14.47        72.23         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
       29.98         8.98         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
              0.1               0.0 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
            65.10            105.07 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
           14.055            12.590 
[1] "0.1 - 65.1 (14.1)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.3"
D297V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C5ORF42 MUTATED         1        1        3        1         5         4
  C5ORF42 WILD-TYPE       0        8       24       25        26        40
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C5ORF42 MUTATED           0          3          2          5        1
  C5ORF42 WILD-TYPE         3         46         34         19       23
D297V3, multiclass
            clus
vv           C5ORF42 MUTATED C5ORF42 WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                 1                 8
  STAGE IB                 3                24
  STAGE II                 1                25
  STAGE IIA                5                26
  STAGE IIB                4                40
  STAGE III                0                 3
  STAGE IIIA               3                46
  STAGE IIIB               2                34
  STAGE IIIC               5                19
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C5ORF42 MUTATED     2   5  10   9
  C5ORF42 WILD-TYPE   9  67 112  66
D297V4, multiclass
    clus
vv   C5ORF42 MUTATED C5ORF42 WILD-TYPE
  T1               2                 9
  T2               5                67
  T3              10               112
  T4               9                66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  C5ORF42 MUTATED   11  6  5  4
  C5ORF42 WILD-TYPE 82 75 45 49
D297V5, multiclass
    clus
vv   C5ORF42 MUTATED C5ORF42 WILD-TYPE
  N0              11                82
  N1               6                75
  N2               5                45
  N3               4                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D297V6, binary
                   cls
clus                  0   1
  C5ORF42 MUTATED    23   1
  C5ORF42 WILD-TYPE 234  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF42 MUTATED     23    1
  C5ORF42 WILD-TYPE  234   17
   clus
vv  C5ORF42 MUTATED C5ORF42 WILD-TYPE
  0              23               234
  1               1                17
[1] 2 2
[1] FALSE
D297V7, binary
                   cls
clus                  0   1
  C5ORF42 MUTATED    11  15
  C5ORF42 WILD-TYPE  99 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF42 MUTATED     11   15
  C5ORF42 WILD-TYPE   99  164
        clus
vv       C5ORF42 MUTATED C5ORF42 WILD-TYPE
  FEMALE              11                99
  MALE                15               164
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C5ORF42 MUTATED                                       5
  C5ORF42 WILD-TYPE                                    45
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C5ORF42 MUTATED                                                       11
  C5ORF42 WILD-TYPE                                                    124
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C5ORF42 MUTATED                                                                   4
  C5ORF42 WILD-TYPE                                                                36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C5ORF42 MUTATED                                                  4
  C5ORF42 WILD-TYPE                                               34
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C5ORF42 MUTATED                                                          2
  C5ORF42 WILD-TYPE                                                       14
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C5ORF42 MUTATED                                                           0
  C5ORF42 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C5ORF42 MUTATED                                          0
  C5ORF42 WILD-TYPE                                        3
D297V8, multiclass
                                                                   clus
vv                                                                  C5ORF42 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  C5ORF42 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D297V9, binary
                   cls
clus                  0   1
  C5ORF42 MUTATED     0  26
  C5ORF42 WILD-TYPE   5 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF42 MUTATED      0   26
  C5ORF42 WILD-TYPE    5  258
     clus
vv    C5ORF42 MUTATED C5ORF42 WILD-TYPE
  NO                0                 5
  YES              26               258
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C5ORF42 MUTATED    24   0   0   1
  C5ORF42 WILD-TYPE 203  10  10  23
D297V10, multiclass
    clus
vv   C5ORF42 MUTATED C5ORF42 WILD-TYPE
  R0              24               203
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D297V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C5ORF42 MUTATED       9                         2    12
  C5ORF42 WILD-TYPE    67                         2   156
D297V12, multiclass
                           clus
vv                          C5ORF42 MUTATED C5ORF42 WILD-TYPE
  ASIAN                                   9                67
  BLACK OR AFRICAN AMERICAN               2                 2
  WHITE                                  12               156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(298) Variable = YBX2 MUTATION ANALYSIS
D298V1, survival
                sevent
clus2              0   1
  YBX2 MUTATED     3   1
  YBX2 WILD-TYPE 178  79
  YBX2 MUTATED YBX2 WILD-TYPE 
             4            257 
  YBX2 MUTATED YBX2 WILD-TYPE 
             1             79 
$`YBX2 MUTATED`
TCGA-BR-8368 TCGA-BR-A4QL TCGA-CG-4465 TCGA-HU-A4H4 
        4.31        11.57         9.01        23.84 

$`YBX2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       19.07        12.03         0.00        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       12.95        19.36        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  YBX2 MUTATED YBX2 WILD-TYPE 
          4.31           0.00 
  YBX2 MUTATED YBX2 WILD-TYPE 
         23.84         105.07 
  YBX2 MUTATED YBX2 WILD-TYPE 
         10.29          12.66 
[1] "4.3 - 23.8 (10.3)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1"  
D298V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  YBX2 MUTATED         0        0        1        0         0         1
  YBX2 WILD-TYPE       1        9       26       26        31        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  YBX2 MUTATED           0          0          1          0        1
  YBX2 WILD-TYPE         3         49         35         24       23
D298V3, multiclass
            clus
vv           YBX2 MUTATED YBX2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             0             31
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            1             35
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  YBX2 MUTATED     0   2   1   1
  YBX2 WILD-TYPE  11  70 121  74
D298V4, multiclass
    clus
vv   YBX2 MUTATED YBX2 WILD-TYPE
  T1            0             11
  T2            2             70
  T3            1            121
  T4            1             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  YBX2 MUTATED    1  0  1  2
  YBX2 WILD-TYPE 92 81 49 51
D298V5, multiclass
    clus
vv   YBX2 MUTATED YBX2 WILD-TYPE
  N0            1             92
  N1            0             81
  N2            1             49
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D298V6, binary
                cls
clus               0   1
  YBX2 MUTATED     3   1
  YBX2 WILD-TYPE 254  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  YBX2 MUTATED      3    1
  YBX2 WILD-TYPE  254   17
   clus
vv  YBX2 MUTATED YBX2 WILD-TYPE
  0            3            254
  1            1             17
[1] 2 2
[1] FALSE
D298V7, binary
                cls
clus               0   1
  YBX2 MUTATED     4   0
  YBX2 WILD-TYPE 106 179
[1] "tbl2"
                cls
clus             [,1] [,2]
  YBX2 MUTATED      4    0
  YBX2 WILD-TYPE  106  179
        clus
vv       YBX2 MUTATED YBX2 WILD-TYPE
  FEMALE            4            106
  MALE              0            179
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  YBX2 MUTATED                                       1
  YBX2 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  YBX2 MUTATED                                                        2
  YBX2 WILD-TYPE                                                    133
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  YBX2 MUTATED                                                                   0
  YBX2 WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  YBX2 MUTATED                                                  1
  YBX2 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  YBX2 MUTATED                                                          0
  YBX2 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  YBX2 MUTATED                                                           0
  YBX2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  YBX2 MUTATED                                          0
  YBX2 WILD-TYPE                                        3
D298V8, multiclass
                                                                   clus
vv                                                                  YBX2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  YBX2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D298V9, binary
                cls
clus               0   1
  YBX2 MUTATED     0   4
  YBX2 WILD-TYPE   5 280
[1] "tbl2"
                cls
clus             [,1] [,2]
  YBX2 MUTATED      0    4
  YBX2 WILD-TYPE    5  280
     clus
vv    YBX2 MUTATED YBX2 WILD-TYPE
  NO             0              5
  YES            4            280
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  YBX2 MUTATED     3   0   1   0
  YBX2 WILD-TYPE 224  10   9  24
D298V10, multiclass
    clus
vv   YBX2 MUTATED YBX2 WILD-TYPE
  R0            3            224
  R1            0             10
  R2            1              9
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D298V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  YBX2 MUTATED       1                         0     2
  YBX2 WILD-TYPE    75                         4   166
D298V12, multiclass
                           clus
vv                          YBX2 MUTATED YBX2 WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                2            166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(299) Variable = SH3KBP1 MUTATION ANALYSIS
D299V1, survival
                   sevent
clus2                 0   1
  SH3KBP1 MUTATED     8   4
  SH3KBP1 WILD-TYPE 173  76
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
               12               249 
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
                4                76 
$`SH3KBP1 MUTATED`
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8680 
        6.61         6.97        20.55         4.31         1.12        15.81 
TCGA-CG-4477 TCGA-CG-5721 TCGA-D7-A4YV TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       30.97         6.02         5.92         0.10         6.25        10.19 

$`SH3KBP1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       26.70        11.70         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69        12.26         9.60         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        22.98         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
              0.1               0.0 
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
            30.97            105.07 
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
             6.43             12.79 
[1] "0.1 - 31.0 (6.4)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.6"
D299V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SH3KBP1 MUTATED         0        0        2        0         1         3
  SH3KBP1 WILD-TYPE       1        9       25       26        30        41
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SH3KBP1 MUTATED           0          2          0          2        2
  SH3KBP1 WILD-TYPE         3         47         36         22       22
D299V3, multiclass
            clus
vv           SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 2                25
  STAGE II                 0                26
  STAGE IIA                1                30
  STAGE IIB                3                41
  STAGE III                0                 3
  STAGE IIIA               2                47
  STAGE IIIB               0                36
  STAGE IIIC               2                22
  STAGE IV                 2                22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SH3KBP1 MUTATED     0   2   5   5
  SH3KBP1 WILD-TYPE  11  70 117  70
D299V4, multiclass
    clus
vv   SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  T1               0                11
  T2               2                70
  T3               5               117
  T4               5                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  SH3KBP1 MUTATED    4  6  3  0
  SH3KBP1 WILD-TYPE 89 75 47 53
D299V5, multiclass
    clus
vv   SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  N0               4                89
  N1               6                75
  N2               3                47
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D299V6, binary
                   cls
clus                  0   1
  SH3KBP1 MUTATED    11   1
  SH3KBP1 WILD-TYPE 246  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SH3KBP1 MUTATED     11    1
  SH3KBP1 WILD-TYPE  246   17
   clus
vv  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  0              11               246
  1               1                17
[1] 2 2
[1] FALSE
D299V7, binary
                   cls
clus                  0   1
  SH3KBP1 MUTATED     8   5
  SH3KBP1 WILD-TYPE 102 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SH3KBP1 MUTATED      8    5
  SH3KBP1 WILD-TYPE  102  174
        clus
vv       SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  FEMALE               8               102
  MALE                 5               174
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SH3KBP1 MUTATED                                       2
  SH3KBP1 WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SH3KBP1 MUTATED                                                        6
  SH3KBP1 WILD-TYPE                                                    129
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SH3KBP1 MUTATED                                                                   2
  SH3KBP1 WILD-TYPE                                                                38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SH3KBP1 MUTATED                                                  3
  SH3KBP1 WILD-TYPE                                               35
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SH3KBP1 MUTATED                                                          0
  SH3KBP1 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SH3KBP1 MUTATED                                                           0
  SH3KBP1 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SH3KBP1 MUTATED                                          0
  SH3KBP1 WILD-TYPE                                        3
D299V8, multiclass
                                                                   clus
vv                                                                  SH3KBP1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  SH3KBP1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D299V9, binary
                   cls
clus                  0   1
  SH3KBP1 MUTATED     0  13
  SH3KBP1 WILD-TYPE   5 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SH3KBP1 MUTATED      0   13
  SH3KBP1 WILD-TYPE    5  271
     clus
vv    SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  NO                0                 5
  YES              13               271
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SH3KBP1 MUTATED    10   0   0   3
  SH3KBP1 WILD-TYPE 217  10  10  21
D299V10, multiclass
    clus
vv   SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  R0              10               217
  R1               0                10
  R2               0                10
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D299V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SH3KBP1 MUTATED       4                         0     7
  SH3KBP1 WILD-TYPE    72                         4   161
D299V12, multiclass
                           clus
vv                          SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  ASIAN                                   4                72
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   7               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(300) Variable = USP15 MUTATION ANALYSIS
D300V1, survival
                 sevent
clus2               0   1
  USP15 MUTATED     5   0
  USP15 WILD-TYPE 176  80
  USP15 MUTATED USP15 WILD-TYPE 
              5             256 
  USP15 MUTATED USP15 WILD-TYPE 
              0              80 
$`USP15 MUTATED`
TCGA-B7-5816 TCGA-BR-8081 TCGA-CG-5721 TCGA-CG-5723 TCGA-HU-A4GT 
       26.70        20.55         6.02       105.07         6.51 

$`USP15 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       17.49        14.43         0.69        12.26         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  USP15 MUTATED USP15 WILD-TYPE 
           6.02            0.00 
  USP15 MUTATED USP15 WILD-TYPE 
         105.07           79.07 
  USP15 MUTATED USP15 WILD-TYPE 
         20.550          12.605 
[1] "6.0 - 105.1 (20.6)" "0.0 - 79.1 (12.6)" 
[1] "hr="     "2.9e+07"
D300V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  USP15 MUTATED         0        0        1        1         1         2
  USP15 WILD-TYPE       1        9       26       25        30        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  USP15 MUTATED           0          0          0          0        1
  USP15 WILD-TYPE         3         49         36         24       23
D300V3, multiclass
            clus
vv           USP15 MUTATED USP15 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP15 MUTATED     0   2   1   3
  USP15 WILD-TYPE  11  70 121  72
D300V4, multiclass
    clus
vv   USP15 MUTATED USP15 WILD-TYPE
  T1             0              11
  T2             2              70
  T3             1             121
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  USP15 MUTATED    4  2  0  0
  USP15 WILD-TYPE 89 79 50 53
D300V5, multiclass
    clus
vv   USP15 MUTATED USP15 WILD-TYPE
  N0             4              89
  N1             2              79
  N2             0              50
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D300V6, binary
                 cls
clus                0   1
  USP15 MUTATED     6   0
  USP15 WILD-TYPE 251  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP15 MUTATED      6    0
  USP15 WILD-TYPE  251   18
   clus
vv  USP15 MUTATED USP15 WILD-TYPE
  0             6             251
  1             0              18
[1] 2 2
[1] FALSE
D300V7, binary
                 cls
clus                0   1
  USP15 MUTATED     3   3
  USP15 WILD-TYPE 107 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP15 MUTATED      3    3
  USP15 WILD-TYPE  107  176
        clus
vv       USP15 MUTATED USP15 WILD-TYPE
  FEMALE             3             107
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  USP15 MUTATED                                       1
  USP15 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  USP15 MUTATED                                                        2
  USP15 WILD-TYPE                                                    133
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  USP15 MUTATED                                                                   2
  USP15 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  USP15 MUTATED                                                  1
  USP15 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  USP15 MUTATED                                                          0
  USP15 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  USP15 MUTATED                                                           0
  USP15 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  USP15 MUTATED                                          0
  USP15 WILD-TYPE                                        3
D300V8, multiclass
                                                                   clus
vv                                                                  USP15 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  USP15 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D300V9, binary
                 cls
clus                0   1
  USP15 MUTATED     0   6
  USP15 WILD-TYPE   5 278
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP15 MUTATED      0    6
  USP15 WILD-TYPE    5  278
     clus
vv    USP15 MUTATED USP15 WILD-TYPE
  NO              0               5
  YES             6             278
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USP15 MUTATED     6   0   0   0
  USP15 WILD-TYPE 221  10  10  24
D300V10, multiclass
    clus
vv   USP15 MUTATED USP15 WILD-TYPE
  R0             6             221
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D300V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  USP15 MUTATED       1                         0     2
  USP15 WILD-TYPE    75                         4   166
D300V12, multiclass
                           clus
vv                          USP15 MUTATED USP15 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 2             166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(301) Variable = IGF2BP3 MUTATION ANALYSIS
D301V1, survival
                   sevent
clus2                 0   1
  IGF2BP3 MUTATED     4   0
  IGF2BP3 WILD-TYPE 177  80
  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
                4               257 
  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
                0                80 
$`IGF2BP3 MUTATED`
TCGA-BR-8680 TCGA-CG-4437 TCGA-FP-A4BE TCGA-HU-A4GN 
       15.81         8.05        11.08        29.98 

$`IGF2BP3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        7.99        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 
       59.54         5.03        13.58         0.56         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        11.77         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
             8.05              0.00 
  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
            29.98            105.07 
  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
           13.445            12.620 
[1] "8.1 - 30.0 (13.4)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "9200000"
D301V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IGF2BP3 MUTATED         0        0        0        1         2         0
  IGF2BP3 WILD-TYPE       1        9       27       25        29        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IGF2BP3 MUTATED           0          0          0          0        2
  IGF2BP3 WILD-TYPE         3         49         36         24       22
D301V3, multiclass
            clus
vv           IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 0                27
  STAGE II                 1                25
  STAGE IIA                2                29
  STAGE IIB                0                44
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               0                36
  STAGE IIIC               0                24
  STAGE IV                 2                22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  IGF2BP3 MUTATED     0   2   1   2
  IGF2BP3 WILD-TYPE  11  70 121  73
D301V4, multiclass
    clus
vv   IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  T1               0                11
  T2               2                70
  T3               1               121
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  IGF2BP3 MUTATED    1  2  2  0
  IGF2BP3 WILD-TYPE 92 79 48 53
D301V5, multiclass
    clus
vv   IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  N0               1                92
  N1               2                79
  N2               2                48
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D301V6, binary
                   cls
clus                  0   1
  IGF2BP3 MUTATED     4   1
  IGF2BP3 WILD-TYPE 253  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IGF2BP3 MUTATED      4    1
  IGF2BP3 WILD-TYPE  253   17
   clus
vv  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  0               4               253
  1               1                17
[1] 2 2
[1] FALSE
D301V7, binary
                   cls
clus                  0   1
  IGF2BP3 MUTATED     1   4
  IGF2BP3 WILD-TYPE 109 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IGF2BP3 MUTATED      1    4
  IGF2BP3 WILD-TYPE  109  175
        clus
vv       IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  FEMALE               1               109
  MALE                 4               175
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  IGF2BP3 MUTATED                                       0
  IGF2BP3 WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IGF2BP3 MUTATED                                                        2
  IGF2BP3 WILD-TYPE                                                    133
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IGF2BP3 MUTATED                                                                   1
  IGF2BP3 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  IGF2BP3 MUTATED                                                  2
  IGF2BP3 WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  IGF2BP3 MUTATED                                                          0
  IGF2BP3 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  IGF2BP3 MUTATED                                                           0
  IGF2BP3 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  IGF2BP3 MUTATED                                          0
  IGF2BP3 WILD-TYPE                                        3
D301V8, multiclass
                                                                   clus
vv                                                                  IGF2BP3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  IGF2BP3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D301V9, binary
                   cls
clus                  0   1
  IGF2BP3 MUTATED     0   5
  IGF2BP3 WILD-TYPE   5 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IGF2BP3 MUTATED      0    5
  IGF2BP3 WILD-TYPE    5  279
     clus
vv    IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  NO                0                 5
  YES               5               279
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  IGF2BP3 MUTATED     4   0   0   1
  IGF2BP3 WILD-TYPE 223  10  10  23
D301V10, multiclass
    clus
vv   IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  R0               4               223
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D301V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IGF2BP3 MUTATED       2                         1     1
  IGF2BP3 WILD-TYPE    74                         3   167
D301V12, multiclass
                           clus
vv                          IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  ASIAN                                   2                74
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   1               167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(302) Variable = PLXNA2 MUTATION ANALYSIS
D302V1, survival
                  sevent
clus2                0   1
  PLXNA2 MUTATED    14   5
  PLXNA2 WILD-TYPE 167  75
  PLXNA2 MUTATED PLXNA2 WILD-TYPE 
              19              242 
  PLXNA2 MUTATED PLXNA2 WILD-TYPE 
               5               75 
$`PLXNA2 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-8680 
       26.70         6.97        34.68        20.55         6.18        15.81 
TCGA-BR-A4QL TCGA-CD-A487 TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5733 
       11.57         9.34         6.58         6.02       105.07        21.07 
TCGA-D7-6815 TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4G9 TCGA-HU-A4GQ 
       15.98        11.08        26.47        11.41        24.20         0.10 
TCGA-HU-A4H4 
       23.84 

$`PLXNA2 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69        12.26         9.60         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
       16.31         2.20        15.58         7.40        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 
        0.10         0.10         0.13         0.10         3.42        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.22        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        11.84         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        19.36        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  PLXNA2 MUTATED PLXNA2 WILD-TYPE 
             0.1              0.0 
  PLXNA2 MUTATED PLXNA2 WILD-TYPE 
          105.07            79.07 
  PLXNA2 MUTATED PLXNA2 WILD-TYPE 
          15.810           12.605 
[1] "0.1 - 105.1 (15.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.6"
D302V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLXNA2 MUTATED         0        1        2        1         4         6
  PLXNA2 WILD-TYPE       1        8       25       25        27        38
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLXNA2 MUTATED           0          3          1          1        2
  PLXNA2 WILD-TYPE         3         46         35         23       22
D302V3, multiclass
            clus
vv           PLXNA2 MUTATED PLXNA2 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                2               25
  STAGE II                1               25
  STAGE IIA               4               27
  STAGE IIB               6               38
  STAGE III               0                3
  STAGE IIIA              3               46
  STAGE IIIB              1               35
  STAGE IIIC              1               23
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PLXNA2 MUTATED     1   7   7   7
  PLXNA2 WILD-TYPE  10  65 115  68
D302V4, multiclass
    clus
vv   PLXNA2 MUTATED PLXNA2 WILD-TYPE
  T1              1               10
  T2              7               65
  T3              7              115
  T4              7               68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  PLXNA2 MUTATED   11  5  5  1
  PLXNA2 WILD-TYPE 82 76 45 52
D302V5, multiclass
    clus
vv   PLXNA2 MUTATED PLXNA2 WILD-TYPE
  N0             11               82
  N1              5               76
  N2              5               45
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D302V6, binary
                  cls
clus                 0   1
  PLXNA2 MUTATED    20   1
  PLXNA2 WILD-TYPE 237  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNA2 MUTATED     20    1
  PLXNA2 WILD-TYPE  237   17
   clus
vv  PLXNA2 MUTATED PLXNA2 WILD-TYPE
  0             20              237
  1              1               17
[1] 2 2
[1] FALSE
D302V7, binary
                  cls
clus                 0   1
  PLXNA2 MUTATED    12  11
  PLXNA2 WILD-TYPE  98 168
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNA2 MUTATED     12   11
  PLXNA2 WILD-TYPE   98  168
        clus
vv       PLXNA2 MUTATED PLXNA2 WILD-TYPE
  FEMALE             12               98
  MALE               11              168
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PLXNA2 MUTATED                                       4
  PLXNA2 WILD-TYPE                                    46
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLXNA2 MUTATED                                                        8
  PLXNA2 WILD-TYPE                                                    127
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLXNA2 MUTATED                                                                   4
  PLXNA2 WILD-TYPE                                                                36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PLXNA2 MUTATED                                                  6
  PLXNA2 WILD-TYPE                                               32
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PLXNA2 MUTATED                                                          0
  PLXNA2 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PLXNA2 MUTATED                                                           0
  PLXNA2 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PLXNA2 MUTATED                                          1
  PLXNA2 WILD-TYPE                                        2
D302V8, multiclass
                                                                   clus
vv                                                                  PLXNA2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       1
                                                                   clus
vv                                                                  PLXNA2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D302V9, binary
                  cls
clus                 0   1
  PLXNA2 MUTATED     0  23
  PLXNA2 WILD-TYPE   5 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNA2 MUTATED      0   23
  PLXNA2 WILD-TYPE    5  261
     clus
vv    PLXNA2 MUTATED PLXNA2 WILD-TYPE
  NO               0                5
  YES             23              261
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PLXNA2 MUTATED    18   0   0   4
  PLXNA2 WILD-TYPE 209  10  10  20
D302V10, multiclass
    clus
vv   PLXNA2 MUTATED PLXNA2 WILD-TYPE
  R0             18              209
  R1              0               10
  R2              0               10
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D302V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLXNA2 MUTATED       7                         1    11
  PLXNA2 WILD-TYPE    69                         3   157
D302V12, multiclass
                           clus
vv                          PLXNA2 MUTATED PLXNA2 WILD-TYPE
  ASIAN                                  7               69
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                 11              157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(303) Variable = MOCS2 MUTATION ANALYSIS
D303V1, survival
                 sevent
clus2               0   1
  MOCS2 MUTATED     1   1
  MOCS2 WILD-TYPE 180  79
  MOCS2 MUTATED MOCS2 WILD-TYPE 
              2             259 
  MOCS2 MUTATED MOCS2 WILD-TYPE 
              1              79 
$`MOCS2 MUTATED`
TCGA-BR-4201 TCGA-BR-8361 
        30.9         19.5 

$`MOCS2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  MOCS2 MUTATED MOCS2 WILD-TYPE 
           19.5             0.0 
  MOCS2 MUTATED MOCS2 WILD-TYPE 
          30.90          105.07 
  MOCS2 MUTATED MOCS2 WILD-TYPE 
          25.20           12.59 
[1] "19.5 - 30.9 (25.2)" "0.0 - 105.1 (12.6)"
[1] "Remove cluster labels:" "MOCS2 MUTATED"         
D303V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MOCS2 MUTATED         0        0        0        1         0         0
  MOCS2 WILD-TYPE       1        9       27       25        31        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MOCS2 MUTATED           0          0          0          1        1
  MOCS2 WILD-TYPE         3         49         36         23       23
D303V3, multiclass
            clus
vv           MOCS2 MUTATED MOCS2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              0              31
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MOCS2 MUTATED     0   2   0   2
  MOCS2 WILD-TYPE  11  70 122  73
D303V4, multiclass
    clus
vv   MOCS2 MUTATED MOCS2 WILD-TYPE
  T1             0              11
  T2             2              70
  T3             0             122
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  MOCS2 MUTATED    0  1  2  0
  MOCS2 WILD-TYPE 93 80 48 53
D303V5, multiclass
    clus
vv   MOCS2 MUTATED MOCS2 WILD-TYPE
  N0             0              93
  N1             1              80
  N2             2              48
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D303V6, binary
                 cls
clus                0   1
  MOCS2 MUTATED     4   0
  MOCS2 WILD-TYPE 253  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOCS2 MUTATED      4    0
  MOCS2 WILD-TYPE  253   18
   clus
vv  MOCS2 MUTATED MOCS2 WILD-TYPE
  0             4             253
  1             0              18
[1] 2 2
[1] FALSE
D303V7, binary
                 cls
clus                0   1
  MOCS2 MUTATED     3   1
  MOCS2 WILD-TYPE 107 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOCS2 MUTATED      3    1
  MOCS2 WILD-TYPE  107  178
        clus
vv       MOCS2 MUTATED MOCS2 WILD-TYPE
  FEMALE             3             107
  MALE               1             178
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MOCS2 MUTATED                                       0
  MOCS2 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MOCS2 MUTATED                                                        3
  MOCS2 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MOCS2 MUTATED                                                                   0
  MOCS2 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MOCS2 MUTATED                                                  0
  MOCS2 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MOCS2 MUTATED                                                          1
  MOCS2 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MOCS2 MUTATED                                                           0
  MOCS2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MOCS2 MUTATED                                          0
  MOCS2 WILD-TYPE                                        3
D303V8, multiclass
                                                                   clus
vv                                                                  MOCS2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  MOCS2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D303V9, binary
                 cls
clus                0   1
  MOCS2 MUTATED     1   3
  MOCS2 WILD-TYPE   4 281
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOCS2 MUTATED      1    3
  MOCS2 WILD-TYPE    4  281
     clus
vv    MOCS2 MUTATED MOCS2 WILD-TYPE
  NO              1               4
  YES             3             281
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MOCS2 MUTATED     2   0   0   2
  MOCS2 WILD-TYPE 225  10  10  22
D303V10, multiclass
    clus
vv   MOCS2 MUTATED MOCS2 WILD-TYPE
  R0             2             225
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D303V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MOCS2 MUTATED       0                         0     3
  MOCS2 WILD-TYPE    76                         4   165
D303V12, multiclass
                           clus
vv                          MOCS2 MUTATED MOCS2 WILD-TYPE
  ASIAN                                 0              76
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(304) Variable = PIK3R3 MUTATION ANALYSIS
D304V1, survival
                  sevent
clus2                0   1
  PIK3R3 MUTATED     4   2
  PIK3R3 WILD-TYPE 177  78
  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
               6              255 
  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
               2               78 
$`PIK3R3 MUTATED`
TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-5801 TCGA-CG-4477 TCGA-HJ-7597 TCGA-HU-A4G8 
       13.45        15.81        13.18        30.97        26.47        11.84 

$`PIK3R3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       15.81         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56        11.08         5.52         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
           11.84             0.00 
  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
           30.97           105.07 
  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
           14.63            12.56 
[1] "11.8 - 31.0 (14.6)" "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D304V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIK3R3 MUTATED         0        0        3        0         0         1
  PIK3R3 WILD-TYPE       1        9       24       26        31        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3R3 MUTATED           0          1          0          1        1
  PIK3R3 WILD-TYPE         3         48         36         23       23
D304V3, multiclass
            clus
vv           PIK3R3 MUTATED PIK3R3 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                3               24
  STAGE II                0               26
  STAGE IIA               0               31
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PIK3R3 MUTATED     0   3   2   2
  PIK3R3 WILD-TYPE  11  69 120  73
D304V4, multiclass
    clus
vv   PIK3R3 MUTATED PIK3R3 WILD-TYPE
  T1              0               11
  T2              3               69
  T3              2              120
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  PIK3R3 MUTATED    3  3  1  1
  PIK3R3 WILD-TYPE 90 78 49 52
D304V5, multiclass
    clus
vv   PIK3R3 MUTATED PIK3R3 WILD-TYPE
  N0              3               90
  N1              3               78
  N2              1               49
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D304V6, binary
                  cls
clus                 0   1
  PIK3R3 MUTATED     6   1
  PIK3R3 WILD-TYPE 251  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R3 MUTATED      6    1
  PIK3R3 WILD-TYPE  251   17
   clus
vv  PIK3R3 MUTATED PIK3R3 WILD-TYPE
  0              6              251
  1              1               17
[1] 2 2
[1] FALSE
D304V7, binary
                  cls
clus                 0   1
  PIK3R3 MUTATED     4   4
  PIK3R3 WILD-TYPE 106 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R3 MUTATED      4    4
  PIK3R3 WILD-TYPE  106  175
        clus
vv       PIK3R3 MUTATED PIK3R3 WILD-TYPE
  FEMALE              4              106
  MALE                4              175
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PIK3R3 MUTATED                                       1
  PIK3R3 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIK3R3 MUTATED                                                        4
  PIK3R3 WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIK3R3 MUTATED                                                                   1
  PIK3R3 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PIK3R3 MUTATED                                                  1
  PIK3R3 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PIK3R3 MUTATED                                                          0
  PIK3R3 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PIK3R3 MUTATED                                                           0
  PIK3R3 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PIK3R3 MUTATED                                          1
  PIK3R3 WILD-TYPE                                        2
D304V8, multiclass
                                                                   clus
vv                                                                  PIK3R3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       1
                                                                   clus
vv                                                                  PIK3R3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D304V9, binary
                  cls
clus                 0   1
  PIK3R3 MUTATED     0   8
  PIK3R3 WILD-TYPE   5 276
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R3 MUTATED      0    8
  PIK3R3 WILD-TYPE    5  276
     clus
vv    PIK3R3 MUTATED PIK3R3 WILD-TYPE
  NO               0                5
  YES              8              276
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PIK3R3 MUTATED     6   0   0   1
  PIK3R3 WILD-TYPE 221  10  10  23
D304V10, multiclass
    clus
vv   PIK3R3 MUTATED PIK3R3 WILD-TYPE
  R0              6              221
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D304V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3R3 MUTATED       3                         0     4
  PIK3R3 WILD-TYPE    73                         4   164
D304V12, multiclass
                           clus
vv                          PIK3R3 MUTATED PIK3R3 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(305) Variable = CR1 MUTATION ANALYSIS
D305V1, survival
               sevent
clus2             0   1
  CR1 MUTATED    16   5
  CR1 WILD-TYPE 165  75
  CR1 MUTATED CR1 WILD-TYPE 
           21           240 
  CR1 MUTATED CR1 WILD-TYPE 
            5            75 
$`CR1 MUTATED`
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-8078 
        6.61        34.68        30.90        23.93        12.43        12.26 
TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8592 
       20.55         0.26        15.85         1.12        15.81         6.28 
TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-5721 TCGA-CG-5728 
        6.58        12.62        15.95         7.99         6.02        65.10 
TCGA-D7-6527 TCGA-D7-A4YY TCGA-HU-A4GX 
       10.26        13.78        10.19 

$`CR1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
       18.35        30.90         6.18         9.57        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 
       31.20        32.94        12.82         9.21        24.76        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       28.01        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 
       12.76        18.71        17.49        14.43         0.69         9.60 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        19.50        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 
       20.22        12.79         9.34        13.45         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
       20.02         3.02        27.02         1.02         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        79.07         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  CR1 MUTATED CR1 WILD-TYPE 
         0.26          0.00 
  CR1 MUTATED CR1 WILD-TYPE 
        65.10        105.07 
  CR1 MUTATED CR1 WILD-TYPE 
        12.43         12.71 
[1] "0.3 - 65.1 (12.4)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.4"
D305V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CR1 MUTATED         0        0        6        3         3         3
  CR1 WILD-TYPE       1        9       21       23        28        41
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CR1 MUTATED           1          2          3          2        1
  CR1 WILD-TYPE         2         47         33         22       23
D305V3, multiclass
            clus
vv           CR1 MUTATED CR1 WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             9
  STAGE IB             6            21
  STAGE II             3            23
  STAGE IIA            3            28
  STAGE IIB            3            41
  STAGE III            1             2
  STAGE IIIA           2            47
  STAGE IIIB           3            33
  STAGE IIIC           2            22
  STAGE IV             1            23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CR1 MUTATED     0  10   5   9
  CR1 WILD-TYPE  11  62 117  66
D305V4, multiclass
    clus
vv   CR1 MUTATED CR1 WILD-TYPE
  T1           0            11
  T2          10            62
  T3           5           117
  T4           9            66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  CR1 MUTATED   13  7  2  2
  CR1 WILD-TYPE 80 74 48 51
D305V5, multiclass
    clus
vv   CR1 MUTATED CR1 WILD-TYPE
  N0          13            80
  N1           7            74
  N2           2            48
  N3           2            51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D305V6, binary
               cls
clus              0   1
  CR1 MUTATED    25   0
  CR1 WILD-TYPE 232  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR1 MUTATED     25    0
  CR1 WILD-TYPE  232   18
   clus
vv  CR1 MUTATED CR1 WILD-TYPE
  0          25           232
  1           0            18
[1] 2 2
[1] FALSE
D305V7, binary
               cls
clus              0   1
  CR1 MUTATED    13  12
  CR1 WILD-TYPE  97 167
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR1 MUTATED     13   12
  CR1 WILD-TYPE   97  167
        clus
vv       CR1 MUTATED CR1 WILD-TYPE
  FEMALE          13            97
  MALE            12           167
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CR1 MUTATED                                       3
  CR1 WILD-TYPE                                    47
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CR1 MUTATED                                                       15
  CR1 WILD-TYPE                                                    120
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CR1 MUTATED                                                                   5
  CR1 WILD-TYPE                                                                35
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CR1 MUTATED                                                  0
  CR1 WILD-TYPE                                               38
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CR1 MUTATED                                                          1
  CR1 WILD-TYPE                                                       15
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CR1 MUTATED                                                           1
  CR1 WILD-TYPE                                                         5
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CR1 MUTATED                                          0
  CR1 WILD-TYPE                                        3
D305V8, multiclass
                                                                   clus
vv                                                                  CR1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                     15
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  CR1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      120
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D305V9, binary
               cls
clus              0   1
  CR1 MUTATED     1  24
  CR1 WILD-TYPE   4 260
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR1 MUTATED      1   24
  CR1 WILD-TYPE    4  260
     clus
vv    CR1 MUTATED CR1 WILD-TYPE
  NO            1             4
  YES          24           260
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  CR1 MUTATED    20   0   0   3
  CR1 WILD-TYPE 207  10  10  21
D305V10, multiclass
    clus
vv   CR1 MUTATED CR1 WILD-TYPE
  R0          20           207
  R1           0            10
  R2           0            10
  RX           3            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D305V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CR1 MUTATED       3                         0    16
  CR1 WILD-TYPE    73                         4   152
D305V12, multiclass
                           clus
vv                          CR1 MUTATED CR1 WILD-TYPE
  ASIAN                               3            73
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                              16           152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(306) Variable = IL2RG MUTATION ANALYSIS
D306V1, survival
                 sevent
clus2               0   1
  IL2RG MUTATED     4   0
  IL2RG WILD-TYPE 177  80
  IL2RG MUTATED IL2RG WILD-TYPE 
              4             257 
  IL2RG MUTATED IL2RG WILD-TYPE 
              0              80 
$`IL2RG MUTATED`
TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8680 TCGA-CG-5728 
       34.68         6.18        15.81        65.10 

$`IL2RG WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        0.99       105.07        12.03        28.96        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  IL2RG MUTATED IL2RG WILD-TYPE 
           6.18            0.00 
  IL2RG MUTATED IL2RG WILD-TYPE 
          65.10          105.07 
  IL2RG MUTATED IL2RG WILD-TYPE 
         25.245          12.590 
[1] "6.2 - 65.1 (25.2)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "2.6e+07"
D306V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IL2RG MUTATED         0        0        1        1         2         0
  IL2RG WILD-TYPE       1        9       26       25        29        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IL2RG MUTATED           0          0          0          0        1
  IL2RG WILD-TYPE         3         49         36         24       23
D306V3, multiclass
            clus
vv           IL2RG MUTATED IL2RG WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              2              29
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IL2RG MUTATED     0   2   3   1
  IL2RG WILD-TYPE  11  70 119  74
D306V4, multiclass
    clus
vv   IL2RG MUTATED IL2RG WILD-TYPE
  T1             0              11
  T2             2              70
  T3             3             119
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  IL2RG MUTATED    3  1  1  0
  IL2RG WILD-TYPE 90 80 49 53
D306V5, multiclass
    clus
vv   IL2RG MUTATED IL2RG WILD-TYPE
  N0             3              90
  N1             1              80
  N2             1              49
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D306V6, binary
                 cls
clus                0   1
  IL2RG MUTATED     4   1
  IL2RG WILD-TYPE 253  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL2RG MUTATED      4    1
  IL2RG WILD-TYPE  253   17
   clus
vv  IL2RG MUTATED IL2RG WILD-TYPE
  0             4             253
  1             1              17
[1] 2 2
[1] FALSE
D306V7, binary
                 cls
clus                0   1
  IL2RG MUTATED     3   3
  IL2RG WILD-TYPE 107 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL2RG MUTATED      3    3
  IL2RG WILD-TYPE  107  176
        clus
vv       IL2RG MUTATED IL2RG WILD-TYPE
  FEMALE             3             107
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  IL2RG MUTATED                                       0
  IL2RG WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IL2RG MUTATED                                                        2
  IL2RG WILD-TYPE                                                    133
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IL2RG MUTATED                                                                   2
  IL2RG WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  IL2RG MUTATED                                                  1
  IL2RG WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  IL2RG MUTATED                                                          1
  IL2RG WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  IL2RG MUTATED                                                           0
  IL2RG WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  IL2RG MUTATED                                          0
  IL2RG WILD-TYPE                                        3
D306V8, multiclass
                                                                   clus
vv                                                                  IL2RG MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  IL2RG WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D306V9, binary
                 cls
clus                0   1
  IL2RG MUTATED     1   5
  IL2RG WILD-TYPE   4 279
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL2RG MUTATED      1    5
  IL2RG WILD-TYPE    4  279
     clus
vv    IL2RG MUTATED IL2RG WILD-TYPE
  NO              1               4
  YES             5             279
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IL2RG MUTATED     5   0   0   1
  IL2RG WILD-TYPE 222  10  10  23
D306V10, multiclass
    clus
vv   IL2RG MUTATED IL2RG WILD-TYPE
  R0             5             222
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D306V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IL2RG MUTATED       1                         0     3
  IL2RG WILD-TYPE    75                         4   165
D306V12, multiclass
                           clus
vv                          IL2RG MUTATED IL2RG WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(307) Variable = FAM70B MUTATION ANALYSIS
D307V1, survival
                  sevent
clus2                0   1
  FAM70B MUTATED     7   3
  FAM70B WILD-TYPE 174  77
  FAM70B MUTATED FAM70B WILD-TYPE 
              10              251 
  FAM70B MUTATED FAM70B WILD-TYPE 
               3               77 
$`FAM70B MUTATED`
TCGA-BR-8360 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4PF TCGA-CD-A4MG TCGA-CG-4465 
        6.18         1.12        15.81         1.15         6.58         9.01 
TCGA-CG-5721 TCGA-CG-5726 TCGA-F1-A448 TCGA-HU-A4G9 
        6.02        28.96        21.27        24.20 

$`FAM70B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
       19.36        13.51        20.65        20.42        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 
        1.02         0.99         0.99       105.07        12.03        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        11.84         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  FAM70B MUTATED FAM70B WILD-TYPE 
            1.12             0.00 
  FAM70B MUTATED FAM70B WILD-TYPE 
           28.96           105.07 
  FAM70B MUTATED FAM70B WILD-TYPE 
           7.795           12.660 
[1] "1.1 - 29.0 (7.8)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.1"
D307V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM70B MUTATED         0        2        1        0         3         0
  FAM70B WILD-TYPE       1        7       26       26        28        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM70B MUTATED           0          0          2          0        3
  FAM70B WILD-TYPE         3         49         34         24       21
D307V3, multiclass
            clus
vv           FAM70B MUTATED FAM70B WILD-TYPE
  STAGE I                 0                1
  STAGE IA                2                7
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               3               28
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              2               34
  STAGE IIIC              0               24
  STAGE IV                3               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM70B MUTATED     2   1   4   4
  FAM70B WILD-TYPE   9  71 118  71
D307V4, multiclass
    clus
vv   FAM70B MUTATED FAM70B WILD-TYPE
  T1              2                9
  T2              1               71
  T3              4              118
  T4              4               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  FAM70B MUTATED    6  3  2  2
  FAM70B WILD-TYPE 87 78 48 51
D307V5, multiclass
    clus
vv   FAM70B MUTATED FAM70B WILD-TYPE
  N0              6               87
  N1              3               78
  N2              2               48
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D307V6, binary
                  cls
clus                 0   1
  FAM70B MUTATED    11   2
  FAM70B WILD-TYPE 246  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM70B MUTATED     11    2
  FAM70B WILD-TYPE  246   16
   clus
vv  FAM70B MUTATED FAM70B WILD-TYPE
  0             11              246
  1              2               16
[1] 2 2
[1] FALSE
D307V7, binary
                  cls
clus                 0   1
  FAM70B MUTATED     4   9
  FAM70B WILD-TYPE 106 170
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM70B MUTATED      4    9
  FAM70B WILD-TYPE  106  170
        clus
vv       FAM70B MUTATED FAM70B WILD-TYPE
  FEMALE              4              106
  MALE                9              170
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FAM70B MUTATED                                       2
  FAM70B WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAM70B MUTATED                                                        4
  FAM70B WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAM70B MUTATED                                                                   4
  FAM70B WILD-TYPE                                                                36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FAM70B MUTATED                                                  2
  FAM70B WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FAM70B MUTATED                                                          1
  FAM70B WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FAM70B MUTATED                                                           0
  FAM70B WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FAM70B MUTATED                                          0
  FAM70B WILD-TYPE                                        3
D307V8, multiclass
                                                                   clus
vv                                                                  FAM70B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  FAM70B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D307V9, binary
                  cls
clus                 0   1
  FAM70B MUTATED     0  13
  FAM70B WILD-TYPE   5 271
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM70B MUTATED      0   13
  FAM70B WILD-TYPE    5  271
     clus
vv    FAM70B MUTATED FAM70B WILD-TYPE
  NO               0                5
  YES             13              271
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FAM70B MUTATED     9   0   1   2
  FAM70B WILD-TYPE 218  10   9  22
D307V10, multiclass
    clus
vv   FAM70B MUTATED FAM70B WILD-TYPE
  R0              9              218
  R1              0               10
  R2              1                9
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D307V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM70B MUTATED       3                         0     6
  FAM70B WILD-TYPE    73                         4   162
D307V12, multiclass
                           clus
vv                          FAM70B MUTATED FAM70B WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(308) Variable = COL12A1 MUTATION ANALYSIS
D308V1, survival
                   sevent
clus2                 0   1
  COL12A1 MUTATED    29  11
  COL12A1 WILD-TYPE 152  69
  COL12A1 MUTATED COL12A1 WILD-TYPE 
               40               221 
  COL12A1 MUTATED COL12A1 WILD-TYPE 
               11                69 
$`COL12A1 MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6458 
       11.70         6.97         6.61        34.68        13.87        19.33 
TCGA-BR-8289 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8591 
        2.66        19.50        22.19         9.21         1.12        13.45 
TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-A48C TCGA-CD-A4MG 
       15.81        11.57         0.13         0.16        11.61         6.58 
TCGA-CD-A4MI TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4444 TCGA-CG-5721 TCGA-CG-5722 
        0.10        15.95         1.02        47.05         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6527 TCGA-D7-6528 
      105.07        79.07        65.10        21.07        10.26        15.22 
TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-A4BE TCGA-HU-A4GN 
       12.33         7.99        14.47        21.27        11.08        29.98 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H8 
        6.51        10.19         0.26         8.88 

$`COL12A1 WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       26.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
        6.18         9.57        15.95        17.29        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
       20.55         8.05        12.95        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        7.40         6.18         0.26        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 
        0.26        15.85         3.72         5.39        25.18        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        15.81         9.34         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.07         0.07         0.10         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH 
        0.10         3.42         9.34        11.31        12.43        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 
       12.62        20.02         3.02        27.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5724 TCGA-CG-5726 
        6.97        36.00         1.02         0.99        12.03        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       13.35        17.19        15.98        12.79        10.55        11.31 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7735 
       13.78        14.76         0.62        16.24        72.23         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H0 
       25.81        11.77         8.98         0.10         6.25         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
       12.95        19.36        23.84        12.30         9.67        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  COL12A1 MUTATED COL12A1 WILD-TYPE 
              0.1               0.0 
  COL12A1 MUTATED COL12A1 WILD-TYPE 
           105.07             72.23 
  COL12A1 MUTATED COL12A1 WILD-TYPE 
            11.59             12.79 
[1] "0.1 - 105.1 (11.6)" "0.0 - 72.2 (12.8)" 
[1] "hr=" "1.4"
D308V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  COL12A1 MUTATED         1        0        6        6         6         4
  COL12A1 WILD-TYPE       0        9       21       20        25        40
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COL12A1 MUTATED           1          4          3          6        7
  COL12A1 WILD-TYPE         2         45         33         18       17
D308V3, multiclass
            clus
vv           COL12A1 MUTATED COL12A1 WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                 0                 9
  STAGE IB                 6                21
  STAGE II                 6                20
  STAGE IIA                6                25
  STAGE IIB                4                40
  STAGE III                1                 2
  STAGE IIIA               4                45
  STAGE IIIB               3                33
  STAGE IIIC               6                18
  STAGE IV                 7                17
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  COL12A1 MUTATED     3  13  17  12
  COL12A1 WILD-TYPE   8  59 105  63
D308V4, multiclass
    clus
vv   COL12A1 MUTATED COL12A1 WILD-TYPE
  T1               3                 8
  T2              13                59
  T3              17               105
  T4              12                63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  COL12A1 MUTATED   13 17  9  6
  COL12A1 WILD-TYPE 80 64 41 47
D308V5, multiclass
    clus
vv   COL12A1 MUTATED COL12A1 WILD-TYPE
  N0              13                80
  N1              17                64
  N2               9                41
  N3               6                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D308V6, binary
                   cls
clus                  0   1
  COL12A1 MUTATED    38   5
  COL12A1 WILD-TYPE 219  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL12A1 MUTATED     38    5
  COL12A1 WILD-TYPE  219   13
   clus
vv  COL12A1 MUTATED COL12A1 WILD-TYPE
  0              38               219
  1               5                13
[1] 2 2
[1] FALSE
D308V7, binary
                   cls
clus                  0   1
  COL12A1 MUTATED    20  26
  COL12A1 WILD-TYPE  90 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL12A1 MUTATED     20   26
  COL12A1 WILD-TYPE   90  153
        clus
vv       COL12A1 MUTATED COL12A1 WILD-TYPE
  FEMALE              20                90
  MALE                26               153
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  COL12A1 MUTATED                                       8
  COL12A1 WILD-TYPE                                    42
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  COL12A1 MUTATED                                                       20
  COL12A1 WILD-TYPE                                                    115
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  COL12A1 MUTATED                                                                   8
  COL12A1 WILD-TYPE                                                                32
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  COL12A1 MUTATED                                                  6
  COL12A1 WILD-TYPE                                               32
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  COL12A1 MUTATED                                                          3
  COL12A1 WILD-TYPE                                                       13
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  COL12A1 MUTATED                                                           1
  COL12A1 WILD-TYPE                                                         5
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  COL12A1 MUTATED                                          0
  COL12A1 WILD-TYPE                                        3
D308V8, multiclass
                                                                   clus
vv                                                                  COL12A1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         20
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  COL12A1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            42
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          115
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D308V9, binary
                   cls
clus                  0   1
  COL12A1 MUTATED     1  45
  COL12A1 WILD-TYPE   4 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL12A1 MUTATED      1   45
  COL12A1 WILD-TYPE    4  239
     clus
vv    COL12A1 MUTATED COL12A1 WILD-TYPE
  NO                1                 4
  YES              45               239
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  COL12A1 MUTATED    35   0   2   5
  COL12A1 WILD-TYPE 192  10   8  19
D308V10, multiclass
    clus
vv   COL12A1 MUTATED COL12A1 WILD-TYPE
  R0              35               192
  R1               0                10
  R2               2                 8
  RX               5                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D308V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  COL12A1 MUTATED      11                         2    22
  COL12A1 WILD-TYPE    65                         2   146
D308V12, multiclass
                           clus
vv                          COL12A1 MUTATED COL12A1 WILD-TYPE
  ASIAN                                  11                65
  BLACK OR AFRICAN AMERICAN               2                 2
  WHITE                                  22               146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(309) Variable = NFE2L1 MUTATION ANALYSIS
D309V1, survival
                  sevent
clus2                0   1
  NFE2L1 MUTATED     5   2
  NFE2L1 WILD-TYPE 176  78
  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
               7              254 
  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
               2               78 
$`NFE2L1 MUTATED`
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-8487 TCGA-CD-8529 TCGA-EQ-A4SO TCGA-F1-6874 
       18.35        30.90         1.12         0.13        16.24        14.47 
TCGA-HU-A4GN 
       29.98 

$`NFE2L1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.07         0.10         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        7.99        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
            0.13             0.00 
  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
           30.90           105.07 
  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
          16.240           12.575 
[1] "0.1 - 30.9 (16.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D309V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NFE2L1 MUTATED         0        0        1        0         2         0
  NFE2L1 WILD-TYPE       1        9       26       26        29        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NFE2L1 MUTATED           0          0          1          0        1
  NFE2L1 WILD-TYPE         3         49         35         24       23
D309V3, multiclass
            clus
vv           NFE2L1 MUTATED NFE2L1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               2               29
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              1               35
  STAGE IIIC              0               24
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NFE2L1 MUTATED     1   3   1   2
  NFE2L1 WILD-TYPE  10  69 121  73
D309V4, multiclass
    clus
vv   NFE2L1 MUTATED NFE2L1 WILD-TYPE
  T1              1               10
  T2              3               69
  T3              1              121
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  NFE2L1 MUTATED    3  4  0  0
  NFE2L1 WILD-TYPE 90 77 50 53
D309V5, multiclass
    clus
vv   NFE2L1 MUTATED NFE2L1 WILD-TYPE
  N0              3               90
  N1              4               77
  N2              0               50
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D309V6, binary
                  cls
clus                 0   1
  NFE2L1 MUTATED     7   1
  NFE2L1 WILD-TYPE 250  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L1 MUTATED      7    1
  NFE2L1 WILD-TYPE  250   17
   clus
vv  NFE2L1 MUTATED NFE2L1 WILD-TYPE
  0              7              250
  1              1               17
[1] 2 2
[1] FALSE
D309V7, binary
                  cls
clus                 0   1
  NFE2L1 MUTATED     4   5
  NFE2L1 WILD-TYPE 106 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L1 MUTATED      4    5
  NFE2L1 WILD-TYPE  106  174
        clus
vv       NFE2L1 MUTATED NFE2L1 WILD-TYPE
  FEMALE              4              106
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NFE2L1 MUTATED                                       0
  NFE2L1 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NFE2L1 MUTATED                                                        6
  NFE2L1 WILD-TYPE                                                    129
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NFE2L1 MUTATED                                                                   1
  NFE2L1 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NFE2L1 MUTATED                                                  1
  NFE2L1 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NFE2L1 MUTATED                                                          1
  NFE2L1 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NFE2L1 MUTATED                                                           0
  NFE2L1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NFE2L1 MUTATED                                          0
  NFE2L1 WILD-TYPE                                        3
D309V8, multiclass
                                                                   clus
vv                                                                  NFE2L1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  NFE2L1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D309V9, binary
                  cls
clus                 0   1
  NFE2L1 MUTATED     0   9
  NFE2L1 WILD-TYPE   5 275
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L1 MUTATED      0    9
  NFE2L1 WILD-TYPE    5  275
     clus
vv    NFE2L1 MUTATED NFE2L1 WILD-TYPE
  NO               0                5
  YES              9              275
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NFE2L1 MUTATED     5   0   0   4
  NFE2L1 WILD-TYPE 222  10  10  20
D309V10, multiclass
    clus
vv   NFE2L1 MUTATED NFE2L1 WILD-TYPE
  R0              5              222
  R1              0               10
  R2              0               10
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D309V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NFE2L1 MUTATED       2                         0     7
  NFE2L1 WILD-TYPE    74                         4   161
D309V12, multiclass
                           clus
vv                          NFE2L1 MUTATED NFE2L1 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  7              161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(310) Variable = TCHP MUTATION ANALYSIS
D310V1, survival
                sevent
clus2              0   1
  TCHP MUTATED     6   4
  TCHP WILD-TYPE 175  76
  TCHP MUTATED TCHP WILD-TYPE 
            10            251 
  TCHP MUTATED TCHP WILD-TYPE 
             4             76 
$`TCHP MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-8078 TCGA-BR-8372 
       26.70         6.97        30.90         6.61        12.26        19.17 
TCGA-CD-A4MG TCGA-CG-5723 TCGA-D7-8572 TCGA-D7-A4YT 
        6.58       105.07        16.80        14.27 

$`TCHP WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 
       11.70         6.61         4.64         7.43        18.35         6.18 
TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        20.55         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         6.02         0.99        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  TCHP MUTATED TCHP WILD-TYPE 
          6.58           0.00 
  TCHP MUTATED TCHP WILD-TYPE 
        105.07          79.07 
  TCHP MUTATED TCHP WILD-TYPE 
        15.535         12.590 
[1] "6.6 - 105.1 (15.5)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.2"
D310V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TCHP MUTATED         0        0        0        1         1         3
  TCHP WILD-TYPE       1        9       27       25        30        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TCHP MUTATED           1          2          0          1        0
  TCHP WILD-TYPE         2         47         36         23       24
D310V3, multiclass
            clus
vv           TCHP MUTATED TCHP WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              1             25
  STAGE IIA             1             30
  STAGE IIB             3             41
  STAGE III             1              2
  STAGE IIIA            2             47
  STAGE IIIB            0             36
  STAGE IIIC            1             23
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TCHP MUTATED     0   5   2   3
  TCHP WILD-TYPE  11  67 120  72
D310V4, multiclass
    clus
vv   TCHP MUTATED TCHP WILD-TYPE
  T1            0             11
  T2            5             67
  T3            2            120
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  TCHP MUTATED    3  3  1  2
  TCHP WILD-TYPE 90 78 49 51
D310V5, multiclass
    clus
vv   TCHP MUTATED TCHP WILD-TYPE
  N0            3             90
  N1            3             78
  N2            1             49
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D310V6, binary
                cls
clus               0   1
  TCHP MUTATED     9   0
  TCHP WILD-TYPE 248  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHP MUTATED      9    0
  TCHP WILD-TYPE  248   18
   clus
vv  TCHP MUTATED TCHP WILD-TYPE
  0            9            248
  1            0             18
[1] 2 2
[1] FALSE
D310V7, binary
                cls
clus               0   1
  TCHP MUTATED     4   6
  TCHP WILD-TYPE 106 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHP MUTATED      4    6
  TCHP WILD-TYPE  106  173
        clus
vv       TCHP MUTATED TCHP WILD-TYPE
  FEMALE            4            106
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TCHP MUTATED                                       2
  TCHP WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TCHP MUTATED                                                        7
  TCHP WILD-TYPE                                                    128
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TCHP MUTATED                                                                   0
  TCHP WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TCHP MUTATED                                                  1
  TCHP WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TCHP MUTATED                                                          0
  TCHP WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TCHP MUTATED                                                           0
  TCHP WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TCHP MUTATED                                          0
  TCHP WILD-TYPE                                        3
D310V8, multiclass
                                                                   clus
vv                                                                  TCHP MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  TCHP WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D310V9, binary
                cls
clus               0   1
  TCHP MUTATED     0  10
  TCHP WILD-TYPE   5 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHP MUTATED      0   10
  TCHP WILD-TYPE    5  274
     clus
vv    TCHP MUTATED TCHP WILD-TYPE
  NO             0              5
  YES           10            274
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TCHP MUTATED     6   0   0   3
  TCHP WILD-TYPE 221  10  10  21
D310V10, multiclass
    clus
vv   TCHP MUTATED TCHP WILD-TYPE
  R0            6            221
  R1            0             10
  R2            0             10
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D310V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TCHP MUTATED       1                         0     8
  TCHP WILD-TYPE    75                         4   160
D310V12, multiclass
                           clus
vv                          TCHP MUTATED TCHP WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                8            160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(311) Variable = WNT1 MUTATION ANALYSIS
D311V1, survival
                sevent
clus2              0   1
  WNT1 MUTATED     4   2
  WNT1 WILD-TYPE 177  78
  WNT1 MUTATED WNT1 WILD-TYPE 
             6            255 
  WNT1 MUTATED WNT1 WILD-TYPE 
             2             78 
$`WNT1 MUTATED`
TCGA-BR-6565 TCGA-BR-6852 TCGA-BR-8078 TCGA-D7-A4YV TCGA-EQ-A4SO TCGA-FP-A4BE 
        9.17        32.94        12.26         5.92        16.24        11.08 

$`WNT1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       14.27        16.44        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  WNT1 MUTATED WNT1 WILD-TYPE 
          5.92           0.00 
  WNT1 MUTATED WNT1 WILD-TYPE 
         32.94         105.07 
  WNT1 MUTATED WNT1 WILD-TYPE 
         11.67          12.66 
[1] "5.9 - 32.9 (11.7)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1"  
D311V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WNT1 MUTATED         1        0        0        1         2         3
  WNT1 WILD-TYPE       0        9       27       25        29        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WNT1 MUTATED           0          0          1          0        0
  WNT1 WILD-TYPE         3         49         35         24       24
D311V3, multiclass
            clus
vv           WNT1 MUTATED WNT1 WILD-TYPE
  STAGE I               1              0
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              1             25
  STAGE IIA             2             29
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            1             35
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WNT1 MUTATED     1   1   3   3
  WNT1 WILD-TYPE  10  71 119  72
D311V4, multiclass
    clus
vv   WNT1 MUTATED WNT1 WILD-TYPE
  T1            1             10
  T2            1             71
  T3            3            119
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  WNT1 MUTATED    4  4  0  0
  WNT1 WILD-TYPE 89 77 50 53
D311V5, multiclass
    clus
vv   WNT1 MUTATED WNT1 WILD-TYPE
  N0            4             89
  N1            4             77
  N2            0             50
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D311V6, binary
                cls
clus               0   1
  WNT1 MUTATED     6   0
  WNT1 WILD-TYPE 251  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT1 MUTATED      6    0
  WNT1 WILD-TYPE  251   18
   clus
vv  WNT1 MUTATED WNT1 WILD-TYPE
  0            6            251
  1            0             18
[1] 2 2
[1] FALSE
D311V7, binary
                cls
clus               0   1
  WNT1 MUTATED     3   5
  WNT1 WILD-TYPE 107 174
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT1 MUTATED      3    5
  WNT1 WILD-TYPE  107  174
        clus
vv       WNT1 MUTATED WNT1 WILD-TYPE
  FEMALE            3            107
  MALE              5            174
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  WNT1 MUTATED                                       0
  WNT1 WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WNT1 MUTATED                                                        6
  WNT1 WILD-TYPE                                                    129
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WNT1 MUTATED                                                                   0
  WNT1 WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  WNT1 MUTATED                                                  1
  WNT1 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  WNT1 MUTATED                                                          1
  WNT1 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  WNT1 MUTATED                                                           0
  WNT1 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  WNT1 MUTATED                                          0
  WNT1 WILD-TYPE                                        3
D311V8, multiclass
                                                                   clus
vv                                                                  WNT1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  WNT1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D311V9, binary
                cls
clus               0   1
  WNT1 MUTATED     1   7
  WNT1 WILD-TYPE   4 277
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT1 MUTATED      1    7
  WNT1 WILD-TYPE    4  277
     clus
vv    WNT1 MUTATED WNT1 WILD-TYPE
  NO             1              4
  YES            7            277
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  WNT1 MUTATED     8   0   0   0
  WNT1 WILD-TYPE 219  10  10  24
D311V10, multiclass
    clus
vv   WNT1 MUTATED WNT1 WILD-TYPE
  R0            8            219
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D311V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WNT1 MUTATED       0                         2     5
  WNT1 WILD-TYPE    76                         2   163
D311V12, multiclass
                           clus
vv                          WNT1 MUTATED WNT1 WILD-TYPE
  ASIAN                                0             76
  BLACK OR AFRICAN AMERICAN            2              2
  WHITE                                5            163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(312) Variable = UBC MUTATION ANALYSIS
D312V1, survival
               sevent
clus2             0   1
  UBC MUTATED     5   2
  UBC WILD-TYPE 176  78
  UBC MUTATED UBC WILD-TYPE 
            7           254 
  UBC MUTATED UBC WILD-TYPE 
            2            78 
$`UBC MUTATED`
TCGA-BR-4184 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8360 TCGA-CG-4301 
        6.97        30.90        32.94        23.93         6.18         3.02 
TCGA-HU-A4GQ 
        0.10 

$`UBC WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 
       21.11        31.20        12.82         9.21        24.76        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
       16.31         2.20        15.58         7.40        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
       12.20         0.10        12.62        20.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  UBC MUTATED UBC WILD-TYPE 
          0.1           0.0 
  UBC MUTATED UBC WILD-TYPE 
        32.94        105.07 
  UBC MUTATED UBC WILD-TYPE 
         6.97         12.64 
[1] "0.1 - 32.9 (7.0)"   "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D312V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UBC MUTATED         0        0        1        0         2         0
  UBC WILD-TYPE       1        9       26       26        29        44
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UBC MUTATED           0          2          0          1        1
  UBC WILD-TYPE         3         47         36         23       23
D312V3, multiclass
            clus
vv           UBC MUTATED UBC WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             9
  STAGE IB             1            26
  STAGE II             0            26
  STAGE IIA            2            29
  STAGE IIB            0            44
  STAGE III            0             3
  STAGE IIIA           2            47
  STAGE IIIB           0            36
  STAGE IIIC           1            23
  STAGE IV             1            23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  UBC MUTATED     0   1   4   2
  UBC WILD-TYPE  11  71 118  73
D312V4, multiclass
    clus
vv   UBC MUTATED UBC WILD-TYPE
  T1           0            11
  T2           1            71
  T3           4           118
  T4           2            73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  UBC MUTATED    3  3  2  0
  UBC WILD-TYPE 90 78 48 53
D312V5, multiclass
    clus
vv   UBC MUTATED UBC WILD-TYPE
  N0           3            90
  N1           3            78
  N2           2            48
  N3           0            53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D312V6, binary
               cls
clus              0   1
  UBC MUTATED     6   1
  UBC WILD-TYPE 251  17
[1] "tbl2"
               cls
clus            [,1] [,2]
  UBC MUTATED      6    1
  UBC WILD-TYPE  251   17
   clus
vv  UBC MUTATED UBC WILD-TYPE
  0           6           251
  1           1            17
[1] 2 2
[1] FALSE
D312V7, binary
               cls
clus              0   1
  UBC MUTATED     4   4
  UBC WILD-TYPE 106 175
[1] "tbl2"
               cls
clus            [,1] [,2]
  UBC MUTATED      4    4
  UBC WILD-TYPE  106  175
        clus
vv       UBC MUTATED UBC WILD-TYPE
  FEMALE           4           106
  MALE             4           175
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  UBC MUTATED                                       0
  UBC WILD-TYPE                                    50
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  UBC MUTATED                                                        6
  UBC WILD-TYPE                                                    129
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  UBC MUTATED                                                                   1
  UBC WILD-TYPE                                                                39
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  UBC MUTATED                                                  1
  UBC WILD-TYPE                                               37
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  UBC MUTATED                                                          0
  UBC WILD-TYPE                                                       16
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  UBC MUTATED                                                           0
  UBC WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  UBC MUTATED                                          0
  UBC WILD-TYPE                                        3
D312V8, multiclass
                                                                   clus
vv                                                                  UBC MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  UBC WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D312V9, binary
               cls
clus              0   1
  UBC MUTATED     0   8
  UBC WILD-TYPE   5 276
[1] "tbl2"
               cls
clus            [,1] [,2]
  UBC MUTATED      0    8
  UBC WILD-TYPE    5  276
     clus
vv    UBC MUTATED UBC WILD-TYPE
  NO            0             5
  YES           8           276
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  UBC MUTATED     5   0   1   2
  UBC WILD-TYPE 222  10   9  22
D312V10, multiclass
    clus
vv   UBC MUTATED UBC WILD-TYPE
  R0           5           222
  R1           0            10
  R2           1             9
  RX           2            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D312V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UBC MUTATED       1                         0     6
  UBC WILD-TYPE    75                         4   162
D312V12, multiclass
                           clus
vv                          UBC MUTATED UBC WILD-TYPE
  ASIAN                               1            75
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                               6           162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(313) Variable = XK MUTATION ANALYSIS
D313V1, survival
              sevent
clus2            0   1
  XK MUTATED     3   1
  XK WILD-TYPE 178  79
  XK MUTATED XK WILD-TYPE 
           4          257 
  XK MUTATED XK WILD-TYPE 
           1           79 
$`XK MUTATED`
TCGA-BR-4280 TCGA-BR-A4J8 TCGA-CG-5723 TCGA-HU-A4GH 
        6.61        13.51       105.07        11.77 

$`XK WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.53         0.66        19.36        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  XK MUTATED XK WILD-TYPE 
        6.61         0.00 
  XK MUTATED XK WILD-TYPE 
      105.07        79.07 
  XK MUTATED XK WILD-TYPE 
       12.64        12.62 
[1] "6.6 - 105.1 (12.6)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "2.5"
D313V2, continuous
              vv
clus           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  XK MUTATED         0        1        0        1         0         0         1
  XK WILD-TYPE       1        8       27       25        31        44         2
              vv
clus           STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XK MUTATED            0          1          0        0
  XK WILD-TYPE         49         35         24       24
D313V3, multiclass
            clus
vv           XK MUTATED XK WILD-TYPE
  STAGE I             0            1
  STAGE IA            1            8
  STAGE IB            0           27
  STAGE II            1           25
  STAGE IIA           0           31
  STAGE IIB           0           44
  STAGE III           1            2
  STAGE IIIA          0           49
  STAGE IIIB          1           35
  STAGE IIIC          0           24
  STAGE IV            0           24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            T1  T2  T3  T4
  XK MUTATED     1   2   1   0
  XK WILD-TYPE  10  70 121  75
D313V4, multiclass
    clus
vv   XK MUTATED XK WILD-TYPE
  T1          1           10
  T2          2           70
  T3          1          121
  T4          0           75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           N0 N1 N2 N3
  XK MUTATED    1  3  0  1
  XK WILD-TYPE 92 78 50 52
D313V5, multiclass
    clus
vv   XK MUTATED XK WILD-TYPE
  N0          1           92
  N1          3           78
  N2          0           50
  N3          1           52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D313V6, binary
              cls
clus             0   1
  XK MUTATED     5   0
  XK WILD-TYPE 252  18
[1] "tbl2"
              cls
clus           [,1] [,2]
  XK MUTATED      5    0
  XK WILD-TYPE  252   18
   clus
vv  XK MUTATED XK WILD-TYPE
  0          5          252
  1          0           18
[1] 2 2
[1] FALSE
D313V7, binary
              cls
clus             0   1
  XK MUTATED     3   2
  XK WILD-TYPE 107 177
[1] "tbl2"
              cls
clus           [,1] [,2]
  XK MUTATED      3    2
  XK WILD-TYPE  107  177
        clus
vv       XK MUTATED XK WILD-TYPE
  FEMALE          3          107
  MALE            2          177
[1] 2 2
[1] FALSE
              vv
clus           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  XK MUTATED                                       0
  XK WILD-TYPE                                    50
              vv
clus           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XK MUTATED                                                        4
  XK WILD-TYPE                                                    131
              vv
clus           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XK MUTATED                                                                   0
  XK WILD-TYPE                                                                40
              vv
clus           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  XK MUTATED                                                  1
  XK WILD-TYPE                                               37
              vv
clus           STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  XK MUTATED                                                          0
  XK WILD-TYPE                                                       16
              vv
clus           STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  XK MUTATED                                                           0
  XK WILD-TYPE                                                         6
              vv
clus           STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  XK MUTATED                                          0
  XK WILD-TYPE                                        3
D313V8, multiclass
                                                                   clus
vv                                                                  XK MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                      0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                     4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)          0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                           1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                  0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                   0
                                                                   clus
vv                                                                  XK WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                     131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D313V9, binary
              cls
clus             0   1
  XK MUTATED     0   5
  XK WILD-TYPE   5 279
[1] "tbl2"
              cls
clus           [,1] [,2]
  XK MUTATED      0    5
  XK WILD-TYPE    5  279
     clus
vv    XK MUTATED XK WILD-TYPE
  NO           0            5
  YES          5          279
[1] 2 2
[1] FALSE
              vv
clus            R0  R1  R2  RX
  XK MUTATED     3   0   0   2
  XK WILD-TYPE 224  10  10  22
D313V10, multiclass
    clus
vv   XK MUTATED XK WILD-TYPE
  R0          3          224
  R1          0           10
  R2          0           10
  RX          2           22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D313V11, continuous
              vv
clus           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XK MUTATED       1                         0     3
  XK WILD-TYPE    75                         4   165
D313V12, multiclass
                           clus
vv                          XK MUTATED XK WILD-TYPE
  ASIAN                              1           75
  BLACK OR AFRICAN AMERICAN          0            4
  WHITE                              3          165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(314) Variable = CTSA MUTATION ANALYSIS
D314V1, survival
                sevent
clus2              0   1
  CTSA MUTATED     4   0
  CTSA WILD-TYPE 177  80
  CTSA MUTATED CTSA WILD-TYPE 
             4            257 
  CTSA MUTATED CTSA WILD-TYPE 
             0             80 
$`CTSA MUTATED`
TCGA-BR-6803 TCGA-CG-4305 TCGA-CG-5723 TCGA-FP-A4BE 
       31.20        15.95       105.07        11.08 

$`CTSA WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        30.90        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
        5.03        13.58         0.56         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  CTSA MUTATED CTSA WILD-TYPE 
         11.08           0.00 
  CTSA MUTATED CTSA WILD-TYPE 
        105.07          79.07 
  CTSA MUTATED CTSA WILD-TYPE 
        23.575         12.590 
[1] "11.1 - 105.1 (23.6)" "0.0 - 79.1 (12.6)"  
[1] "hr="     "2.9e+07"
D314V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CTSA MUTATED         0        0        0        2         2         0
  CTSA WILD-TYPE       1        9       27       24        29        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTSA MUTATED           0          0          0          0        0
  CTSA WILD-TYPE         3         49         36         24       24
D314V3, multiclass
            clus
vv           CTSA MUTATED CTSA WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              2             24
  STAGE IIA             2             29
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CTSA MUTATED     0   2   2   0
  CTSA WILD-TYPE  11  70 120  75
D314V4, multiclass
    clus
vv   CTSA MUTATED CTSA WILD-TYPE
  T1            0             11
  T2            2             70
  T3            2            120
  T4            0             75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  CTSA MUTATED    2  2  0  0
  CTSA WILD-TYPE 91 79 50 53
D314V5, multiclass
    clus
vv   CTSA MUTATED CTSA WILD-TYPE
  N0            2             91
  N1            2             79
  N2            0             50
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D314V6, binary
                cls
clus               0   1
  CTSA MUTATED     4   0
  CTSA WILD-TYPE 253  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSA MUTATED      4    0
  CTSA WILD-TYPE  253   18
   clus
vv  CTSA MUTATED CTSA WILD-TYPE
  0            4            253
  1            0             18
[1] 2 2
[1] FALSE
D314V7, binary
                cls
clus               0   1
  CTSA MUTATED     1   3
  CTSA WILD-TYPE 109 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSA MUTATED      1    3
  CTSA WILD-TYPE  109  176
        clus
vv       CTSA MUTATED CTSA WILD-TYPE
  FEMALE            1            109
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CTSA MUTATED                                       1
  CTSA WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CTSA MUTATED                                                        3
  CTSA WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CTSA MUTATED                                                                   0
  CTSA WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CTSA MUTATED                                                  0
  CTSA WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CTSA MUTATED                                                          0
  CTSA WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CTSA MUTATED                                                           0
  CTSA WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CTSA MUTATED                                          0
  CTSA WILD-TYPE                                        3
D314V8, multiclass
                                                                   clus
vv                                                                  CTSA MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  CTSA WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D314V9, binary
                cls
clus               0   1
  CTSA MUTATED     0   4
  CTSA WILD-TYPE   5 280
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSA MUTATED      0    4
  CTSA WILD-TYPE    5  280
     clus
vv    CTSA MUTATED CTSA WILD-TYPE
  NO             0              5
  YES            4            280
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CTSA MUTATED     4   0   0   0
  CTSA WILD-TYPE 223  10  10  24
D314V10, multiclass
    clus
vv   CTSA MUTATED CTSA WILD-TYPE
  R0            4            223
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D314V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CTSA MUTATED       0                         1     1
  CTSA WILD-TYPE    76                         3   167
D314V12, multiclass
[1] "Remove cluster labels:" "CTSA MUTATED"          
clus
  CTSA MUTATED CTSA WILD-TYPE 
             2            246 
    TCGA-B7-5816     TCGA-B7-5818     TCGA-BR-4183     TCGA-BR-4184 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-4187     TCGA-BR-4188     TCGA-BR-4191     TCGA-BR-4201 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-4253     TCGA-BR-4255     TCGA-BR-4256     TCGA-BR-4257 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-4267     TCGA-BR-4279     TCGA-BR-4280     TCGA-BR-4292 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-4294     TCGA-BR-4357     TCGA-BR-4361     TCGA-BR-4362 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-4363     TCGA-BR-4366     TCGA-BR-4368     TCGA-BR-4369 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-4370     TCGA-BR-4371     TCGA-BR-6452     TCGA-BR-6453 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-6454     TCGA-BR-6455     TCGA-BR-6456     TCGA-BR-6457 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-6458     TCGA-BR-6563     TCGA-BR-6564     TCGA-BR-6565 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-6566     TCGA-BR-6705     TCGA-BR-6706     TCGA-BR-6707 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-6710     TCGA-BR-6801     TCGA-BR-6802     TCGA-BR-6852 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-7196     TCGA-BR-7197     TCGA-BR-7703     TCGA-BR-7707 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-7715     TCGA-BR-7716     TCGA-BR-7717     TCGA-BR-7722 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-7723     TCGA-BR-7851     TCGA-BR-7901     TCGA-BR-7957 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-7958     TCGA-BR-7959     TCGA-BR-8058     TCGA-BR-8059 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-8077     TCGA-BR-8078     TCGA-BR-8080     TCGA-BR-8081 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-8284     TCGA-BR-8286     TCGA-BR-8289     TCGA-BR-8291 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-8295     TCGA-BR-8296     TCGA-BR-8297     TCGA-BR-8360 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-8361     TCGA-BR-8363     TCGA-BR-8364     TCGA-BR-8365 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-8366     TCGA-BR-8367     TCGA-BR-8368     TCGA-BR-8369 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-8370     TCGA-BR-8371     TCGA-BR-8372     TCGA-BR-8373 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-8380     TCGA-BR-8381     TCGA-BR-8382     TCGA-BR-8384 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-8483     TCGA-BR-8484     TCGA-BR-8485     TCGA-BR-8486 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-8487     TCGA-BR-8588     TCGA-BR-8589     TCGA-BR-8590 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-8591     TCGA-BR-8592     TCGA-BR-8676     TCGA-BR-8677 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-8678     TCGA-BR-8679     TCGA-BR-8680     TCGA-BR-8682 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-8683     TCGA-BR-8686     TCGA-BR-8687     TCGA-BR-8690 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-A44T     TCGA-BR-A44U     TCGA-BR-A452     TCGA-BR-A453 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-A4CQ     TCGA-BR-A4CR     TCGA-BR-A4CS     TCGA-BR-A4IU 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-A4IV     TCGA-BR-A4IY     TCGA-BR-A4IZ     TCGA-BR-A4J1 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-A4J2     TCGA-BR-A4J4     TCGA-BR-A4J6     TCGA-BR-A4J7 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-A4J8     TCGA-BR-A4PD     TCGA-BR-A4PE     TCGA-BR-A4PF 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-BR-A4QI     TCGA-BR-A4QL     TCGA-BR-A4QM     TCGA-CD-5798 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-CD-5799     TCGA-CD-5800     TCGA-CD-5801     TCGA-CD-5802 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-CD-5803     TCGA-CD-5804     TCGA-CD-5813     TCGA-CD-8524 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-CD-8525     TCGA-CD-8526     TCGA-CD-8527     TCGA-CD-8528 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-CD-8529     TCGA-CD-8530     TCGA-CD-8531     TCGA-CD-8532 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-CD-8534     TCGA-CD-8535     TCGA-CD-8536     TCGA-CD-A486 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-CD-A487     TCGA-CD-A489     TCGA-CD-A48A     TCGA-CD-A48C 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-CD-A4MG     TCGA-CD-A4MH     TCGA-CD-A4MI     TCGA-CD-A4MJ 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-D7-5577     TCGA-D7-5578     TCGA-D7-5579     TCGA-D7-6518 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-D7-6519     TCGA-D7-6520     TCGA-D7-6521     TCGA-D7-6522 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-D7-6524     TCGA-D7-6525     TCGA-D7-6526     TCGA-D7-6527 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-D7-6528     TCGA-D7-6815     TCGA-D7-6817     TCGA-D7-6818 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-D7-6820     TCGA-D7-6822     TCGA-D7-8570     TCGA-D7-8572 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-D7-8573     TCGA-D7-8574     TCGA-D7-8575     TCGA-D7-8576 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-D7-8578     TCGA-D7-8579     TCGA-D7-A4YT     TCGA-D7-A4YU 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-D7-A4YV     TCGA-D7-A4YX     TCGA-D7-A4YY     TCGA-D7-A4Z0 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-EQ-5647     TCGA-EQ-8122     TCGA-EQ-A4SO     TCGA-F1-6177 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-F1-6874     TCGA-F1-6875     TCGA-F1-A448     TCGA-FP-7735 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-FP-7829     TCGA-FP-7916     TCGA-FP-7998     TCGA-FP-8099 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-FP-8209     TCGA-FP-8210     TCGA-FP-8211     TCGA-FP-8631 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-FP-A4BF     TCGA-HJ-7597     TCGA-HU-8243     TCGA-HU-8245 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-HU-8249     TCGA-HU-8602     TCGA-HU-8604     TCGA-HU-8608 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-HU-8610     TCGA-HU-A4G2     TCGA-HU-A4G3     TCGA-HU-A4G6 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-HU-A4G8     TCGA-HU-A4G9     TCGA-HU-A4GC     TCGA-HU-A4GD 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-HU-A4GF     TCGA-HU-A4GH     TCGA-HU-A4GN     TCGA-HU-A4GP 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-HU-A4GQ     TCGA-HU-A4GT     TCGA-HU-A4GU     TCGA-HU-A4GX 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-HU-A4GY     TCGA-HU-A4H0     TCGA-HU-A4H2     TCGA-HU-A4H3 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-HU-A4H4     TCGA-HU-A4H5     TCGA-HU-A4H6     TCGA-HU-A4H8 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-HU-A4HD     TCGA-IN-7806     TCGA-IN-7808     TCGA-IN-8462 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" "CTSA WILD-TYPE" 
    TCGA-IN-8663     TCGA-IP-7968 
"CTSA WILD-TYPE" "CTSA WILD-TYPE" 

Clustering(315) Variable = TMEM41B MUTATION ANALYSIS
D315V1, survival
                   sevent
clus2                 0   1
  TMEM41B MUTATED     2   1
  TMEM41B WILD-TYPE 179  79
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                3               258 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                1                79 
$`TMEM41B MUTATED`
TCGA-BR-4184 TCGA-BR-A4QL TCGA-CD-8527 
        6.97        11.57         0.07 

$`TMEM41B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  TMEM41B MUTATED TMEM41B WILD-TYPE 
             0.07              0.00 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
            11.57            105.07 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
             6.97             12.71 
[1] "0.1 - 11.6 (7.0)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "2.8"
D315V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEM41B MUTATED         1        0        0        1         0         0
  TMEM41B WILD-TYPE       0        9       27       25        31        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM41B MUTATED           0          1          1          0        0
  TMEM41B WILD-TYPE         3         48         35         24       24
D315V3, multiclass
            clus
vv           TMEM41B MUTATED TMEM41B WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                 0                 9
  STAGE IB                 0                27
  STAGE II                 1                25
  STAGE IIA                0                31
  STAGE IIB                0                44
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               1                35
  STAGE IIIC               0                24
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM41B MUTATED     1   1   2   0
  TMEM41B WILD-TYPE  10  71 120  75
D315V4, multiclass
    clus
vv   TMEM41B MUTATED TMEM41B WILD-TYPE
  T1               1                10
  T2               1                71
  T3               2               120
  T4               0                75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  TMEM41B MUTATED    0  3  0  1
  TMEM41B WILD-TYPE 93 78 50 52
D315V5, multiclass
    clus
vv   TMEM41B MUTATED TMEM41B WILD-TYPE
  N0               0                93
  N1               3                78
  N2               0                50
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D315V6, binary
                   cls
clus                  0   1
  TMEM41B MUTATED     2   0
  TMEM41B WILD-TYPE 255  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      2    0
  TMEM41B WILD-TYPE  255   18
   clus
vv  TMEM41B MUTATED TMEM41B WILD-TYPE
  0               2               255
  1               0                18
[1] 2 2
[1] FALSE
D315V7, binary
                   cls
clus                  0   1
  TMEM41B MUTATED     2   2
  TMEM41B WILD-TYPE 108 177
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      2    2
  TMEM41B WILD-TYPE  108  177
        clus
vv       TMEM41B MUTATED TMEM41B WILD-TYPE
  FEMALE               2               108
  MALE                 2               177
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TMEM41B MUTATED                                       0
  TMEM41B WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TMEM41B MUTATED                                                        3
  TMEM41B WILD-TYPE                                                    132
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TMEM41B MUTATED                                                                   1
  TMEM41B WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TMEM41B MUTATED                                                  0
  TMEM41B WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TMEM41B MUTATED                                                          0
  TMEM41B WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TMEM41B MUTATED                                                           0
  TMEM41B WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TMEM41B MUTATED                                          0
  TMEM41B WILD-TYPE                                        3
D315V8, multiclass
                                                                   clus
vv                                                                  TMEM41B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  TMEM41B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D315V9, binary
                   cls
clus                  0   1
  TMEM41B MUTATED     0   4
  TMEM41B WILD-TYPE   5 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      0    4
  TMEM41B WILD-TYPE    5  280
     clus
vv    TMEM41B MUTATED TMEM41B WILD-TYPE
  NO                0                 5
  YES               4               280
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TMEM41B MUTATED     3   0   0   1
  TMEM41B WILD-TYPE 224  10  10  23
D315V10, multiclass
    clus
vv   TMEM41B MUTATED TMEM41B WILD-TYPE
  R0               3               224
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D315V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMEM41B MUTATED       1                         1     2
  TMEM41B WILD-TYPE    75                         3   166
D315V12, multiclass
                           clus
vv                          TMEM41B MUTATED TMEM41B WILD-TYPE
  ASIAN                                   1                75
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   2               166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(316) Variable = ENTPD2 MUTATION ANALYSIS
D316V1, survival
                  sevent
clus2                0   1
  ENTPD2 MUTATED     2   1
  ENTPD2 WILD-TYPE 179  79
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               3              258 
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               1               79 
$`ENTPD2 MUTATED`
TCGA-B7-5816 TCGA-D7-A4YV TCGA-HU-A4G9 
       26.70         5.92        24.20 

$`ENTPD2 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
            5.92             0.00 
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
           26.70           105.07 
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
          24.200           12.605 
[1] "5.9 - 26.7 (24.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D316V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ENTPD2 MUTATED         0        1        0        0         0         2
  ENTPD2 WILD-TYPE       1        8       27       26        31        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ENTPD2 MUTATED           0          0          0          0        0
  ENTPD2 WILD-TYPE         3         49         36         24       24
D316V3, multiclass
            clus
vv           ENTPD2 MUTATED ENTPD2 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               0               31
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ENTPD2 MUTATED     1   0   1   1
  ENTPD2 WILD-TYPE  10  72 121  74
D316V4, multiclass
    clus
vv   ENTPD2 MUTATED ENTPD2 WILD-TYPE
  T1              1               10
  T2              0               72
  T3              1              121
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ENTPD2 MUTATED    2  2  0  0
  ENTPD2 WILD-TYPE 91 79 50 53
D316V5, multiclass
    clus
vv   ENTPD2 MUTATED ENTPD2 WILD-TYPE
  N0              2               91
  N1              2               79
  N2              0               50
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D316V6, binary
                  cls
clus                 0   1
  ENTPD2 MUTATED     4   0
  ENTPD2 WILD-TYPE 253  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD2 MUTATED      4    0
  ENTPD2 WILD-TYPE  253   18
   clus
vv  ENTPD2 MUTATED ENTPD2 WILD-TYPE
  0              4              253
  1              0               18
[1] 2 2
[1] FALSE
D316V7, binary
                  cls
clus                 0   1
  ENTPD2 MUTATED     4   0
  ENTPD2 WILD-TYPE 106 179
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD2 MUTATED      4    0
  ENTPD2 WILD-TYPE  106  179
        clus
vv       ENTPD2 MUTATED ENTPD2 WILD-TYPE
  FEMALE              4              106
  MALE                0              179
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ENTPD2 MUTATED                                       1
  ENTPD2 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ENTPD2 MUTATED                                                        1
  ENTPD2 WILD-TYPE                                                    134
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ENTPD2 MUTATED                                                                   0
  ENTPD2 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ENTPD2 MUTATED                                                  2
  ENTPD2 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ENTPD2 MUTATED                                                          0
  ENTPD2 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ENTPD2 MUTATED                                                           0
  ENTPD2 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ENTPD2 MUTATED                                          0
  ENTPD2 WILD-TYPE                                        3
D316V8, multiclass
                                                                   clus
vv                                                                  ENTPD2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         1
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ENTPD2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D316V9, binary
                  cls
clus                 0   1
  ENTPD2 MUTATED     0   4
  ENTPD2 WILD-TYPE   5 280
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD2 MUTATED      0    4
  ENTPD2 WILD-TYPE    5  280
     clus
vv    ENTPD2 MUTATED ENTPD2 WILD-TYPE
  NO               0                5
  YES              4              280
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ENTPD2 MUTATED     3   0   0   1
  ENTPD2 WILD-TYPE 224  10  10  23
D316V10, multiclass
    clus
vv   ENTPD2 MUTATED ENTPD2 WILD-TYPE
  R0              3              224
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D316V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ENTPD2 MUTATED       1                         0     3
  ENTPD2 WILD-TYPE    75                         4   165
D316V12, multiclass
                           clus
vv                          ENTPD2 MUTATED ENTPD2 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  3              165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(317) Variable = IRS4 MUTATION ANALYSIS
D317V1, survival
                sevent
clus2              0   1
  IRS4 MUTATED    16   2
  IRS4 WILD-TYPE 165  78
  IRS4 MUTATED IRS4 WILD-TYPE 
            18            243 
  IRS4 MUTATED IRS4 WILD-TYPE 
             2             78 
$`IRS4 MUTATED`
TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8382 
       11.70        34.68        23.93         4.31        19.17        15.85 
TCGA-BR-8680 TCGA-CD-A4MI TCGA-CG-5733 TCGA-D7-6526 TCGA-FP-7998 TCGA-HU-8602 
       15.81         0.10        21.07        17.19        22.29        11.41 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H3 
        8.98         0.10         6.51        10.19         2.10        19.36 

$`IRS4 WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
       14.04         3.32        11.80        14.79         0.26         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        14.07        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H4 
       11.77        29.98         6.25         0.26        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  IRS4 MUTATED IRS4 WILD-TYPE 
           0.1            0.0 
  IRS4 MUTATED IRS4 WILD-TYPE 
         34.68         105.07 
  IRS4 MUTATED IRS4 WILD-TYPE 
        13.755         12.620 
[1] "0.1 - 34.7 (13.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.8"
D317V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IRS4 MUTATED         0        0        3        0         3         1
  IRS4 WILD-TYPE       1        9       24       26        28        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IRS4 MUTATED           0          3          1          8        2
  IRS4 WILD-TYPE         3         46         35         16       22
D317V3, multiclass
            clus
vv           IRS4 MUTATED IRS4 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              3             24
  STAGE II              0             26
  STAGE IIA             3             28
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            3             46
  STAGE IIIB            1             35
  STAGE IIIC            8             16
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IRS4 MUTATED     1   5   4  12
  IRS4 WILD-TYPE  10  67 118  63
D317V4, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  T1            1             10
  T2            5             67
  T3            4            118
  T4           12             63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  IRS4 MUTATED    7  3  6  6
  IRS4 WILD-TYPE 86 78 44 47
D317V5, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  N0            7             86
  N1            3             78
  N2            6             44
  N3            6             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D317V6, binary
                cls
clus               0   1
  IRS4 MUTATED    21   1
  IRS4 WILD-TYPE 236  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED     21    1
  IRS4 WILD-TYPE  236   17
   clus
vv  IRS4 MUTATED IRS4 WILD-TYPE
  0           21            236
  1            1             17
[1] 2 2
[1] FALSE
D317V7, binary
                cls
clus               0   1
  IRS4 MUTATED    16   7
  IRS4 WILD-TYPE  94 172
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED     16    7
  IRS4 WILD-TYPE   94  172
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  FEMALE           16             94
  MALE              7            172
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  IRS4 MUTATED                                       7
  IRS4 WILD-TYPE                                    43
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IRS4 MUTATED                                                       11
  IRS4 WILD-TYPE                                                    124
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IRS4 MUTATED                                                                   1
  IRS4 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  IRS4 MUTATED                                                  4
  IRS4 WILD-TYPE                                               34
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  IRS4 MUTATED                                                          0
  IRS4 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  IRS4 MUTATED                                                           0
  IRS4 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  IRS4 MUTATED                                          0
  IRS4 WILD-TYPE                                        3
D317V8, multiclass
                                                                   clus
vv                                                                  IRS4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  IRS4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         43
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D317V9, binary
                cls
clus               0   1
  IRS4 MUTATED     0  23
  IRS4 WILD-TYPE   5 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      0   23
  IRS4 WILD-TYPE    5  261
     clus
vv    IRS4 MUTATED IRS4 WILD-TYPE
  NO             0              5
  YES           23            261
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IRS4 MUTATED    18   0   0   4
  IRS4 WILD-TYPE 209  10  10  20
D317V10, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  R0           18            209
  R1            0             10
  R2            0             10
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D317V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IRS4 MUTATED       9                         0    13
  IRS4 WILD-TYPE    67                         4   155
D317V12, multiclass
                           clus
vv                          IRS4 MUTATED IRS4 WILD-TYPE
  ASIAN                                9             67
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               13            155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(318) Variable = EVL MUTATION ANALYSIS
D318V1, survival
               sevent
clus2             0   1
  EVL MUTATED     4   2
  EVL WILD-TYPE 177  78
  EVL MUTATED EVL WILD-TYPE 
            6           255 
  EVL MUTATED EVL WILD-TYPE 
            2            78 
$`EVL MUTATED`
TCGA-BR-4201 TCGA-BR-7851 TCGA-BR-8369 TCGA-CD-8536 TCGA-CG-4477 TCGA-HJ-7597 
       30.90        12.43        14.04         0.10        30.97        26.47 

$`EVL WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        22.98         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56        11.08         5.52         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  EVL MUTATED EVL WILD-TYPE 
          0.1           0.0 
  EVL MUTATED EVL WILD-TYPE 
        30.97        105.07 
  EVL MUTATED EVL WILD-TYPE 
       20.255        12.590 
[1] "0.1 - 31.0 (20.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.5"
D318V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EVL MUTATED         0        0        2        1         0         1
  EVL WILD-TYPE       1        9       25       25        31        43
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EVL MUTATED           0          1          1          0        0
  EVL WILD-TYPE         3         48         35         24       24
D318V3, multiclass
            clus
vv           EVL MUTATED EVL WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             9
  STAGE IB             2            25
  STAGE II             1            25
  STAGE IIA            0            31
  STAGE IIB            1            43
  STAGE III            0             3
  STAGE IIIA           1            48
  STAGE IIIB           1            35
  STAGE IIIC           0            24
  STAGE IV             0            24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  EVL MUTATED     0   3   2   2
  EVL WILD-TYPE  11  69 120  73
D318V4, multiclass
    clus
vv   EVL MUTATED EVL WILD-TYPE
  T1           0            11
  T2           3            69
  T3           2           120
  T4           2            73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  EVL MUTATED    5  0  0  1
  EVL WILD-TYPE 88 81 50 52
D318V5, multiclass
    clus
vv   EVL MUTATED EVL WILD-TYPE
  N0           5            88
  N1           0            81
  N2           0            50
  N3           1            52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D318V6, binary
               cls
clus              0   1
  EVL MUTATED     6   0
  EVL WILD-TYPE 251  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  EVL MUTATED      6    0
  EVL WILD-TYPE  251   18
   clus
vv  EVL MUTATED EVL WILD-TYPE
  0           6           251
  1           0            18
[1] 2 2
[1] FALSE
D318V7, binary
               cls
clus              0   1
  EVL MUTATED     5   2
  EVL WILD-TYPE 105 177
[1] "tbl2"
               cls
clus            [,1] [,2]
  EVL MUTATED      5    2
  EVL WILD-TYPE  105  177
        clus
vv       EVL MUTATED EVL WILD-TYPE
  FEMALE           5           105
  MALE             2           177
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  EVL MUTATED                                       0
  EVL WILD-TYPE                                    50
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EVL MUTATED                                                        4
  EVL WILD-TYPE                                                    131
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EVL MUTATED                                                                   2
  EVL WILD-TYPE                                                                38
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  EVL MUTATED                                                  0
  EVL WILD-TYPE                                               38
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  EVL MUTATED                                                          0
  EVL WILD-TYPE                                                       16
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  EVL MUTATED                                                           0
  EVL WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  EVL MUTATED                                          1
  EVL WILD-TYPE                                        2
D318V8, multiclass
                                                                   clus
vv                                                                  EVL MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    1
                                                                   clus
vv                                                                  EVL WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D318V9, binary
               cls
clus              0   1
  EVL MUTATED     0   7
  EVL WILD-TYPE   5 277
[1] "tbl2"
               cls
clus            [,1] [,2]
  EVL MUTATED      0    7
  EVL WILD-TYPE    5  277
     clus
vv    EVL MUTATED EVL WILD-TYPE
  NO            0             5
  YES           7           277
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  EVL MUTATED     5   0   0   2
  EVL WILD-TYPE 222  10  10  22
D318V10, multiclass
    clus
vv   EVL MUTATED EVL WILD-TYPE
  R0           5           222
  R1           0            10
  R2           0            10
  RX           2            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D318V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EVL MUTATED       1                         0     5
  EVL WILD-TYPE    75                         4   163
D318V12, multiclass
                           clus
vv                          EVL MUTATED EVL WILD-TYPE
  ASIAN                               1            75
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                               5           163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(319) Variable = OR5M3 MUTATION ANALYSIS
D319V1, survival
                 sevent
clus2               0   1
  OR5M3 MUTATED    10   3
  OR5M3 WILD-TYPE 171  77
  OR5M3 MUTATED OR5M3 WILD-TYPE 
             13             248 
  OR5M3 MUTATED OR5M3 WILD-TYPE 
              3              77 
$`OR5M3 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7851 TCGA-BR-8295 TCGA-BR-8382 TCGA-BR-8487 
       30.90        34.68        12.43         2.20        15.85         1.12 
TCGA-BR-8588 TCGA-BR-A452 TCGA-CD-8528 TCGA-D7-6526 TCGA-HU-A4GT TCGA-HU-A4GU 
       12.79         7.53         0.10        17.19         6.51         6.25 
TCGA-HU-A4H8 
        8.88 

$`OR5M3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       18.35         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        16.31        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 
        3.72         5.39        25.18         9.21        20.22        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56        13.87         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       12.30         9.67        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  OR5M3 MUTATED OR5M3 WILD-TYPE 
            0.1             0.0 
  OR5M3 MUTATED OR5M3 WILD-TYPE 
          34.68          105.07 
  OR5M3 MUTATED OR5M3 WILD-TYPE 
           8.88           12.71 
[1] "0.1 - 34.7 (8.9)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.2"
D319V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OR5M3 MUTATED         0        0        2        1         3         4
  OR5M3 WILD-TYPE       1        9       25       25        28        40
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR5M3 MUTATED           0          3          0          1        0
  OR5M3 WILD-TYPE         3         46         36         23       24
D319V3, multiclass
            clus
vv           OR5M3 MUTATED OR5M3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               1              25
  STAGE IIA              3              28
  STAGE IIB              4              40
  STAGE III              0               3
  STAGE IIIA             3              46
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR5M3 MUTATED     1   3   5   6
  OR5M3 WILD-TYPE  10  69 117  69
D319V4, multiclass
    clus
vv   OR5M3 MUTATED OR5M3 WILD-TYPE
  T1             1              10
  T2             3              69
  T3             5             117
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  OR5M3 MUTATED    8  4  1  1
  OR5M3 WILD-TYPE 85 77 49 52
D319V5, multiclass
    clus
vv   OR5M3 MUTATED OR5M3 WILD-TYPE
  N0             8              85
  N1             4              77
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D319V6, binary
                 cls
clus                0   1
  OR5M3 MUTATED    15   0
  OR5M3 WILD-TYPE 242  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5M3 MUTATED     15    0
  OR5M3 WILD-TYPE  242   18
   clus
vv  OR5M3 MUTATED OR5M3 WILD-TYPE
  0            15             242
  1             0              18
[1] 2 2
[1] FALSE
D319V7, binary
                 cls
clus                0   1
  OR5M3 MUTATED     9   6
  OR5M3 WILD-TYPE 101 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5M3 MUTATED      9    6
  OR5M3 WILD-TYPE  101  173
        clus
vv       OR5M3 MUTATED OR5M3 WILD-TYPE
  FEMALE             9             101
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  OR5M3 MUTATED                                       1
  OR5M3 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OR5M3 MUTATED                                                        7
  OR5M3 WILD-TYPE                                                    128
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OR5M3 MUTATED                                                                   2
  OR5M3 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  OR5M3 MUTATED                                                  4
  OR5M3 WILD-TYPE                                               34
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  OR5M3 MUTATED                                                          1
  OR5M3 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  OR5M3 MUTATED                                                           0
  OR5M3 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  OR5M3 MUTATED                                          0
  OR5M3 WILD-TYPE                                        3
D319V8, multiclass
                                                                   clus
vv                                                                  OR5M3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  OR5M3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D319V9, binary
                 cls
clus                0   1
  OR5M3 MUTATED     1  14
  OR5M3 WILD-TYPE   4 270
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5M3 MUTATED      1   14
  OR5M3 WILD-TYPE    4  270
     clus
vv    OR5M3 MUTATED OR5M3 WILD-TYPE
  NO              1               4
  YES            14             270
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR5M3 MUTATED    14   0   0   1
  OR5M3 WILD-TYPE 213  10  10  23
D319V10, multiclass
    clus
vv   OR5M3 MUTATED OR5M3 WILD-TYPE
  R0            14             213
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D319V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR5M3 MUTATED       5                         0     8
  OR5M3 WILD-TYPE    71                         4   160
D319V12, multiclass
                           clus
vv                          OR5M3 MUTATED OR5M3 WILD-TYPE
  ASIAN                                 5              71
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 8             160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(320) Variable = MYEOV MUTATION ANALYSIS
D320V1, survival
                 sevent
clus2               0   1
  MYEOV MUTATED     5   1
  MYEOV WILD-TYPE 176  79
  MYEOV MUTATED MYEOV WILD-TYPE 
              6             255 
  MYEOV MUTATED MYEOV WILD-TYPE 
              1              79 
$`MYEOV MUTATED`
TCGA-BR-8078 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-8536 TCGA-CD-A4MG TCGA-HU-A4G9 
       12.26        13.45        15.81         0.10         6.58        24.20 

$`MYEOV WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        9.34         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        11.84         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  MYEOV MUTATED MYEOV WILD-TYPE 
            0.1             0.0 
  MYEOV MUTATED MYEOV WILD-TYPE 
          24.20          105.07 
  MYEOV MUTATED MYEOV WILD-TYPE 
         12.855          12.620 
[1] "0.1 - 24.2 (12.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.5"
D320V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MYEOV MUTATED         1        1        0        1         1         1
  MYEOV WILD-TYPE       0        8       27       25        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MYEOV MUTATED           0          0          0          1        1
  MYEOV WILD-TYPE         3         49         36         23       23
D320V3, multiclass
            clus
vv           MYEOV MUTATED MYEOV WILD-TYPE
  STAGE I                1               0
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYEOV MUTATED     3   0   2   3
  MYEOV WILD-TYPE   8  72 120  72
D320V4, multiclass
    clus
vv   MYEOV MUTATED MYEOV WILD-TYPE
  T1             3               8
  T2             0              72
  T3             2             120
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  MYEOV MUTATED    4  1  1  1
  MYEOV WILD-TYPE 89 80 49 52
D320V5, multiclass
    clus
vv   MYEOV MUTATED MYEOV WILD-TYPE
  N0             4              89
  N1             1              80
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D320V6, binary
                 cls
clus                0   1
  MYEOV MUTATED     6   1
  MYEOV WILD-TYPE 251  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYEOV MUTATED      6    1
  MYEOV WILD-TYPE  251   17
   clus
vv  MYEOV MUTATED MYEOV WILD-TYPE
  0             6             251
  1             1              17
[1] 2 2
[1] FALSE
D320V7, binary
                 cls
clus                0   1
  MYEOV MUTATED     3   5
  MYEOV WILD-TYPE 107 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYEOV MUTATED      3    5
  MYEOV WILD-TYPE  107  174
        clus
vv       MYEOV MUTATED MYEOV WILD-TYPE
  FEMALE             3             107
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MYEOV MUTATED                                       1
  MYEOV WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MYEOV MUTATED                                                        5
  MYEOV WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MYEOV MUTATED                                                                   0
  MYEOV WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MYEOV MUTATED                                                  2
  MYEOV WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MYEOV MUTATED                                                          0
  MYEOV WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MYEOV MUTATED                                                           0
  MYEOV WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MYEOV MUTATED                                          0
  MYEOV WILD-TYPE                                        3
D320V8, multiclass
                                                                   clus
vv                                                                  MYEOV MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  MYEOV WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D320V9, binary
                 cls
clus                0   1
  MYEOV MUTATED     0   8
  MYEOV WILD-TYPE   5 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYEOV MUTATED      0    8
  MYEOV WILD-TYPE    5  276
     clus
vv    MYEOV MUTATED MYEOV WILD-TYPE
  NO              0               5
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MYEOV MUTATED     6   0   0   1
  MYEOV WILD-TYPE 221  10  10  23
D320V10, multiclass
    clus
vv   MYEOV MUTATED MYEOV WILD-TYPE
  R0             6             221
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D320V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MYEOV MUTATED       4                         1     3
  MYEOV WILD-TYPE    72                         3   165
D320V12, multiclass
                           clus
vv                          MYEOV MUTATED MYEOV WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(321) Variable = C15ORF52 MUTATION ANALYSIS
D321V1, survival
                    sevent
clus2                  0   1
  C15ORF52 MUTATED     4   1
  C15ORF52 WILD-TYPE 177  79
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                 5                256 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                 1                 79 
$`C15ORF52 MUTATED`
TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-A4MG TCGA-F1-A448 TCGA-HU-A4GT 
        1.12        13.45         6.58        21.27         6.51 

$`C15ORF52 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        0.62         7.99        16.24        14.47        72.23         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
              1.12               0.00 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
             21.27             105.07 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
              6.58              12.64 
[1] "1.1 - 21.3 (6.6)"   "0.0 - 105.1 (12.6)"
[1] "hr=" "1"  
D321V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C15ORF52 MUTATED         0        0        0        1         3         0
  C15ORF52 WILD-TYPE       1        9       27       25        28        44
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C15ORF52 MUTATED           0          0          1          1        0
  C15ORF52 WILD-TYPE         3         49         35         23       24
D321V3, multiclass
            clus
vv           C15ORF52 MUTATED C15ORF52 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  0                 27
  STAGE II                  1                 25
  STAGE IIA                 3                 28
  STAGE IIB                 0                 44
  STAGE III                 0                  3
  STAGE IIIA                0                 49
  STAGE IIIB                1                 35
  STAGE IIIC                1                 23
  STAGE IV                  0                 24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C15ORF52 MUTATED     0   1   5   1
  C15ORF52 WILD-TYPE  11  71 117  74
D321V4, multiclass
    clus
vv   C15ORF52 MUTATED C15ORF52 WILD-TYPE
  T1                0                 11
  T2                1                 71
  T3                5                117
  T4                1                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  C15ORF52 MUTATED    3  1  0  2
  C15ORF52 WILD-TYPE 90 80 50 51
D321V5, multiclass
    clus
vv   C15ORF52 MUTATED C15ORF52 WILD-TYPE
  N0                3                 90
  N1                1                 80
  N2                0                 50
  N3                2                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D321V6, binary
                    cls
clus                   0   1
  C15ORF52 MUTATED     7   0
  C15ORF52 WILD-TYPE 250  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF52 MUTATED      7    0
  C15ORF52 WILD-TYPE  250   18
   clus
vv  C15ORF52 MUTATED C15ORF52 WILD-TYPE
  0                7                250
  1                0                 18
[1] 2 2
[1] FALSE
D321V7, binary
                    cls
clus                   0   1
  C15ORF52 MUTATED     4   4
  C15ORF52 WILD-TYPE 106 175
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF52 MUTATED      4    4
  C15ORF52 WILD-TYPE  106  175
        clus
vv       C15ORF52 MUTATED C15ORF52 WILD-TYPE
  FEMALE                4                106
  MALE                  4                175
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C15ORF52 MUTATED                                       1
  C15ORF52 WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C15ORF52 MUTATED                                                        4
  C15ORF52 WILD-TYPE                                                    131
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C15ORF52 MUTATED                                                                   0
  C15ORF52 WILD-TYPE                                                                40
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C15ORF52 MUTATED                                                  1
  C15ORF52 WILD-TYPE                                               37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C15ORF52 MUTATED                                                          2
  C15ORF52 WILD-TYPE                                                       14
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C15ORF52 MUTATED                                                           0
  C15ORF52 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C15ORF52 MUTATED                                          0
  C15ORF52 WILD-TYPE                                        3
D321V8, multiclass
                                                                   clus
vv                                                                  C15ORF52 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  C15ORF52 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D321V9, binary
                    cls
clus                   0   1
  C15ORF52 MUTATED     1   7
  C15ORF52 WILD-TYPE   4 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF52 MUTATED      1    7
  C15ORF52 WILD-TYPE    4  277
     clus
vv    C15ORF52 MUTATED C15ORF52 WILD-TYPE
  NO                 1                  4
  YES                7                277
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C15ORF52 MUTATED     5   0   0   2
  C15ORF52 WILD-TYPE 222  10  10  22
D321V10, multiclass
    clus
vv   C15ORF52 MUTATED C15ORF52 WILD-TYPE
  R0                5                222
  R1                0                 10
  R2                0                 10
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D321V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C15ORF52 MUTATED       2                         0     5
  C15ORF52 WILD-TYPE    74                         4   163
D321V12, multiclass
                           clus
vv                          C15ORF52 MUTATED C15ORF52 WILD-TYPE
  ASIAN                                    2                 74
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    5                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(322) Variable = PKN2 MUTATION ANALYSIS
D322V1, survival
                sevent
clus2              0   1
  PKN2 MUTATED     8   2
  PKN2 WILD-TYPE 173  78
  PKN2 MUTATED PKN2 WILD-TYPE 
            10            251 
  PKN2 MUTATED PKN2 WILD-TYPE 
             2             78 
$`PKN2 MUTATED`
TCGA-BR-4280 TCGA-BR-8080 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4QL 
        6.61         9.60         4.31         1.12        15.81        11.57 
TCGA-CG-5728 TCGA-D7-6524 TCGA-HU-A4G8 TCGA-HU-A4GU 
       65.10        17.85        11.84         6.25 

$`PKN2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69        12.26        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.54        18.61        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  PKN2 MUTATED PKN2 WILD-TYPE 
          1.12           0.00 
  PKN2 MUTATED PKN2 WILD-TYPE 
         65.10         105.07 
  PKN2 MUTATED PKN2 WILD-TYPE 
        10.585         12.760 
[1] "1.1 - 65.1 (10.6)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.4"
D322V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PKN2 MUTATED         0        0        2        1         1         2
  PKN2 WILD-TYPE       1        9       25       25        30        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PKN2 MUTATED           1          0          1          1        1
  PKN2 WILD-TYPE         2         49         35         23       23
D322V3, multiclass
            clus
vv           PKN2 MUTATED PKN2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              1             25
  STAGE IIA             1             30
  STAGE IIB             2             42
  STAGE III             1              2
  STAGE IIIA            0             49
  STAGE IIIB            1             35
  STAGE IIIC            1             23
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PKN2 MUTATED     0   4   4   2
  PKN2 WILD-TYPE  11  68 118  73
D322V4, multiclass
    clus
vv   PKN2 MUTATED PKN2 WILD-TYPE
  T1            0             11
  T2            4             68
  T3            4            118
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  PKN2 MUTATED    3  4  1  2
  PKN2 WILD-TYPE 90 77 49 51
D322V5, multiclass
    clus
vv   PKN2 MUTATED PKN2 WILD-TYPE
  N0            3             90
  N1            4             77
  N2            1             49
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D322V6, binary
                cls
clus               0   1
  PKN2 MUTATED     9   1
  PKN2 WILD-TYPE 248  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN2 MUTATED      9    1
  PKN2 WILD-TYPE  248   17
   clus
vv  PKN2 MUTATED PKN2 WILD-TYPE
  0            9            248
  1            1             17
[1] 2 2
[1] FALSE
D322V7, binary
                cls
clus               0   1
  PKN2 MUTATED     7   3
  PKN2 WILD-TYPE 103 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN2 MUTATED      7    3
  PKN2 WILD-TYPE  103  176
        clus
vv       PKN2 MUTATED PKN2 WILD-TYPE
  FEMALE            7            103
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PKN2 MUTATED                                       3
  PKN2 WILD-TYPE                                    47
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PKN2 MUTATED                                                        4
  PKN2 WILD-TYPE                                                    131
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PKN2 MUTATED                                                                   1
  PKN2 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PKN2 MUTATED                                                  1
  PKN2 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PKN2 MUTATED                                                          1
  PKN2 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PKN2 MUTATED                                                           0
  PKN2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PKN2 MUTATED                                          0
  PKN2 WILD-TYPE                                        3
D322V8, multiclass
                                                                   clus
vv                                                                  PKN2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  PKN2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D322V9, binary
                cls
clus               0   1
  PKN2 MUTATED     0  10
  PKN2 WILD-TYPE   5 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN2 MUTATED      0   10
  PKN2 WILD-TYPE    5  274
     clus
vv    PKN2 MUTATED PKN2 WILD-TYPE
  NO             0              5
  YES           10            274
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PKN2 MUTATED     7   1   0   1
  PKN2 WILD-TYPE 220   9  10  23
D322V10, multiclass
    clus
vv   PKN2 MUTATED PKN2 WILD-TYPE
  R0            7            220
  R1            1              9
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D322V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PKN2 MUTATED       3                         0     6
  PKN2 WILD-TYPE    73                         4   162
D322V12, multiclass
                           clus
vv                          PKN2 MUTATED PKN2 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                6            162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(323) Variable = IPO11 MUTATION ANALYSIS
D323V1, survival
                 sevent
clus2               0   1
  IPO11 MUTATED     9   0
  IPO11 WILD-TYPE 172  80
  IPO11 MUTATED IPO11 WILD-TYPE 
              9             252 
  IPO11 MUTATED IPO11 WILD-TYPE 
              0              80 
$`IPO11 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8589 TCGA-CD-8536 TCGA-CD-A4MI 
       26.70        34.68         6.18        15.81         0.10         0.10 
TCGA-D7-6818 TCGA-F1-6874 TCGA-FP-A4BE 
       10.55        14.47        11.08 

$`IPO11 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        12.79         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.22        15.98        12.79        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
       13.78        14.76         0.62         7.99        16.24        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 
       59.54         5.03        13.58         0.56         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  IPO11 MUTATED IPO11 WILD-TYPE 
            0.1             0.0 
  IPO11 MUTATED IPO11 WILD-TYPE 
          34.68          105.07 
  IPO11 MUTATED IPO11 WILD-TYPE 
          11.08           12.64 
[1] "0.1 - 34.7 (11.1)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "2.6e+07"
D323V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IPO11 MUTATED         0        0        1        1         3         1
  IPO11 WILD-TYPE       1        9       26       25        28        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IPO11 MUTATED           0          2          2          0        1
  IPO11 WILD-TYPE         3         47         34         24       23
D323V3, multiclass
            clus
vv           IPO11 MUTATED IPO11 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              3              28
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             2              34
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IPO11 MUTATED     0   2   5   4
  IPO11 WILD-TYPE  11  70 117  71
D323V4, multiclass
    clus
vv   IPO11 MUTATED IPO11 WILD-TYPE
  T1             0              11
  T2             2              70
  T3             5             117
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  IPO11 MUTATED    7  2  1  1
  IPO11 WILD-TYPE 86 79 49 52
D323V5, multiclass
    clus
vv   IPO11 MUTATED IPO11 WILD-TYPE
  N0             7              86
  N1             2              79
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D323V6, binary
                 cls
clus                0   1
  IPO11 MUTATED    12   0
  IPO11 WILD-TYPE 245  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IPO11 MUTATED     12    0
  IPO11 WILD-TYPE  245   18
   clus
vv  IPO11 MUTATED IPO11 WILD-TYPE
  0            12             245
  1             0              18
[1] 2 2
[1] FALSE
D323V7, binary
                 cls
clus                0   1
  IPO11 MUTATED     5   7
  IPO11 WILD-TYPE 105 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IPO11 MUTATED      5    7
  IPO11 WILD-TYPE  105  172
        clus
vv       IPO11 MUTATED IPO11 WILD-TYPE
  FEMALE             5             105
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  IPO11 MUTATED                                       2
  IPO11 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IPO11 MUTATED                                                        8
  IPO11 WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IPO11 MUTATED                                                                   2
  IPO11 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  IPO11 MUTATED                                                  0
  IPO11 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  IPO11 MUTATED                                                          0
  IPO11 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  IPO11 MUTATED                                                           0
  IPO11 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  IPO11 MUTATED                                          0
  IPO11 WILD-TYPE                                        3
D323V8, multiclass
                                                                   clus
vv                                                                  IPO11 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  IPO11 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D323V9, binary
                 cls
clus                0   1
  IPO11 MUTATED     1  11
  IPO11 WILD-TYPE   4 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IPO11 MUTATED      1   11
  IPO11 WILD-TYPE    4  273
     clus
vv    IPO11 MUTATED IPO11 WILD-TYPE
  NO              1               4
  YES            11             273
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IPO11 MUTATED     8   0   0   3
  IPO11 WILD-TYPE 219  10  10  21
D323V10, multiclass
    clus
vv   IPO11 MUTATED IPO11 WILD-TYPE
  R0             8             219
  R1             0              10
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D323V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IPO11 MUTATED       2                         1     9
  IPO11 WILD-TYPE    74                         3   159
D323V12, multiclass
                           clus
vv                          IPO11 MUTATED IPO11 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 9             159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(324) Variable = INTS12 MUTATION ANALYSIS
D324V1, survival
                  sevent
clus2                0   1
  INTS12 MUTATED     3   1
  INTS12 WILD-TYPE 178  79
  INTS12 MUTATED INTS12 WILD-TYPE 
               4              257 
  INTS12 MUTATED INTS12 WILD-TYPE 
               1               79 
$`INTS12 MUTATED`
TCGA-BR-6452 TCGA-BR-8059 TCGA-BR-8360 TCGA-BR-A4QL 
       34.68        14.43         6.18        11.57 

$`INTS12 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  INTS12 MUTATED INTS12 WILD-TYPE 
            6.18             0.00 
  INTS12 MUTATED INTS12 WILD-TYPE 
           34.68           105.07 
  INTS12 MUTATED INTS12 WILD-TYPE 
           13.00            12.62 
[1] "6.2 - 34.7 (13.0)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.5"
D324V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  INTS12 MUTATED         0        0        0        0         2         0
  INTS12 WILD-TYPE       1        9       27       26        29        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  INTS12 MUTATED           1          0          1          0        1
  INTS12 WILD-TYPE         2         49         35         24       23
D324V3, multiclass
            clus
vv           INTS12 MUTATED INTS12 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               2               29
  STAGE IIB               0               44
  STAGE III               1                2
  STAGE IIIA              0               49
  STAGE IIIB              1               35
  STAGE IIIC              0               24
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  INTS12 MUTATED     0   0   3   2
  INTS12 WILD-TYPE  11  72 119  73
D324V4, multiclass
    clus
vv   INTS12 MUTATED INTS12 WILD-TYPE
  T1              0               11
  T2              0               72
  T3              3              119
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  INTS12 MUTATED    2  2  1  1
  INTS12 WILD-TYPE 91 79 49 52
D324V5, multiclass
    clus
vv   INTS12 MUTATED INTS12 WILD-TYPE
  N0              2               91
  N1              2               79
  N2              1               49
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D324V6, binary
                  cls
clus                 0   1
  INTS12 MUTATED     6   0
  INTS12 WILD-TYPE 251  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INTS12 MUTATED      6    0
  INTS12 WILD-TYPE  251   18
   clus
vv  INTS12 MUTATED INTS12 WILD-TYPE
  0              6              251
  1              0               18
[1] 2 2
[1] FALSE
D324V7, binary
                  cls
clus                 0   1
  INTS12 MUTATED     4   2
  INTS12 WILD-TYPE 106 177
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INTS12 MUTATED      4    2
  INTS12 WILD-TYPE  106  177
        clus
vv       INTS12 MUTATED INTS12 WILD-TYPE
  FEMALE              4              106
  MALE                2              177
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  INTS12 MUTATED                                       0
  INTS12 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  INTS12 MUTATED                                                        4
  INTS12 WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  INTS12 MUTATED                                                                   2
  INTS12 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  INTS12 MUTATED                                                  0
  INTS12 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  INTS12 MUTATED                                                          0
  INTS12 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  INTS12 MUTATED                                                           0
  INTS12 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  INTS12 MUTATED                                          0
  INTS12 WILD-TYPE                                        3
D324V8, multiclass
                                                                   clus
vv                                                                  INTS12 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  INTS12 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D324V9, binary
                  cls
clus                 0   1
  INTS12 MUTATED     0   6
  INTS12 WILD-TYPE   5 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INTS12 MUTATED      0    6
  INTS12 WILD-TYPE    5  278
     clus
vv    INTS12 MUTATED INTS12 WILD-TYPE
  NO               0                5
  YES              6              278
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  INTS12 MUTATED     4   0   0   2
  INTS12 WILD-TYPE 223  10  10  22
D324V10, multiclass
    clus
vv   INTS12 MUTATED INTS12 WILD-TYPE
  R0              4              223
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D324V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  INTS12 MUTATED       0                         0     6
  INTS12 WILD-TYPE    76                         4   162
D324V12, multiclass
                           clus
vv                          INTS12 MUTATED INTS12 WILD-TYPE
  ASIAN                                  0               76
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(325) Variable = PGBD1 MUTATION ANALYSIS
D325V1, survival
                 sevent
clus2               0   1
  PGBD1 MUTATED     8   2
  PGBD1 WILD-TYPE 173  78
  PGBD1 MUTATED PGBD1 WILD-TYPE 
             10             251 
  PGBD1 MUTATED PGBD1 WILD-TYPE 
              2              78 
$`PGBD1 MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8372 TCGA-CD-A4MJ TCGA-CG-4305 
       11.70         6.97        34.68        19.17        12.62        15.95 
TCGA-CG-5720 TCGA-CG-5728 TCGA-HU-8602 TCGA-HU-A4GX 
        0.99        65.10        11.41        10.19 

$`PGBD1 WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       26.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20         0.10        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       26.47         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  PGBD1 MUTATED PGBD1 WILD-TYPE 
           0.99            0.00 
  PGBD1 MUTATED PGBD1 WILD-TYPE 
          65.10          105.07 
  PGBD1 MUTATED PGBD1 WILD-TYPE 
          12.16           12.66 
[1] "1.0 - 65.1 (12.2)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "2"  
D325V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PGBD1 MUTATED         0        0        4        1         1         1
  PGBD1 WILD-TYPE       1        9       23       25        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PGBD1 MUTATED           0          1          0          2        0
  PGBD1 WILD-TYPE         3         48         36         22       24
D325V3, multiclass
            clus
vv           PGBD1 MUTATED PGBD1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               4              23
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             2              22
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PGBD1 MUTATED     1   5   2   3
  PGBD1 WILD-TYPE  10  67 120  72
D325V4, multiclass
    clus
vv   PGBD1 MUTATED PGBD1 WILD-TYPE
  T1             1              10
  T2             5              67
  T3             2             120
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PGBD1 MUTATED    6  2  1  1
  PGBD1 WILD-TYPE 87 79 49 52
D325V5, multiclass
    clus
vv   PGBD1 MUTATED PGBD1 WILD-TYPE
  N0             6              87
  N1             2              79
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D325V6, binary
                 cls
clus                0   1
  PGBD1 MUTATED    11   0
  PGBD1 WILD-TYPE 246  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGBD1 MUTATED     11    0
  PGBD1 WILD-TYPE  246   18
   clus
vv  PGBD1 MUTATED PGBD1 WILD-TYPE
  0            11             246
  1             0              18
[1] 2 2
[1] FALSE
D325V7, binary
                 cls
clus                0   1
  PGBD1 MUTATED     6   6
  PGBD1 WILD-TYPE 104 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGBD1 MUTATED      6    6
  PGBD1 WILD-TYPE  104  173
        clus
vv       PGBD1 MUTATED PGBD1 WILD-TYPE
  FEMALE             6             104
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PGBD1 MUTATED                                       3
  PGBD1 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PGBD1 MUTATED                                                        8
  PGBD1 WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PGBD1 MUTATED                                                                   1
  PGBD1 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PGBD1 MUTATED                                                  0
  PGBD1 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PGBD1 MUTATED                                                          0
  PGBD1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PGBD1 MUTATED                                                           0
  PGBD1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PGBD1 MUTATED                                          0
  PGBD1 WILD-TYPE                                        3
D325V8, multiclass
                                                                   clus
vv                                                                  PGBD1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  PGBD1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D325V9, binary
                 cls
clus                0   1
  PGBD1 MUTATED     0  12
  PGBD1 WILD-TYPE   5 272
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGBD1 MUTATED      0   12
  PGBD1 WILD-TYPE    5  272
     clus
vv    PGBD1 MUTATED PGBD1 WILD-TYPE
  NO              0               5
  YES            12             272
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PGBD1 MUTATED     8   0   0   3
  PGBD1 WILD-TYPE 219  10  10  21
D325V10, multiclass
    clus
vv   PGBD1 MUTATED PGBD1 WILD-TYPE
  R0             8             219
  R1             0              10
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D325V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PGBD1 MUTATED       3                         0     6
  PGBD1 WILD-TYPE    73                         4   162
D325V12, multiclass
                           clus
vv                          PGBD1 MUTATED PGBD1 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(326) Variable = NCAPH MUTATION ANALYSIS
D326V1, survival
                 sevent
clus2               0   1
  NCAPH MUTATED     4   3
  NCAPH WILD-TYPE 177  77
  NCAPH MUTATED NCAPH WILD-TYPE 
              7             254 
  NCAPH MUTATED NCAPH WILD-TYPE 
              3              77 
$`NCAPH MUTATED`
TCGA-BR-4184 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5730 TCGA-FP-A4BE 
        6.97         6.02       105.07        28.96         4.01        11.08 
TCGA-HU-A4GQ 
        0.10 

$`NCAPH WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 
        0.99         0.99        12.03        79.07        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  NCAPH MUTATED NCAPH WILD-TYPE 
            0.1             0.0 
  NCAPH MUTATED NCAPH WILD-TYPE 
         105.07           79.07 
  NCAPH MUTATED NCAPH WILD-TYPE 
           6.97           12.71 
[1] "0.1 - 105.1 (7.0)" "0.0 - 79.1 (12.7)"
[1] "hr=" "1"  
D326V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NCAPH MUTATED         0        1        0        1         1         0
  NCAPH WILD-TYPE       1        8       27       25        30        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NCAPH MUTATED           0          2          0          2        2
  NCAPH WILD-TYPE         3         47         36         22       22
D326V3, multiclass
            clus
vv           NCAPH MUTATED NCAPH WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             0              36
  STAGE IIIC             2              22
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NCAPH MUTATED     1   2   2   4
  NCAPH WILD-TYPE  10  70 120  71
D326V4, multiclass
    clus
vv   NCAPH MUTATED NCAPH WILD-TYPE
  T1             1              10
  T2             2              70
  T3             2             120
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  NCAPH MUTATED    3  4  1  1
  NCAPH WILD-TYPE 90 77 49 52
D326V5, multiclass
    clus
vv   NCAPH MUTATED NCAPH WILD-TYPE
  N0             3              90
  N1             4              77
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D326V6, binary
                 cls
clus                0   1
  NCAPH MUTATED     8   1
  NCAPH WILD-TYPE 249  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCAPH MUTATED      8    1
  NCAPH WILD-TYPE  249   17
   clus
vv  NCAPH MUTATED NCAPH WILD-TYPE
  0             8             249
  1             1              17
[1] 2 2
[1] FALSE
D326V7, binary
                 cls
clus                0   1
  NCAPH MUTATED     3   7
  NCAPH WILD-TYPE 107 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCAPH MUTATED      3    7
  NCAPH WILD-TYPE  107  172
        clus
vv       NCAPH MUTATED NCAPH WILD-TYPE
  FEMALE             3             107
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NCAPH MUTATED                                       1
  NCAPH WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NCAPH MUTATED                                                        5
  NCAPH WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NCAPH MUTATED                                                                   3
  NCAPH WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NCAPH MUTATED                                                  1
  NCAPH WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NCAPH MUTATED                                                          0
  NCAPH WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NCAPH MUTATED                                                           0
  NCAPH WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NCAPH MUTATED                                          0
  NCAPH WILD-TYPE                                        3
D326V8, multiclass
                                                                   clus
vv                                                                  NCAPH MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  NCAPH WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D326V9, binary
                 cls
clus                0   1
  NCAPH MUTATED     0  10
  NCAPH WILD-TYPE   5 274
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCAPH MUTATED      0   10
  NCAPH WILD-TYPE    5  274
     clus
vv    NCAPH MUTATED NCAPH WILD-TYPE
  NO              0               5
  YES            10             274
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NCAPH MUTATED     6   0   1   3
  NCAPH WILD-TYPE 221  10   9  21
D326V10, multiclass
    clus
vv   NCAPH MUTATED NCAPH WILD-TYPE
  R0             6             221
  R1             0              10
  R2             1               9
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D326V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NCAPH MUTATED       1                         1     3
  NCAPH WILD-TYPE    75                         3   165
D326V12, multiclass
                           clus
vv                          NCAPH MUTATED NCAPH WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(327) Variable = AQP8 MUTATION ANALYSIS
D327V1, survival
                sevent
clus2              0   1
  AQP8 MUTATED     7   2
  AQP8 WILD-TYPE 174  78
  AQP8 MUTATED AQP8 WILD-TYPE 
             9            252 
  AQP8 MUTATED AQP8 WILD-TYPE 
             2             78 
$`AQP8 MUTATED`
TCGA-BR-4280 TCGA-BR-6457 TCGA-BR-7851 TCGA-BR-8370 TCGA-BR-8382 TCGA-BR-8487 
        6.61        13.68        12.43         3.32        15.85         1.12 
TCGA-CG-4437 TCGA-HJ-7597 TCGA-HU-A4GC 
        8.05        26.47         3.25 

$`AQP8 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04        11.80        19.17        14.79         0.26 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.52         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  AQP8 MUTATED AQP8 WILD-TYPE 
          1.12           0.00 
  AQP8 MUTATED AQP8 WILD-TYPE 
         26.47         105.07 
  AQP8 MUTATED AQP8 WILD-TYPE 
          8.05          12.71 
[1] "1.1 - 26.5 (8.1)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1"  
D327V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AQP8 MUTATED         0        0        1        2         2         1
  AQP8 WILD-TYPE       1        9       26       24        29        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AQP8 MUTATED           1          1          2          1        0
  AQP8 WILD-TYPE         2         48         34         23       24
D327V3, multiclass
            clus
vv           AQP8 MUTATED AQP8 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              2             24
  STAGE IIA             2             29
  STAGE IIB             1             43
  STAGE III             1              2
  STAGE IIIA            1             48
  STAGE IIIB            2             34
  STAGE IIIC            1             23
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AQP8 MUTATED     0   4   3   4
  AQP8 WILD-TYPE  11  68 119  71
D327V4, multiclass
    clus
vv   AQP8 MUTATED AQP8 WILD-TYPE
  T1            0             11
  T2            4             68
  T3            3            119
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  AQP8 MUTATED    5  3  1  2
  AQP8 WILD-TYPE 88 78 49 51
D327V5, multiclass
    clus
vv   AQP8 MUTATED AQP8 WILD-TYPE
  N0            5             88
  N1            3             78
  N2            1             49
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D327V6, binary
                cls
clus               0   1
  AQP8 MUTATED    10   0
  AQP8 WILD-TYPE 247  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP8 MUTATED     10    0
  AQP8 WILD-TYPE  247   18
   clus
vv  AQP8 MUTATED AQP8 WILD-TYPE
  0           10            247
  1            0             18
[1] 2 2
[1] FALSE
D327V7, binary
                cls
clus               0   1
  AQP8 MUTATED     5   6
  AQP8 WILD-TYPE 105 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP8 MUTATED      5    6
  AQP8 WILD-TYPE  105  173
        clus
vv       AQP8 MUTATED AQP8 WILD-TYPE
  FEMALE            5            105
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AQP8 MUTATED                                       2
  AQP8 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AQP8 MUTATED                                                        5
  AQP8 WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AQP8 MUTATED                                                                   2
  AQP8 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AQP8 MUTATED                                                  0
  AQP8 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AQP8 MUTATED                                                          1
  AQP8 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AQP8 MUTATED                                                           0
  AQP8 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AQP8 MUTATED                                          1
  AQP8 WILD-TYPE                                        2
D327V8, multiclass
                                                                   clus
vv                                                                  AQP8 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  AQP8 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D327V9, binary
                cls
clus               0   1
  AQP8 MUTATED     1  10
  AQP8 WILD-TYPE   4 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP8 MUTATED      1   10
  AQP8 WILD-TYPE    4  274
     clus
vv    AQP8 MUTATED AQP8 WILD-TYPE
  NO             1              4
  YES           10            274
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  AQP8 MUTATED     9   0   0   2
  AQP8 WILD-TYPE 218  10  10  22
D327V10, multiclass
    clus
vv   AQP8 MUTATED AQP8 WILD-TYPE
  R0            9            218
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D327V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AQP8 MUTATED       1                         0     8
  AQP8 WILD-TYPE    75                         4   160
D327V12, multiclass
                           clus
vv                          AQP8 MUTATED AQP8 WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                8            160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(328) Variable = EXO1 MUTATION ANALYSIS
D328V1, survival
                sevent
clus2              0   1
  EXO1 MUTATED    12   1
  EXO1 WILD-TYPE 169  79
  EXO1 MUTATED EXO1 WILD-TYPE 
            13            248 
  EXO1 MUTATED EXO1 WILD-TYPE 
             1             79 
$`EXO1 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       26.70        34.68        32.94        12.82        24.76        23.93 
TCGA-BR-A4J8 TCGA-CG-5733 TCGA-HU-8602 TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU 
       13.51        21.07        11.41        29.98         6.51         6.25 
TCGA-HU-A4H4 
       23.84 

$`EXO1 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       30.90        31.20         9.21        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE 
       14.17         0.53         0.66        19.36        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10         4.01        69.04         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       26.47         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        11.77         8.98         0.10 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        19.36        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  EXO1 MUTATED EXO1 WILD-TYPE 
          6.25           0.00 
  EXO1 MUTATED EXO1 WILD-TYPE 
         34.68         105.07 
  EXO1 MUTATED EXO1 WILD-TYPE 
         23.84          12.43 
[1] "6.2 - 34.7 (23.8)"  "0.0 - 105.1 (12.4)"
[1] "hr=" "6.6"
D328V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EXO1 MUTATED         0        1        2        0         4         4
  EXO1 WILD-TYPE       1        8       25       26        27        40
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EXO1 MUTATED           0          2          1          0        1
  EXO1 WILD-TYPE         3         47         35         24       23
D328V3, multiclass
            clus
vv           EXO1 MUTATED EXO1 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              2             25
  STAGE II              0             26
  STAGE IIA             4             27
  STAGE IIB             4             40
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            1             35
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EXO1 MUTATED     2   5   6   3
  EXO1 WILD-TYPE   9  67 116  72
D328V4, multiclass
    clus
vv   EXO1 MUTATED EXO1 WILD-TYPE
  T1            2              9
  T2            5             67
  T3            6            116
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  EXO1 MUTATED    9  2  2  2
  EXO1 WILD-TYPE 84 79 48 51
D328V5, multiclass
    clus
vv   EXO1 MUTATED EXO1 WILD-TYPE
  N0            9             84
  N1            2             79
  N2            2             48
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D328V6, binary
                cls
clus               0   1
  EXO1 MUTATED    15   1
  EXO1 WILD-TYPE 242  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXO1 MUTATED     15    1
  EXO1 WILD-TYPE  242   17
   clus
vv  EXO1 MUTATED EXO1 WILD-TYPE
  0           15            242
  1            1             17
[1] 2 2
[1] FALSE
D328V7, binary
                cls
clus               0   1
  EXO1 MUTATED    11   5
  EXO1 WILD-TYPE  99 174
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXO1 MUTATED     11    5
  EXO1 WILD-TYPE   99  174
        clus
vv       EXO1 MUTATED EXO1 WILD-TYPE
  FEMALE           11             99
  MALE              5            174
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  EXO1 MUTATED                                       3
  EXO1 WILD-TYPE                                    47
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EXO1 MUTATED                                                        7
  EXO1 WILD-TYPE                                                    128
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EXO1 MUTATED                                                                   2
  EXO1 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  EXO1 MUTATED                                                  3
  EXO1 WILD-TYPE                                               35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  EXO1 MUTATED                                                          0
  EXO1 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  EXO1 MUTATED                                                           1
  EXO1 WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  EXO1 MUTATED                                          0
  EXO1 WILD-TYPE                                        3
D328V8, multiclass
                                                                   clus
vv                                                                  EXO1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  EXO1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D328V9, binary
                cls
clus               0   1
  EXO1 MUTATED     0  16
  EXO1 WILD-TYPE   5 268
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXO1 MUTATED      0   16
  EXO1 WILD-TYPE    5  268
     clus
vv    EXO1 MUTATED EXO1 WILD-TYPE
  NO             0              5
  YES           16            268
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EXO1 MUTATED    14   0   0   2
  EXO1 WILD-TYPE 213  10  10  22
D328V10, multiclass
    clus
vv   EXO1 MUTATED EXO1 WILD-TYPE
  R0           14            213
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D328V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EXO1 MUTATED       5                         0     9
  EXO1 WILD-TYPE    71                         4   159
D328V12, multiclass
                           clus
vv                          EXO1 MUTATED EXO1 WILD-TYPE
  ASIAN                                5             71
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                9            159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(329) Variable = PRMT8 MUTATION ANALYSIS
D329V1, survival
                 sevent
clus2               0   1
  PRMT8 MUTATED     7   0
  PRMT8 WILD-TYPE 174  80
  PRMT8 MUTATED PRMT8 WILD-TYPE 
              7             254 
  PRMT8 MUTATED PRMT8 WILD-TYPE 
              0              80 
$`PRMT8 MUTATED`
TCGA-BR-6452 TCGA-BR-8368 TCGA-BR-A4QL TCGA-CG-5721 TCGA-CG-5723 TCGA-HU-A4G8 
       34.68         4.31        11.57         6.02       105.07        11.84 
TCGA-HU-A4GT 
        6.51 

$`PRMT8 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         0.10         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  PRMT8 MUTATED PRMT8 WILD-TYPE 
           4.31            0.00 
  PRMT8 MUTATED PRMT8 WILD-TYPE 
         105.07           79.07 
  PRMT8 MUTATED PRMT8 WILD-TYPE 
          11.57           12.71 
[1] "4.3 - 105.1 (11.6)" "0.0 - 79.1 (12.7)" 
[1] "hr="     "2.9e+07"
D329V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRMT8 MUTATED         0        0        1        1         2         1
  PRMT8 WILD-TYPE       1        9       26       25        29        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRMT8 MUTATED           0          0          1          0        1
  PRMT8 WILD-TYPE         3         49         35         24       23
D329V3, multiclass
            clus
vv           PRMT8 MUTATED PRMT8 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              2              29
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRMT8 MUTATED     0   2   4   1
  PRMT8 WILD-TYPE  11  70 118  74
D329V4, multiclass
    clus
vv   PRMT8 MUTATED PRMT8 WILD-TYPE
  T1             0              11
  T2             2              70
  T3             4             118
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PRMT8 MUTATED    3  3  0  1
  PRMT8 WILD-TYPE 90 78 50 52
D329V5, multiclass
    clus
vv   PRMT8 MUTATED PRMT8 WILD-TYPE
  N0             3              90
  N1             3              78
  N2             0              50
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D329V6, binary
                 cls
clus                0   1
  PRMT8 MUTATED     8   0
  PRMT8 WILD-TYPE 249  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT8 MUTATED      8    0
  PRMT8 WILD-TYPE  249   18
   clus
vv  PRMT8 MUTATED PRMT8 WILD-TYPE
  0             8             249
  1             0              18
[1] 2 2
[1] FALSE
D329V7, binary
                 cls
clus                0   1
  PRMT8 MUTATED     6   2
  PRMT8 WILD-TYPE 104 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT8 MUTATED      6    2
  PRMT8 WILD-TYPE  104  177
        clus
vv       PRMT8 MUTATED PRMT8 WILD-TYPE
  FEMALE             6             104
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PRMT8 MUTATED                                       1
  PRMT8 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PRMT8 MUTATED                                                        5
  PRMT8 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PRMT8 MUTATED                                                                   1
  PRMT8 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PRMT8 MUTATED                                                  1
  PRMT8 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PRMT8 MUTATED                                                          0
  PRMT8 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PRMT8 MUTATED                                                           0
  PRMT8 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PRMT8 MUTATED                                          0
  PRMT8 WILD-TYPE                                        3
D329V8, multiclass
                                                                   clus
vv                                                                  PRMT8 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  PRMT8 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D329V9, binary
                 cls
clus                0   1
  PRMT8 MUTATED     0   8
  PRMT8 WILD-TYPE   5 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT8 MUTATED      0    8
  PRMT8 WILD-TYPE    5  276
     clus
vv    PRMT8 MUTATED PRMT8 WILD-TYPE
  NO              0               5
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PRMT8 MUTATED     6   0   0   1
  PRMT8 WILD-TYPE 221  10  10  23
D329V10, multiclass
    clus
vv   PRMT8 MUTATED PRMT8 WILD-TYPE
  R0             6             221
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D329V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRMT8 MUTATED       2                         0     4
  PRMT8 WILD-TYPE    74                         4   164
D329V12, multiclass
                           clus
vv                          PRMT8 MUTATED PRMT8 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(330) Variable = ACP1 MUTATION ANALYSIS
D330V1, survival
                sevent
clus2              0   1
  ACP1 MUTATED     3   2
  ACP1 WILD-TYPE 178  78
  ACP1 MUTATED ACP1 WILD-TYPE 
             5            256 
  ACP1 MUTATED ACP1 WILD-TYPE 
             2             78 
$`ACP1 MUTATED`
TCGA-BR-4184 TCGA-CD-8536 TCGA-D7-A4YV TCGA-HU-A4G8 TCGA-HU-A4GN 
        6.97         0.10         5.92        11.84        29.98 

$`ACP1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.13         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       22.75        25.81        11.77         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  ACP1 MUTATED ACP1 WILD-TYPE 
           0.1            0.0 
  ACP1 MUTATED ACP1 WILD-TYPE 
         29.98         105.07 
  ACP1 MUTATED ACP1 WILD-TYPE 
          6.97          12.71 
[1] "0.1 - 30.0 (7.0)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.6"
D330V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ACP1 MUTATED         0        0        0        1         1         2
  ACP1 WILD-TYPE       1        9       27       25        30        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACP1 MUTATED           0          1          0          0        0
  ACP1 WILD-TYPE         3         48         36         24       24
D330V3, multiclass
            clus
vv           ACP1 MUTATED ACP1 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              1             25
  STAGE IIA             1             30
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ACP1 MUTATED     0   1   4   0
  ACP1 WILD-TYPE  11  71 118  75
D330V4, multiclass
    clus
vv   ACP1 MUTATED ACP1 WILD-TYPE
  T1            0             11
  T2            1             71
  T3            4            118
  T4            0             75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  ACP1 MUTATED    1  4  0  0
  ACP1 WILD-TYPE 92 77 50 53
D330V5, multiclass
    clus
vv   ACP1 MUTATED ACP1 WILD-TYPE
  N0            1             92
  N1            4             77
  N2            0             50
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D330V6, binary
                cls
clus               0   1
  ACP1 MUTATED     4   0
  ACP1 WILD-TYPE 253  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACP1 MUTATED      4    0
  ACP1 WILD-TYPE  253   18
   clus
vv  ACP1 MUTATED ACP1 WILD-TYPE
  0            4            253
  1            0             18
[1] 2 2
[1] FALSE
D330V7, binary
                cls
clus               0   1
  ACP1 MUTATED     2   3
  ACP1 WILD-TYPE 108 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACP1 MUTATED      2    3
  ACP1 WILD-TYPE  108  176
        clus
vv       ACP1 MUTATED ACP1 WILD-TYPE
  FEMALE            2            108
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ACP1 MUTATED                                       1
  ACP1 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ACP1 MUTATED                                                        2
  ACP1 WILD-TYPE                                                    133
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ACP1 MUTATED                                                                   0
  ACP1 WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ACP1 MUTATED                                                  2
  ACP1 WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ACP1 MUTATED                                                          0
  ACP1 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ACP1 MUTATED                                                           0
  ACP1 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ACP1 MUTATED                                          0
  ACP1 WILD-TYPE                                        3
D330V8, multiclass
                                                                   clus
vv                                                                  ACP1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  ACP1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D330V9, binary
                cls
clus               0   1
  ACP1 MUTATED     0   5
  ACP1 WILD-TYPE   5 279
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACP1 MUTATED      0    5
  ACP1 WILD-TYPE    5  279
     clus
vv    ACP1 MUTATED ACP1 WILD-TYPE
  NO             0              5
  YES            5            279
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ACP1 MUTATED     3   0   0   1
  ACP1 WILD-TYPE 224  10  10  23
D330V10, multiclass
    clus
vv   ACP1 MUTATED ACP1 WILD-TYPE
  R0            3            224
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D330V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACP1 MUTATED       3                         0     2
  ACP1 WILD-TYPE    73                         4   166
D330V12, multiclass
                           clus
vv                          ACP1 MUTATED ACP1 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                2            166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(331) Variable = ANKRD40 MUTATION ANALYSIS
D331V1, survival
                   sevent
clus2                 0   1
  ANKRD40 MUTATED     5   0
  ANKRD40 WILD-TYPE 176  80
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
                5               256 
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
                0                80 
$`ANKRD40 MUTATED`
TCGA-BR-8361 TCGA-BR-8382 TCGA-CG-4477 TCGA-D7-6518 TCGA-HU-A4G8 
       19.50        15.85        30.97        19.13        11.84 

$`ANKRD40 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       19.17        14.79         0.26         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       11.93        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
            11.84              0.00 
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
            30.97            105.07 
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
           19.130            12.575 
[1] "11.8 - 31.0 (19.1)" "0.0 - 105.1 (12.6)"
[1] "hr="     "2.5e+07"
D331V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANKRD40 MUTATED         0        0        1        0         0         1
  ANKRD40 WILD-TYPE       1        9       26       26        31        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD40 MUTATED           0          1          0          2        0
  ANKRD40 WILD-TYPE         3         48         36         22       24
D331V3, multiclass
            clus
vv           ANKRD40 MUTATED ANKRD40 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 0                26
  STAGE IIA                0                31
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               0                36
  STAGE IIIC               2                22
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANKRD40 MUTATED     0   2   1   2
  ANKRD40 WILD-TYPE  11  70 121  73
D331V4, multiclass
    clus
vv   ANKRD40 MUTATED ANKRD40 WILD-TYPE
  T1               0                11
  T2               2                70
  T3               1               121
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  ANKRD40 MUTATED    1  1  1  2
  ANKRD40 WILD-TYPE 92 80 49 51
D331V5, multiclass
    clus
vv   ANKRD40 MUTATED ANKRD40 WILD-TYPE
  N0               1                92
  N1               1                80
  N2               1                49
  N3               2                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D331V6, binary
                   cls
clus                  0   1
  ANKRD40 MUTATED     5   0
  ANKRD40 WILD-TYPE 252  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD40 MUTATED      5    0
  ANKRD40 WILD-TYPE  252   18
   clus
vv  ANKRD40 MUTATED ANKRD40 WILD-TYPE
  0               5               252
  1               0                18
[1] 2 2
[1] FALSE
D331V7, binary
                   cls
clus                  0   1
  ANKRD40 MUTATED     4   1
  ANKRD40 WILD-TYPE 106 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD40 MUTATED      4    1
  ANKRD40 WILD-TYPE  106  178
        clus
vv       ANKRD40 MUTATED ANKRD40 WILD-TYPE
  FEMALE               4               106
  MALE                 1               178
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ANKRD40 MUTATED                                       2
  ANKRD40 WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ANKRD40 MUTATED                                                        2
  ANKRD40 WILD-TYPE                                                    133
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ANKRD40 MUTATED                                                                   1
  ANKRD40 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ANKRD40 MUTATED                                                  0
  ANKRD40 WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ANKRD40 MUTATED                                                          0
  ANKRD40 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ANKRD40 MUTATED                                                           0
  ANKRD40 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ANKRD40 MUTATED                                          0
  ANKRD40 WILD-TYPE                                        3
D331V8, multiclass
                                                                   clus
vv                                                                  ANKRD40 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  ANKRD40 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D331V9, binary
                   cls
clus                  0   1
  ANKRD40 MUTATED     0   5
  ANKRD40 WILD-TYPE   5 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD40 MUTATED      0    5
  ANKRD40 WILD-TYPE    5  279
     clus
vv    ANKRD40 MUTATED ANKRD40 WILD-TYPE
  NO                0                 5
  YES               5               279
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ANKRD40 MUTATED     3   1   0   0
  ANKRD40 WILD-TYPE 224   9  10  24
D331V10, multiclass
    clus
vv   ANKRD40 MUTATED ANKRD40 WILD-TYPE
  R0               3               224
  R1               1                 9
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D331V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ANKRD40 MUTATED       1                         0     3
  ANKRD40 WILD-TYPE    75                         4   165
D331V12, multiclass
                           clus
vv                          ANKRD40 MUTATED ANKRD40 WILD-TYPE
  ASIAN                                   1                75
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   3               165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(332) Variable = RBM6 MUTATION ANALYSIS
D332V1, survival
                sevent
clus2              0   1
  RBM6 MUTATED    11   4
  RBM6 WILD-TYPE 170  76
  RBM6 MUTATED RBM6 WILD-TYPE 
            15            246 
  RBM6 MUTATED RBM6 WILD-TYPE 
             4             76 
$`RBM6 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8382 
        6.97        30.90         6.61        34.68        32.94        15.85 
TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-5728 TCGA-F1-6874 
       13.45        15.81         6.58        15.95        65.10        14.47 
TCGA-HU-8245 TCGA-HU-A4G8 TCGA-HU-A4H4 
       12.59        11.84        23.84 

$`RBM6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       12.82         9.21        24.76        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        20.55         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
        3.32        11.80        19.17        14.79         0.26         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       15.81         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        28.96        79.07         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       16.24        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8602 
       11.08         5.52        26.47         5.92        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        19.36        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  RBM6 MUTATED RBM6 WILD-TYPE 
          6.58           0.00 
  RBM6 MUTATED RBM6 WILD-TYPE 
         65.10         105.07 
  RBM6 MUTATED RBM6 WILD-TYPE 
         15.81          12.43 
[1] "6.6 - 65.1 (15.8)"  "0.0 - 105.1 (12.4)"
[1] "hr=" "1.7"
D332V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RBM6 MUTATED         1        0        3        1         4         2
  RBM6 WILD-TYPE       0        9       24       25        27        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RBM6 MUTATED           1          2          0          2        2
  RBM6 WILD-TYPE         2         47         36         22       22
D332V3, multiclass
            clus
vv           RBM6 MUTATED RBM6 WILD-TYPE
  STAGE I               1              0
  STAGE IA              0              9
  STAGE IB              3             24
  STAGE II              1             25
  STAGE IIA             4             27
  STAGE IIB             2             42
  STAGE III             1              2
  STAGE IIIA            2             47
  STAGE IIIB            0             36
  STAGE IIIC            2             22
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RBM6 MUTATED     2   7   6   5
  RBM6 WILD-TYPE   9  65 116  70
D332V4, multiclass
    clus
vv   RBM6 MUTATED RBM6 WILD-TYPE
  T1            2              9
  T2            7             65
  T3            6            116
  T4            5             70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  RBM6 MUTATED    8  5  3  2
  RBM6 WILD-TYPE 85 76 47 51
D332V5, multiclass
    clus
vv   RBM6 MUTATED RBM6 WILD-TYPE
  N0            8             85
  N1            5             76
  N2            3             47
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D332V6, binary
                cls
clus               0   1
  RBM6 MUTATED    17   1
  RBM6 WILD-TYPE 240  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM6 MUTATED     17    1
  RBM6 WILD-TYPE  240   17
   clus
vv  RBM6 MUTATED RBM6 WILD-TYPE
  0           17            240
  1            1             17
[1] 2 2
[1] FALSE
D332V7, binary
                cls
clus               0   1
  RBM6 MUTATED    11   9
  RBM6 WILD-TYPE  99 170
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM6 MUTATED     11    9
  RBM6 WILD-TYPE   99  170
        clus
vv       RBM6 MUTATED RBM6 WILD-TYPE
  FEMALE           11             99
  MALE              9            170
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RBM6 MUTATED                                       2
  RBM6 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RBM6 MUTATED                                                       12
  RBM6 WILD-TYPE                                                    123
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RBM6 MUTATED                                                                   3
  RBM6 WILD-TYPE                                                                37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RBM6 MUTATED                                                  2
  RBM6 WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RBM6 MUTATED                                                          0
  RBM6 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RBM6 MUTATED                                                           1
  RBM6 WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RBM6 MUTATED                                          0
  RBM6 WILD-TYPE                                        3
D332V8, multiclass
                                                                   clus
vv                                                                  RBM6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      12
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  RBM6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       123
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D332V9, binary
                cls
clus               0   1
  RBM6 MUTATED     0  20
  RBM6 WILD-TYPE   5 264
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM6 MUTATED      0   20
  RBM6 WILD-TYPE    5  264
     clus
vv    RBM6 MUTATED RBM6 WILD-TYPE
  NO             0              5
  YES           20            264
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RBM6 MUTATED    12   0   0   6
  RBM6 WILD-TYPE 215  10  10  18
D332V10, multiclass
    clus
vv   RBM6 MUTATED RBM6 WILD-TYPE
  R0           12            215
  R1            0             10
  R2            0             10
  RX            6             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D332V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM6 MUTATED       5                         1    11
  RBM6 WILD-TYPE    71                         3   157
D332V12, multiclass
                           clus
vv                          RBM6 MUTATED RBM6 WILD-TYPE
  ASIAN                                5             71
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                               11            157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(333) Variable = SLC12A7 MUTATION ANALYSIS
D333V1, survival
                   sevent
clus2                 0   1
  SLC12A7 MUTATED    14   2
  SLC12A7 WILD-TYPE 167  78
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
               16               245 
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
                2                78 
$`SLC12A7 MUTATED`
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8487 
       34.68        32.78        23.93         6.18         0.26         1.12 
TCGA-BR-8591 TCGA-CD-8536 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CG-5721 TCGA-FP-A4BE 
       13.45         0.10        12.43         6.58         6.02        11.08 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4H5 TCGA-HU-A4H8 
        5.59        11.84        12.30         8.88 

$`SLC12A7 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        2.66        16.31         2.20        15.58         7.40        19.50 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       15.81         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.13         3.42         9.34        11.31 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 
       11.41        12.10        10.62         0.76        24.30        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD 
        2.10        12.95        19.36        23.84         9.67        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
              0.1               0.0 
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
            34.68            105.07 
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
             9.98             12.79 
[1] "0.1 - 34.7 (10.0)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "2.1"
D333V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC12A7 MUTATED         0        0        5        1         7         2
  SLC12A7 WILD-TYPE       1        9       22       25        24        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC12A7 MUTATED           0          0          0          1        1
  SLC12A7 WILD-TYPE         3         49         36         23       23
D333V3, multiclass
            clus
vv           SLC12A7 MUTATED SLC12A7 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 5                22
  STAGE II                 1                25
  STAGE IIA                7                24
  STAGE IIB                2                42
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               0                36
  STAGE IIIC               1                23
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC12A7 MUTATED     1   5   9   2
  SLC12A7 WILD-TYPE  10  67 113  73
D333V4, multiclass
    clus
vv   SLC12A7 MUTATED SLC12A7 WILD-TYPE
  T1               1                10
  T2               5                67
  T3               9               113
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  SLC12A7 MUTATED   12  3  1  1
  SLC12A7 WILD-TYPE 81 78 49 52
D333V5, multiclass
    clus
vv   SLC12A7 MUTATED SLC12A7 WILD-TYPE
  N0              12                81
  N1               3                78
  N2               1                49
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D333V6, binary
                   cls
clus                  0   1
  SLC12A7 MUTATED    18   0
  SLC12A7 WILD-TYPE 239  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A7 MUTATED     18    0
  SLC12A7 WILD-TYPE  239   18
   clus
vv  SLC12A7 MUTATED SLC12A7 WILD-TYPE
  0              18               239
  1               0                18
[1] 2 2
[1] FALSE
D333V7, binary
                   cls
clus                  0   1
  SLC12A7 MUTATED     7  11
  SLC12A7 WILD-TYPE 103 168
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A7 MUTATED      7   11
  SLC12A7 WILD-TYPE  103  168
        clus
vv       SLC12A7 MUTATED SLC12A7 WILD-TYPE
  FEMALE               7               103
  MALE                11               168
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SLC12A7 MUTATED                                       2
  SLC12A7 WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC12A7 MUTATED                                                       10
  SLC12A7 WILD-TYPE                                                    125
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC12A7 MUTATED                                                                   3
  SLC12A7 WILD-TYPE                                                                37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SLC12A7 MUTATED                                                  2
  SLC12A7 WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SLC12A7 MUTATED                                                          0
  SLC12A7 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SLC12A7 MUTATED                                                           1
  SLC12A7 WILD-TYPE                                                         5
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SLC12A7 MUTATED                                          0
  SLC12A7 WILD-TYPE                                        3
D333V8, multiclass
                                                                   clus
vv                                                                  SLC12A7 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  SLC12A7 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D333V9, binary
                   cls
clus                  0   1
  SLC12A7 MUTATED     0  18
  SLC12A7 WILD-TYPE   5 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A7 MUTATED      0   18
  SLC12A7 WILD-TYPE    5  266
     clus
vv    SLC12A7 MUTATED SLC12A7 WILD-TYPE
  NO                0                 5
  YES              18               266
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC12A7 MUTATED    14   0   0   1
  SLC12A7 WILD-TYPE 213  10  10  23
D333V10, multiclass
    clus
vv   SLC12A7 MUTATED SLC12A7 WILD-TYPE
  R0              14               213
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D333V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC12A7 MUTATED       7                         1     8
  SLC12A7 WILD-TYPE    69                         3   160
D333V12, multiclass
                           clus
vv                          SLC12A7 MUTATED SLC12A7 WILD-TYPE
  ASIAN                                   7                69
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   8               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(334) Variable = ERBB2 MUTATION ANALYSIS
D334V1, survival
                 sevent
clus2               0   1
  ERBB2 MUTATED     9   3
  ERBB2 WILD-TYPE 172  77
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             12             249 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              3              77 
$`ERBB2 MUTATED`
TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7957 TCGA-BR-8487 TCGA-BR-8588 
       32.78        30.90        32.94         9.07         1.12        12.79 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5730 TCGA-HU-A4H0 TCGA-HU-A4H8 TCGA-IN-8663 
       18.97         7.07         4.01         2.10         8.88         3.39 

$`ERBB2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       21.11        31.20        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        3.45        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 
        0.10         6.51         6.25        10.19         0.26        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
       19.36        23.84        12.30         9.67        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IP-7968 
        3.45        18.81         2.53 

  ERBB2 MUTATED ERBB2 WILD-TYPE 
           1.12            0.00 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          32.94          105.07 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          8.975          12.660 
[1] "1.1 - 32.9 (9.0)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.3"
D334V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ERBB2 MUTATED         0        0        2        1         3         2
  ERBB2 WILD-TYPE       1        9       25       25        28        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ERBB2 MUTATED           0          1          0          1        3
  ERBB2 WILD-TYPE         3         48         36         23       21
D334V3, multiclass
            clus
vv           ERBB2 MUTATED ERBB2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               1              25
  STAGE IIA              3              28
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               3              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ERBB2 MUTATED     1   4   6   2
  ERBB2 WILD-TYPE  10  68 116  73
D334V4, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  T1             1              10
  T2             4              68
  T3             6             116
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ERBB2 MUTATED    5  3  2  3
  ERBB2 WILD-TYPE 88 78 48 50
D334V5, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  N0             5              88
  N1             3              78
  N2             2              48
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D334V6, binary
                 cls
clus                0   1
  ERBB2 MUTATED    12   2
  ERBB2 WILD-TYPE 245  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     12    2
  ERBB2 WILD-TYPE  245   16
   clus
vv  ERBB2 MUTATED ERBB2 WILD-TYPE
  0            12             245
  1             2              16
[1] 2 2
[1] FALSE
D334V7, binary
                 cls
clus                0   1
  ERBB2 MUTATED     8   6
  ERBB2 WILD-TYPE 102 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      8    6
  ERBB2 WILD-TYPE  102  173
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  FEMALE             8             102
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ERBB2 MUTATED                                       1
  ERBB2 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ERBB2 MUTATED                                                        7
  ERBB2 WILD-TYPE                                                    128
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ERBB2 MUTATED                                                                   4
  ERBB2 WILD-TYPE                                                                36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ERBB2 MUTATED                                                  1
  ERBB2 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ERBB2 MUTATED                                                          1
  ERBB2 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ERBB2 MUTATED                                                           0
  ERBB2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ERBB2 MUTATED                                          0
  ERBB2 WILD-TYPE                                        3
D334V8, multiclass
                                                                   clus
vv                                                                  ERBB2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ERBB2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D334V9, binary
                 cls
clus                0   1
  ERBB2 MUTATED     1  13
  ERBB2 WILD-TYPE   4 271
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      1   13
  ERBB2 WILD-TYPE    4  271
     clus
vv    ERBB2 MUTATED ERBB2 WILD-TYPE
  NO              1               4
  YES            13             271
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ERBB2 MUTATED    11   1   1   1
  ERBB2 WILD-TYPE 216   9   9  23
D334V10, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  R0            11             216
  R1             1               9
  R2             1               9
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D334V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERBB2 MUTATED       2                         0     8
  ERBB2 WILD-TYPE    74                         4   160
D334V12, multiclass
                           clus
vv                          ERBB2 MUTATED ERBB2 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 8             160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(335) Variable = CASP8 MUTATION ANALYSIS
D335V1, survival
                 sevent
clus2               0   1
  CASP8 MUTATED    10   5
  CASP8 WILD-TYPE 171  75
  CASP8 MUTATED CASP8 WILD-TYPE 
             15             246 
  CASP8 MUTATED CASP8 WILD-TYPE 
              5              75 
$`CASP8 MUTATED`
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8059 TCGA-BR-8487 TCGA-CD-A4MG 
        6.61        34.68        32.94        14.43         1.12         6.58 
TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-5723 TCGA-D7-8570 TCGA-D7-A4YV TCGA-D7-A4Z0 
        0.10         1.02       105.07        24.72         5.92        14.76 
TCGA-EQ-A4SO TCGA-HU-8602 TCGA-HU-A4G8 
       16.24        11.41        11.84 

$`CASP8 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
       18.35        30.90         6.18         9.57        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 
        3.45         9.07        12.76        18.71        17.49         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 
       12.79        10.55        11.31        12.33        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
       16.44        15.16        13.78         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        5.52        26.47         5.92        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  CASP8 MUTATED CASP8 WILD-TYPE 
            0.1             0.0 
  CASP8 MUTATED CASP8 WILD-TYPE 
         105.07           79.07 
  CASP8 MUTATED CASP8 WILD-TYPE 
          11.84           12.64 
[1] "0.1 - 105.1 (11.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.2"
D335V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CASP8 MUTATED         0        0        0        1         4         4
  CASP8 WILD-TYPE       1        9       27       25        27        40
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CASP8 MUTATED           2          0          3          0        1
  CASP8 WILD-TYPE         1         49         33         24       23
D335V3, multiclass
            clus
vv           CASP8 MUTATED CASP8 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              4              27
  STAGE IIB              4              40
  STAGE III              2               1
  STAGE IIIA             0              49
  STAGE IIIB             3              33
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CASP8 MUTATED     1   3  10   3
  CASP8 WILD-TYPE  10  69 112  72
D335V4, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  T1             1              10
  T2             3              69
  T3            10             112
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CASP8 MUTATED    5  8  2  1
  CASP8 WILD-TYPE 88 73 48 52
D335V5, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  N0             5              88
  N1             8              73
  N2             2              48
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D335V6, binary
                 cls
clus                0   1
  CASP8 MUTATED    15   1
  CASP8 WILD-TYPE 242  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     15    1
  CASP8 WILD-TYPE  242   17
   clus
vv  CASP8 MUTATED CASP8 WILD-TYPE
  0            15             242
  1             1              17
[1] 2 2
[1] FALSE
D335V7, binary
                 cls
clus                0   1
  CASP8 MUTATED    11   7
  CASP8 WILD-TYPE  99 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     11    7
  CASP8 WILD-TYPE   99  172
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  FEMALE            11              99
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CASP8 MUTATED                                       3
  CASP8 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CASP8 MUTATED                                                       11
  CASP8 WILD-TYPE                                                    124
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CASP8 MUTATED                                                                   1
  CASP8 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CASP8 MUTATED                                                  2
  CASP8 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CASP8 MUTATED                                                          1
  CASP8 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CASP8 MUTATED                                                           0
  CASP8 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CASP8 MUTATED                                          0
  CASP8 WILD-TYPE                                        3
D335V8, multiclass
                                                                   clus
vv                                                                  CASP8 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  CASP8 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D335V9, binary
                 cls
clus                0   1
  CASP8 MUTATED     0  18
  CASP8 WILD-TYPE   5 266
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      0   18
  CASP8 WILD-TYPE    5  266
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  NO              0               5
  YES            18             266
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CASP8 MUTATED    10   0   1   4
  CASP8 WILD-TYPE 217  10   9  20
D335V10, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  R0            10             217
  R1             0              10
  R2             1               9
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D335V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CASP8 MUTATED       4                         0    12
  CASP8 WILD-TYPE    72                         4   156
D335V12, multiclass
                           clus
vv                          CASP8 MUTATED CASP8 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                12             156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(336) Variable = WHSC1L1 MUTATION ANALYSIS
D336V1, survival
                   sevent
clus2                 0   1
  WHSC1L1 MUTATED     9   2
  WHSC1L1 WILD-TYPE 172  78
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
               11               250 
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
                2                78 
$`WHSC1L1 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8368 TCGA-CD-5801 TCGA-CD-8536 TCGA-CD-A4MJ 
       26.70        34.68         4.31        13.18         0.10        12.62 
TCGA-CG-4305 TCGA-D7-6822 TCGA-D7-A4YV TCGA-HU-A4GN TCGA-HU-A4GU 
       15.95        12.33         5.92        29.98         6.25 

$`WHSC1L1 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
       11.57         5.13         2.83         3.25        13.15         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       12.20         0.10        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       15.22        15.98        12.79        10.55        11.31        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        11.77         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
              0.1               0.0 
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
            34.68            105.07 
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
           12.620            12.625 
[1] "0.1 - 34.7 (12.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.9"
D336V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WHSC1L1 MUTATED         0        0        4        2         2         3
  WHSC1L1 WILD-TYPE       1        9       23       24        29        41
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WHSC1L1 MUTATED           0          2          0          0        0
  WHSC1L1 WILD-TYPE         3         47         36         24       24
D336V3, multiclass
            clus
vv           WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 4                23
  STAGE II                 2                24
  STAGE IIA                2                29
  STAGE IIB                3                41
  STAGE III                0                 3
  STAGE IIIA               2                47
  STAGE IIIB               0                36
  STAGE IIIC               0                24
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  WHSC1L1 MUTATED     0   6   5   2
  WHSC1L1 WILD-TYPE  11  66 117  73
D336V4, multiclass
    clus
vv   WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  T1               0                11
  T2               6                66
  T3               5               117
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  WHSC1L1 MUTATED    8  7  0  0
  WHSC1L1 WILD-TYPE 85 74 50 53
D336V5, multiclass
    clus
vv   WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  N0               8                85
  N1               7                74
  N2               0                50
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D336V6, binary
                   cls
clus                  0   1
  WHSC1L1 MUTATED    16   0
  WHSC1L1 WILD-TYPE 241  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WHSC1L1 MUTATED     16    0
  WHSC1L1 WILD-TYPE  241   18
   clus
vv  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  0              16               241
  1               0                18
[1] 2 2
[1] FALSE
D336V7, binary
                   cls
clus                  0   1
  WHSC1L1 MUTATED     7   9
  WHSC1L1 WILD-TYPE 103 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WHSC1L1 MUTATED      7    9
  WHSC1L1 WILD-TYPE  103  170
        clus
vv       WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  FEMALE               7               103
  MALE                 9               170
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  WHSC1L1 MUTATED                                       2
  WHSC1L1 WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WHSC1L1 MUTATED                                                       10
  WHSC1L1 WILD-TYPE                                                    125
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WHSC1L1 MUTATED                                                                   1
  WHSC1L1 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  WHSC1L1 MUTATED                                                  3
  WHSC1L1 WILD-TYPE                                               35
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  WHSC1L1 MUTATED                                                          0
  WHSC1L1 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  WHSC1L1 MUTATED                                                           0
  WHSC1L1 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  WHSC1L1 MUTATED                                          0
  WHSC1L1 WILD-TYPE                                        3
D336V8, multiclass
                                                                   clus
vv                                                                  WHSC1L1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  WHSC1L1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D336V9, binary
                   cls
clus                  0   1
  WHSC1L1 MUTATED     0  16
  WHSC1L1 WILD-TYPE   5 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WHSC1L1 MUTATED      0   16
  WHSC1L1 WILD-TYPE    5  268
     clus
vv    WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  NO                0                 5
  YES              16               268
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  WHSC1L1 MUTATED    11   0   0   4
  WHSC1L1 WILD-TYPE 216  10  10  20
D336V10, multiclass
    clus
vv   WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  R0              11               216
  R1               0                10
  R2               0                10
  RX               4                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D336V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WHSC1L1 MUTATED       5                         0     9
  WHSC1L1 WILD-TYPE    71                         4   159
D336V12, multiclass
                           clus
vv                          WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  ASIAN                                   5                71
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   9               159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(337) Variable = TBL1XR1 MUTATION ANALYSIS
D337V1, survival
                   sevent
clus2                 0   1
  TBL1XR1 MUTATED     2   1
  TBL1XR1 WILD-TYPE 179  79
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
                3               258 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
                1                79 
$`TBL1XR1 MUTATED`
TCGA-BR-8078 TCGA-CG-5726 TCGA-FP-A4BE 
       12.26        28.96        11.08 

$`TBL1XR1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 
        0.99         6.02         0.99       105.07        12.03        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 
       59.54         5.03        13.58         0.56         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
            11.08              0.00 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
            28.96            105.07 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
            12.26             12.64 
[1] "11.1 - 29.0 (12.3)" "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D337V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TBL1XR1 MUTATED         0        1        0        0         1         1
  TBL1XR1 WILD-TYPE       1        8       27       26        30        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBL1XR1 MUTATED           0          1          0          0        1
  TBL1XR1 WILD-TYPE         3         48         36         24       23
D337V3, multiclass
            clus
vv           TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 1                 8
  STAGE IB                 0                27
  STAGE II                 0                26
  STAGE IIA                1                30
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               0                36
  STAGE IIIC               0                24
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TBL1XR1 MUTATED     1   0   1   3
  TBL1XR1 WILD-TYPE  10  72 121  72
D337V4, multiclass
    clus
vv   TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  T1               1                10
  T2               0                72
  T3               1               121
  T4               3                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  TBL1XR1 MUTATED    4  0  1  0
  TBL1XR1 WILD-TYPE 89 81 49 53
D337V5, multiclass
    clus
vv   TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  N0               4                89
  N1               0                81
  N2               1                49
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D337V6, binary
                   cls
clus                  0   1
  TBL1XR1 MUTATED     5   0
  TBL1XR1 WILD-TYPE 252  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBL1XR1 MUTATED      5    0
  TBL1XR1 WILD-TYPE  252   18
   clus
vv  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  0               5               252
  1               0                18
[1] 2 2
[1] FALSE
D337V7, binary
                   cls
clus                  0   1
  TBL1XR1 MUTATED     3   2
  TBL1XR1 WILD-TYPE 107 177
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBL1XR1 MUTATED      3    2
  TBL1XR1 WILD-TYPE  107  177
        clus
vv       TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  FEMALE               3               107
  MALE                 2               177
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TBL1XR1 MUTATED                                       0
  TBL1XR1 WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TBL1XR1 MUTATED                                                        4
  TBL1XR1 WILD-TYPE                                                    131
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TBL1XR1 MUTATED                                                                   1
  TBL1XR1 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TBL1XR1 MUTATED                                                  0
  TBL1XR1 WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TBL1XR1 MUTATED                                                          0
  TBL1XR1 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TBL1XR1 MUTATED                                                           0
  TBL1XR1 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TBL1XR1 MUTATED                                          0
  TBL1XR1 WILD-TYPE                                        3
D337V8, multiclass
                                                                   clus
vv                                                                  TBL1XR1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  TBL1XR1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D337V9, binary
                   cls
clus                  0   1
  TBL1XR1 MUTATED     0   5
  TBL1XR1 WILD-TYPE   5 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBL1XR1 MUTATED      0    5
  TBL1XR1 WILD-TYPE    5  279
     clus
vv    TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  NO                0                 5
  YES               5               279
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TBL1XR1 MUTATED     3   0   0   2
  TBL1XR1 WILD-TYPE 224  10  10  22
D337V10, multiclass
    clus
vv   TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  R0               3               224
  R1               0                10
  R2               0                10
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D337V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TBL1XR1 MUTATED       0                         1     3
  TBL1XR1 WILD-TYPE    76                         3   165
D337V12, multiclass
                           clus
vv                          TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  ASIAN                                   0                76
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   3               165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(338) Variable = NEK7 MUTATION ANALYSIS
D338V1, survival
                sevent
clus2              0   1
  NEK7 MUTATED     2   1
  NEK7 WILD-TYPE 179  79
  NEK7 MUTATED NEK7 WILD-TYPE 
             3            258 
  NEK7 MUTATED NEK7 WILD-TYPE 
             1             79 
$`NEK7 MUTATED`
TCGA-CG-4306 TCGA-F1-6874 TCGA-HU-A4GX 
        1.02        14.47        10.19 

$`NEK7 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
       13.78        14.76         0.62         7.99        16.24        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  NEK7 MUTATED NEK7 WILD-TYPE 
          1.02           0.00 
  NEK7 MUTATED NEK7 WILD-TYPE 
         14.47         105.07 
  NEK7 MUTATED NEK7 WILD-TYPE 
         10.19          12.64 
[1] "1.0 - 14.5 (10.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.8"
D338V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NEK7 MUTATED         1        0        1        0         0         0
  NEK7 WILD-TYPE       0        9       26       26        31        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NEK7 MUTATED           0          0          0          1        1
  NEK7 WILD-TYPE         3         49         36         23       23
D338V3, multiclass
            clus
vv           NEK7 MUTATED NEK7 WILD-TYPE
  STAGE I               1              0
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             0             31
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            1             23
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NEK7 MUTATED     1   1   1   1
  NEK7 WILD-TYPE  10  71 121  74
D338V4, multiclass
    clus
vv   NEK7 MUTATED NEK7 WILD-TYPE
  T1            1             10
  T2            1             71
  T3            1            121
  T4            1             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  NEK7 MUTATED    1  1  2  0
  NEK7 WILD-TYPE 92 80 48 53
D338V5, multiclass
    clus
vv   NEK7 MUTATED NEK7 WILD-TYPE
  N0            1             92
  N1            1             80
  N2            2             48
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D338V6, binary
                cls
clus               0   1
  NEK7 MUTATED     2   1
  NEK7 WILD-TYPE 255  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK7 MUTATED      2    1
  NEK7 WILD-TYPE  255   17
   clus
vv  NEK7 MUTATED NEK7 WILD-TYPE
  0            2            255
  1            1             17
[1] 2 2
[1] FALSE
D338V7, binary
                cls
clus               0   1
  NEK7 MUTATED     1   3
  NEK7 WILD-TYPE 109 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK7 MUTATED      1    3
  NEK7 WILD-TYPE  109  176
        clus
vv       NEK7 MUTATED NEK7 WILD-TYPE
  FEMALE            1            109
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NEK7 MUTATED                                       1
  NEK7 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NEK7 MUTATED                                                        2
  NEK7 WILD-TYPE                                                    133
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NEK7 MUTATED                                                                   1
  NEK7 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NEK7 MUTATED                                                  0
  NEK7 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NEK7 MUTATED                                                          0
  NEK7 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NEK7 MUTATED                                                           0
  NEK7 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NEK7 MUTATED                                          0
  NEK7 WILD-TYPE                                        3
D338V8, multiclass
                                                                   clus
vv                                                                  NEK7 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  NEK7 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D338V9, binary
                cls
clus               0   1
  NEK7 MUTATED     0   4
  NEK7 WILD-TYPE   5 280
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK7 MUTATED      0    4
  NEK7 WILD-TYPE    5  280
     clus
vv    NEK7 MUTATED NEK7 WILD-TYPE
  NO             0              5
  YES            4            280
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NEK7 MUTATED     3   0   1   0
  NEK7 WILD-TYPE 224  10   9  24
D338V10, multiclass
    clus
vv   NEK7 MUTATED NEK7 WILD-TYPE
  R0            3            224
  R1            0             10
  R2            1              9
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D338V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NEK7 MUTATED       1                         1     1
  NEK7 WILD-TYPE    75                         3   167
D338V12, multiclass
                           clus
vv                          NEK7 MUTATED NEK7 WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                                1            167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(339) Variable = CCDC148 MUTATION ANALYSIS
D339V1, survival
                   sevent
clus2                 0   1
  CCDC148 MUTATED     4   1
  CCDC148 WILD-TYPE 177  79
  CCDC148 MUTATED CCDC148 WILD-TYPE 
                5               256 
  CCDC148 MUTATED CCDC148 WILD-TYPE 
                1                79 
$`CCDC148 MUTATED`
TCGA-BR-A4QL TCGA-CG-5726 TCGA-D7-6524 TCGA-HU-A4G8 TCGA-HU-A4GU 
       11.57        28.96        17.85        11.84         6.25 

$`CCDC148 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 
        0.99         6.02         0.99       105.07        12.03        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  CCDC148 MUTATED CCDC148 WILD-TYPE 
             6.25              0.00 
  CCDC148 MUTATED CCDC148 WILD-TYPE 
            28.96            105.07 
  CCDC148 MUTATED CCDC148 WILD-TYPE 
            11.84             12.64 
[1] "6.2 - 29.0 (11.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.7"
D339V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC148 MUTATED         0        1        0        1         0         2
  CCDC148 WILD-TYPE       1        8       27       25        31        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC148 MUTATED           0          0          1          0        0
  CCDC148 WILD-TYPE         3         49         35         24       24
D339V3, multiclass
            clus
vv           CCDC148 MUTATED CCDC148 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 1                 8
  STAGE IB                 0                27
  STAGE II                 1                25
  STAGE IIA                0                31
  STAGE IIB                2                42
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               1                35
  STAGE IIIC               0                24
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC148 MUTATED     1   1   3   0
  CCDC148 WILD-TYPE  10  71 119  75
D339V4, multiclass
    clus
vv   CCDC148 MUTATED CCDC148 WILD-TYPE
  T1               1                10
  T2               1                71
  T3               3               119
  T4               0                75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  CCDC148 MUTATED    1  3  0  1
  CCDC148 WILD-TYPE 92 78 50 52
D339V5, multiclass
    clus
vv   CCDC148 MUTATED CCDC148 WILD-TYPE
  N0               1                92
  N1               3                78
  N2               0                50
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D339V6, binary
                   cls
clus                  0   1
  CCDC148 MUTATED     5   0
  CCDC148 WILD-TYPE 252  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC148 MUTATED      5    0
  CCDC148 WILD-TYPE  252   18
   clus
vv  CCDC148 MUTATED CCDC148 WILD-TYPE
  0               5               252
  1               0                18
[1] 2 2
[1] FALSE
D339V7, binary
                   cls
clus                  0   1
  CCDC148 MUTATED     2   3
  CCDC148 WILD-TYPE 108 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC148 MUTATED      2    3
  CCDC148 WILD-TYPE  108  176
        clus
vv       CCDC148 MUTATED CCDC148 WILD-TYPE
  FEMALE               2               108
  MALE                 3               176
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CCDC148 MUTATED                                       3
  CCDC148 WILD-TYPE                                    47
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CCDC148 MUTATED                                                        1
  CCDC148 WILD-TYPE                                                    134
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CCDC148 MUTATED                                                                   1
  CCDC148 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CCDC148 MUTATED                                                  0
  CCDC148 WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CCDC148 MUTATED                                                          0
  CCDC148 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CCDC148 MUTATED                                                           0
  CCDC148 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CCDC148 MUTATED                                          0
  CCDC148 WILD-TYPE                                        3
D339V8, multiclass
                                                                   clus
vv                                                                  CCDC148 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          1
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  CCDC148 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D339V9, binary
                   cls
clus                  0   1
  CCDC148 MUTATED     0   5
  CCDC148 WILD-TYPE   5 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC148 MUTATED      0    5
  CCDC148 WILD-TYPE    5  279
     clus
vv    CCDC148 MUTATED CCDC148 WILD-TYPE
  NO                0                 5
  YES               5               279
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CCDC148 MUTATED     3   1   0   0
  CCDC148 WILD-TYPE 224   9  10  24
D339V10, multiclass
    clus
vv   CCDC148 MUTATED CCDC148 WILD-TYPE
  R0               3               224
  R1               1                 9
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D339V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC148 MUTATED       2                         0     2
  CCDC148 WILD-TYPE    74                         4   166
D339V12, multiclass
                           clus
vv                          CCDC148 MUTATED CCDC148 WILD-TYPE
  ASIAN                                   2                74
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   2               166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(340) Variable = ANKRD23 MUTATION ANALYSIS
D340V1, survival
                   sevent
clus2                 0   1
  ANKRD23 MUTATED     4   0
  ANKRD23 WILD-TYPE 177  80
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                4               257 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                0                80 
$`ANKRD23 MUTATED`
TCGA-BR-8372 TCGA-CD-A4MH TCGA-CG-5728 TCGA-HU-A4GT 
       19.17        12.20        65.10         6.51 

$`ANKRD23 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
             6.51              0.00 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
            65.10            105.07 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
           15.685            12.620 
[1] "6.5 - 65.1 (15.7)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "9500000"
D340V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANKRD23 MUTATED         0        0        1        0         2         0
  ANKRD23 WILD-TYPE       1        9       26       26        29        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD23 MUTATED           0          0          0          1        0
  ANKRD23 WILD-TYPE         3         49         36         23       24
D340V3, multiclass
            clus
vv           ANKRD23 MUTATED ANKRD23 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 0                26
  STAGE IIA                2                29
  STAGE IIB                0                44
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               0                36
  STAGE IIIC               1                23
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANKRD23 MUTATED     0   1   2   1
  ANKRD23 WILD-TYPE  11  71 120  74
D340V4, multiclass
    clus
vv   ANKRD23 MUTATED ANKRD23 WILD-TYPE
  T1               0                11
  T2               1                71
  T3               2               120
  T4               1                74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  ANKRD23 MUTATED    3  1  0  1
  ANKRD23 WILD-TYPE 90 80 50 52
D340V5, multiclass
    clus
vv   ANKRD23 MUTATED ANKRD23 WILD-TYPE
  N0               3                90
  N1               1                80
  N2               0                50
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D340V6, binary
                   cls
clus                  0   1
  ANKRD23 MUTATED     5   0
  ANKRD23 WILD-TYPE 252  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD23 MUTATED      5    0
  ANKRD23 WILD-TYPE  252   18
   clus
vv  ANKRD23 MUTATED ANKRD23 WILD-TYPE
  0               5               252
  1               0                18
[1] 2 2
[1] FALSE
D340V7, binary
                   cls
clus                  0   1
  ANKRD23 MUTATED     3   2
  ANKRD23 WILD-TYPE 107 177
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD23 MUTATED      3    2
  ANKRD23 WILD-TYPE  107  177
        clus
vv       ANKRD23 MUTATED ANKRD23 WILD-TYPE
  FEMALE               3               107
  MALE                 2               177
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ANKRD23 MUTATED                                       0
  ANKRD23 WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ANKRD23 MUTATED                                                        3
  ANKRD23 WILD-TYPE                                                    132
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ANKRD23 MUTATED                                                                   1
  ANKRD23 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ANKRD23 MUTATED                                                  1
  ANKRD23 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ANKRD23 MUTATED                                                          0
  ANKRD23 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ANKRD23 MUTATED                                                           0
  ANKRD23 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ANKRD23 MUTATED                                          0
  ANKRD23 WILD-TYPE                                        3
D340V8, multiclass
                                                                   clus
vv                                                                  ANKRD23 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  ANKRD23 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D340V9, binary
                   cls
clus                  0   1
  ANKRD23 MUTATED     0   5
  ANKRD23 WILD-TYPE   5 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD23 MUTATED      0    5
  ANKRD23 WILD-TYPE    5  279
     clus
vv    ANKRD23 MUTATED ANKRD23 WILD-TYPE
  NO                0                 5
  YES               5               279
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ANKRD23 MUTATED     3   0   0   1
  ANKRD23 WILD-TYPE 224  10  10  23
D340V10, multiclass
    clus
vv   ANKRD23 MUTATED ANKRD23 WILD-TYPE
  R0               3               224
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D340V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ANKRD23 MUTATED       2                         0     2
  ANKRD23 WILD-TYPE    74                         4   166
D340V12, multiclass
                           clus
vv                          ANKRD23 MUTATED ANKRD23 WILD-TYPE
  ASIAN                                   2                74
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   2               166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(341) Variable = BTBD11 MUTATION ANALYSIS
D341V1, survival
                  sevent
clus2                0   1
  BTBD11 MUTATED    14   5
  BTBD11 WILD-TYPE 167  75
  BTBD11 MUTATED BTBD11 WILD-TYPE 
              19              242 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
               5               75 
$`BTBD11 MUTATED`
TCGA-B7-5816 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6852 
       26.70        18.35         6.18         6.61        34.68        32.94 
TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-A4IY TCGA-BR-A4QM TCGA-CD-A4MG TCGA-CG-4305 
       15.85         1.12        12.89         5.13         6.58        15.95 
TCGA-CG-4443 TCGA-CG-5721 TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-F1-A448 TCGA-HU-8604 
       29.98         6.02         5.92        14.76        21.27        12.10 
TCGA-HU-A4G8 
       11.84 

$`BTBD11 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
       11.70         6.61         6.97         4.64         7.43        30.90 
TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        9.57        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       19.89         8.98        21.11        30.90        31.20        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        19.17        14.79         0.26         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       13.51         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       11.57         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-EQ-5647 
       20.91        14.27        16.44        15.16        13.78         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        7.99        16.24        14.47        72.23         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        11.41        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  BTBD11 MUTATED BTBD11 WILD-TYPE 
            1.12             0.00 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
           34.68           105.07 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
          12.890           12.605 
[1] "1.1 - 34.7 (12.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D341V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BTBD11 MUTATED         0        1        1        1         5         5
  BTBD11 WILD-TYPE       1        8       26       25        26        39
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BTBD11 MUTATED           1          1          1          1        1
  BTBD11 WILD-TYPE         2         48         35         23       23
D341V3, multiclass
            clus
vv           BTBD11 MUTATED BTBD11 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                1               26
  STAGE II                1               25
  STAGE IIA               5               26
  STAGE IIB               5               39
  STAGE III               1                2
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              1               23
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BTBD11 MUTATED     1   5   9   4
  BTBD11 WILD-TYPE  10  67 113  71
D341V4, multiclass
    clus
vv   BTBD11 MUTATED BTBD11 WILD-TYPE
  T1              1               10
  T2              5               67
  T3              9              113
  T4              4               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  BTBD11 MUTATED    9  6  2  2
  BTBD11 WILD-TYPE 84 75 48 51
D341V5, multiclass
    clus
vv   BTBD11 MUTATED BTBD11 WILD-TYPE
  N0              9               84
  N1              6               75
  N2              2               48
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D341V6, binary
                  cls
clus                 0   1
  BTBD11 MUTATED    20   0
  BTBD11 WILD-TYPE 237  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED     20    0
  BTBD11 WILD-TYPE  237   18
   clus
vv  BTBD11 MUTATED BTBD11 WILD-TYPE
  0             20              237
  1              0               18
[1] 2 2
[1] FALSE
D341V7, binary
                  cls
clus                 0   1
  BTBD11 MUTATED    10  10
  BTBD11 WILD-TYPE 100 169
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED     10   10
  BTBD11 WILD-TYPE  100  169
        clus
vv       BTBD11 MUTATED BTBD11 WILD-TYPE
  FEMALE             10              100
  MALE               10              169
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  BTBD11 MUTATED                                       3
  BTBD11 WILD-TYPE                                    47
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BTBD11 MUTATED                                                       10
  BTBD11 WILD-TYPE                                                    125
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BTBD11 MUTATED                                                                   2
  BTBD11 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  BTBD11 MUTATED                                                  3
  BTBD11 WILD-TYPE                                               35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  BTBD11 MUTATED                                                          2
  BTBD11 WILD-TYPE                                                       14
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  BTBD11 MUTATED                                                           0
  BTBD11 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  BTBD11 MUTATED                                          0
  BTBD11 WILD-TYPE                                        3
D341V8, multiclass
                                                                   clus
vv                                                                  BTBD11 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  BTBD11 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D341V9, binary
                  cls
clus                 0   1
  BTBD11 MUTATED     0  20
  BTBD11 WILD-TYPE   5 264
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED      0   20
  BTBD11 WILD-TYPE    5  264
     clus
vv    BTBD11 MUTATED BTBD11 WILD-TYPE
  NO               0                5
  YES             20              264
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  BTBD11 MUTATED    14   0   0   4
  BTBD11 WILD-TYPE 213  10  10  20
D341V10, multiclass
    clus
vv   BTBD11 MUTATED BTBD11 WILD-TYPE
  R0             14              213
  R1              0               10
  R2              0               10
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D341V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BTBD11 MUTATED       4                         0    13
  BTBD11 WILD-TYPE    72                         4   155
D341V12, multiclass
                           clus
vv                          BTBD11 MUTATED BTBD11 WILD-TYPE
  ASIAN                                  4               72
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                 13              155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(342) Variable = FBXO21 MUTATION ANALYSIS
D342V1, survival
                  sevent
clus2                0   1
  FBXO21 MUTATED     5   3
  FBXO21 WILD-TYPE 176  77
  FBXO21 MUTATED FBXO21 WILD-TYPE 
               8              253 
  FBXO21 MUTATED FBXO21 WILD-TYPE 
               3               77 
$`FBXO21 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8059 TCGA-BR-8361 TCGA-BR-8372 
        6.97        30.90        34.68        14.43        19.50        19.17 
TCGA-BR-8591 TCGA-D7-8579 
       13.45        20.91 

$`FBXO21 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 
        3.45         9.07        12.76        18.71        17.49         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
       16.31         2.20        15.58         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       15.81         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  FBXO21 MUTATED FBXO21 WILD-TYPE 
            6.97             0.00 
  FBXO21 MUTATED FBXO21 WILD-TYPE 
           34.68           105.07 
  FBXO21 MUTATED FBXO21 WILD-TYPE 
          19.335           12.430 
[1] "7.0 - 34.7 (19.3)"  "0.0 - 105.1 (12.4)"
[1] "hr=" "1.3"
D342V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FBXO21 MUTATED         0        0        0        0         1         1
  FBXO21 WILD-TYPE       1        9       27       26        30        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO21 MUTATED           1          2          0          3        0
  FBXO21 WILD-TYPE         2         47         36         21       24
D342V3, multiclass
            clus
vv           FBXO21 MUTATED FBXO21 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               1               43
  STAGE III               1                2
  STAGE IIIA              2               47
  STAGE IIIB              0               36
  STAGE IIIC              3               21
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FBXO21 MUTATED     0   2   2   5
  FBXO21 WILD-TYPE  11  70 120  70
D342V4, multiclass
    clus
vv   FBXO21 MUTATED FBXO21 WILD-TYPE
  T1              0               11
  T2              2               70
  T3              2              120
  T4              5               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  FBXO21 MUTATED    2  4  2  2
  FBXO21 WILD-TYPE 91 77 48 51
D342V5, multiclass
    clus
vv   FBXO21 MUTATED FBXO21 WILD-TYPE
  N0              2               91
  N1              4               77
  N2              2               48
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D342V6, binary
                  cls
clus                 0   1
  FBXO21 MUTATED    11   0
  FBXO21 WILD-TYPE 246  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO21 MUTATED     11    0
  FBXO21 WILD-TYPE  246   18
   clus
vv  FBXO21 MUTATED FBXO21 WILD-TYPE
  0             11              246
  1              0               18
[1] 2 2
[1] FALSE
D342V7, binary
                  cls
clus                 0   1
  FBXO21 MUTATED     7   5
  FBXO21 WILD-TYPE 103 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO21 MUTATED      7    5
  FBXO21 WILD-TYPE  103  174
        clus
vv       FBXO21 MUTATED FBXO21 WILD-TYPE
  FEMALE              7              103
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FBXO21 MUTATED                                       0
  FBXO21 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FBXO21 MUTATED                                                       10
  FBXO21 WILD-TYPE                                                    125
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FBXO21 MUTATED                                                                   2
  FBXO21 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FBXO21 MUTATED                                                  0
  FBXO21 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FBXO21 MUTATED                                                          0
  FBXO21 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FBXO21 MUTATED                                                           0
  FBXO21 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FBXO21 MUTATED                                          0
  FBXO21 WILD-TYPE                                        3
D342V8, multiclass
                                                                   clus
vv                                                                  FBXO21 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  FBXO21 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D342V9, binary
                  cls
clus                 0   1
  FBXO21 MUTATED     0  12
  FBXO21 WILD-TYPE   5 272
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO21 MUTATED      0   12
  FBXO21 WILD-TYPE    5  272
     clus
vv    FBXO21 MUTATED FBXO21 WILD-TYPE
  NO               0                5
  YES             12              272
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FBXO21 MUTATED     6   0   0   6
  FBXO21 WILD-TYPE 221  10  10  18
D342V10, multiclass
    clus
vv   FBXO21 MUTATED FBXO21 WILD-TYPE
  R0              6              221
  R1              0               10
  R2              0               10
  RX              6               18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D342V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FBXO21 MUTATED       0                         0    12
  FBXO21 WILD-TYPE    76                         4   156
D342V12, multiclass
                           clus
vv                          FBXO21 MUTATED FBXO21 WILD-TYPE
  ASIAN                                  0               76
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                 12              156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(343) Variable = C19ORF26 MUTATION ANALYSIS
D343V1, survival
                    sevent
clus2                  0   1
  C19ORF26 MUTATED     2   1
  C19ORF26 WILD-TYPE 179  79
  C19ORF26 MUTATED C19ORF26 WILD-TYPE 
                 3                258 
  C19ORF26 MUTATED C19ORF26 WILD-TYPE 
                 1                 79 
$`C19ORF26 MUTATED`
TCGA-BR-6452 TCGA-BR-8059 TCGA-CG-5721 
       34.68        14.43         6.02 

$`C19ORF26 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  C19ORF26 MUTATED C19ORF26 WILD-TYPE 
              6.02               0.00 
  C19ORF26 MUTATED C19ORF26 WILD-TYPE 
             34.68             105.07 
  C19ORF26 MUTATED C19ORF26 WILD-TYPE 
            14.430             12.605 
[1] "6.0 - 34.7 (14.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D343V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C19ORF26 MUTATED         1        0        2        0         1         0
  C19ORF26 WILD-TYPE       0        9       25       26        30        44
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C19ORF26 MUTATED           1          0          0          0        1
  C19ORF26 WILD-TYPE         2         49         36         24       23
D343V3, multiclass
            clus
vv           C19ORF26 MUTATED C19ORF26 WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                  0                  9
  STAGE IB                  2                 25
  STAGE II                  0                 26
  STAGE IIA                 1                 30
  STAGE IIB                 0                 44
  STAGE III                 1                  2
  STAGE IIIA                0                 49
  STAGE IIIB                0                 36
  STAGE IIIC                0                 24
  STAGE IV                  1                 23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C19ORF26 MUTATED     1   2   1   2
  C19ORF26 WILD-TYPE  10  70 121  73
D343V4, multiclass
    clus
vv   C19ORF26 MUTATED C19ORF26 WILD-TYPE
  T1                1                 10
  T2                2                 70
  T3                1                121
  T4                2                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  C19ORF26 MUTATED    3  4  0  0
  C19ORF26 WILD-TYPE 90 77 50 53
D343V5, multiclass
    clus
vv   C19ORF26 MUTATED C19ORF26 WILD-TYPE
  N0                3                 90
  N1                4                 77
  N2                0                 50
  N3                0                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D343V6, binary
                    cls
clus                   0   1
  C19ORF26 MUTATED     6   0
  C19ORF26 WILD-TYPE 251  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF26 MUTATED      6    0
  C19ORF26 WILD-TYPE  251   18
   clus
vv  C19ORF26 MUTATED C19ORF26 WILD-TYPE
  0                6                251
  1                0                 18
[1] 2 2
[1] FALSE
D343V7, binary
                    cls
clus                   0   1
  C19ORF26 MUTATED     3   4
  C19ORF26 WILD-TYPE 107 175
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF26 MUTATED      3    4
  C19ORF26 WILD-TYPE  107  175
        clus
vv       C19ORF26 MUTATED C19ORF26 WILD-TYPE
  FEMALE                3                107
  MALE                  4                175
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C19ORF26 MUTATED                                       0
  C19ORF26 WILD-TYPE                                    50
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C19ORF26 MUTATED                                                        4
  C19ORF26 WILD-TYPE                                                    131
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C19ORF26 MUTATED                                                                   3
  C19ORF26 WILD-TYPE                                                                37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C19ORF26 MUTATED                                                  0
  C19ORF26 WILD-TYPE                                               38
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C19ORF26 MUTATED                                                          0
  C19ORF26 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C19ORF26 MUTATED                                                           0
  C19ORF26 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C19ORF26 MUTATED                                          0
  C19ORF26 WILD-TYPE                                        3
D343V8, multiclass
                                                                   clus
vv                                                                  C19ORF26 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  C19ORF26 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D343V9, binary
                    cls
clus                   0   1
  C19ORF26 MUTATED     0   7
  C19ORF26 WILD-TYPE   5 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF26 MUTATED      0    7
  C19ORF26 WILD-TYPE    5  277
     clus
vv    C19ORF26 MUTATED C19ORF26 WILD-TYPE
  NO                 0                  5
  YES                7                277
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C19ORF26 MUTATED     6   0   0   1
  C19ORF26 WILD-TYPE 221  10  10  23
D343V10, multiclass
    clus
vv   C19ORF26 MUTATED C19ORF26 WILD-TYPE
  R0                6                221
  R1                0                 10
  R2                0                 10
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D343V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C19ORF26 MUTATED       0                         1     4
  C19ORF26 WILD-TYPE    76                         3   164
D343V12, multiclass
                           clus
vv                          C19ORF26 MUTATED C19ORF26 WILD-TYPE
  ASIAN                                    0                 76
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                    4                164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(344) Variable = NAA25 MUTATION ANALYSIS
D344V1, survival
                 sevent
clus2               0   1
  NAA25 MUTATED    10   2
  NAA25 WILD-TYPE 171  78
  NAA25 MUTATED NAA25 WILD-TYPE 
             12             249 
  NAA25 MUTATED NAA25 WILD-TYPE 
              2              78 
$`NAA25 MUTATED`
TCGA-BR-6458 TCGA-BR-7716 TCGA-BR-7851 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8372 
       19.33        28.01        12.43        20.55         0.26        19.17 
TCGA-CD-A486 TCGA-CD-A4MI TCGA-CG-5728 TCGA-D7-A4YU TCGA-HU-A4GX TCGA-HU-A4H3 
        3.42         0.10        65.10        16.44        10.19        19.36 

$`NAA25 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        23.93        15.42        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69        12.26         9.60         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
        0.16         0.10         0.10         0.13         0.10         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       14.27         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.51         6.25         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  NAA25 MUTATED NAA25 WILD-TYPE 
            0.1             0.0 
  NAA25 MUTATED NAA25 WILD-TYPE 
          65.10          105.07 
  NAA25 MUTATED NAA25 WILD-TYPE 
         17.805          12.590 
[1] "0.1 - 65.1 (17.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.3"
D344V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NAA25 MUTATED         1        0        2        1         1         4
  NAA25 WILD-TYPE       0        9       25       25        30        40
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NAA25 MUTATED           0          0          2          3        0
  NAA25 WILD-TYPE         3         49         34         21       24
D344V3, multiclass
            clus
vv           NAA25 MUTATED NAA25 WILD-TYPE
  STAGE I                1               0
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              4              40
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             2              34
  STAGE IIIC             3              21
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NAA25 MUTATED     1   2   6   5
  NAA25 WILD-TYPE  10  70 116  70
D344V4, multiclass
    clus
vv   NAA25 MUTATED NAA25 WILD-TYPE
  T1             1              10
  T2             2              70
  T3             6             116
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  NAA25 MUTATED    6  4  1  3
  NAA25 WILD-TYPE 87 77 49 50
D344V5, multiclass
    clus
vv   NAA25 MUTATED NAA25 WILD-TYPE
  N0             6              87
  N1             4              77
  N2             1              49
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D344V6, binary
                 cls
clus                0   1
  NAA25 MUTATED    13   0
  NAA25 WILD-TYPE 244  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED     13    0
  NAA25 WILD-TYPE  244   18
   clus
vv  NAA25 MUTATED NAA25 WILD-TYPE
  0            13             244
  1             0              18
[1] 2 2
[1] FALSE
D344V7, binary
                 cls
clus                0   1
  NAA25 MUTATED     7   7
  NAA25 WILD-TYPE 103 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED      7    7
  NAA25 WILD-TYPE  103  172
        clus
vv       NAA25 MUTATED NAA25 WILD-TYPE
  FEMALE             7             103
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NAA25 MUTATED                                       3
  NAA25 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NAA25 MUTATED                                                        8
  NAA25 WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NAA25 MUTATED                                                                   2
  NAA25 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NAA25 MUTATED                                                  1
  NAA25 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NAA25 MUTATED                                                          0
  NAA25 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NAA25 MUTATED                                                           0
  NAA25 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NAA25 MUTATED                                          0
  NAA25 WILD-TYPE                                        3
D344V8, multiclass
                                                                   clus
vv                                                                  NAA25 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  NAA25 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D344V9, binary
                 cls
clus                0   1
  NAA25 MUTATED     0  14
  NAA25 WILD-TYPE   5 270
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED      0   14
  NAA25 WILD-TYPE    5  270
     clus
vv    NAA25 MUTATED NAA25 WILD-TYPE
  NO              0               5
  YES            14             270
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NAA25 MUTATED    12   0   0   0
  NAA25 WILD-TYPE 215  10  10  24
D344V10, multiclass
    clus
vv   NAA25 MUTATED NAA25 WILD-TYPE
  R0            12             215
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D344V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NAA25 MUTATED       5                         1     7
  NAA25 WILD-TYPE    71                         3   161
D344V12, multiclass
                           clus
vv                          NAA25 MUTATED NAA25 WILD-TYPE
  ASIAN                                 5              71
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 7             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(345) Variable = MAMSTR MUTATION ANALYSIS
D345V1, survival
                  sevent
clus2                0   1
  MAMSTR MUTATED     3   0
  MAMSTR WILD-TYPE 178  80
  MAMSTR MUTATED MAMSTR WILD-TYPE 
               3              258 
  MAMSTR MUTATED MAMSTR WILD-TYPE 
               0               80 
$`MAMSTR MUTATED`
TCGA-BR-6852 TCGA-BR-8360 TCGA-HU-A4GX 
       32.94         6.18        10.19 

$`MAMSTR WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        30.90        31.20        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  MAMSTR MUTATED MAMSTR WILD-TYPE 
            6.18             0.00 
  MAMSTR MUTATED MAMSTR WILD-TYPE 
           32.94           105.07 
  MAMSTR MUTATED MAMSTR WILD-TYPE 
           10.19            12.64 
[1] "6.2 - 32.9 (10.2)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "9200000"
D345V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAMSTR MUTATED         0        0        0        0         2         0
  MAMSTR WILD-TYPE       1        9       27       26        29        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAMSTR MUTATED           0          0          0          1        0
  MAMSTR WILD-TYPE         3         49         36         23       24
D345V3, multiclass
            clus
vv           MAMSTR MUTATED MAMSTR WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               2               29
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAMSTR MUTATED     0   0   2   1
  MAMSTR WILD-TYPE  11  72 120  74
D345V4, multiclass
    clus
vv   MAMSTR MUTATED MAMSTR WILD-TYPE
  T1              0               11
  T2              0               72
  T3              2              120
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  MAMSTR MUTATED    2  1  1  0
  MAMSTR WILD-TYPE 91 80 49 53
D345V5, multiclass
    clus
vv   MAMSTR MUTATED MAMSTR WILD-TYPE
  N0              2               91
  N1              1               80
  N2              1               49
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D345V6, binary
                  cls
clus                 0   1
  MAMSTR MUTATED     4   0
  MAMSTR WILD-TYPE 253  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAMSTR MUTATED      4    0
  MAMSTR WILD-TYPE  253   18
   clus
vv  MAMSTR MUTATED MAMSTR WILD-TYPE
  0              4              253
  1              0               18
[1] 2 2
[1] FALSE
D345V7, binary
                  cls
clus                 0   1
  MAMSTR MUTATED     3   1
  MAMSTR WILD-TYPE 107 178
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAMSTR MUTATED      3    1
  MAMSTR WILD-TYPE  107  178
        clus
vv       MAMSTR MUTATED MAMSTR WILD-TYPE
  FEMALE              3              107
  MALE                1              178
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MAMSTR MUTATED                                       1
  MAMSTR WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MAMSTR MUTATED                                                        2
  MAMSTR WILD-TYPE                                                    133
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MAMSTR MUTATED                                                                   1
  MAMSTR WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MAMSTR MUTATED                                                  0
  MAMSTR WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MAMSTR MUTATED                                                          0
  MAMSTR WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MAMSTR MUTATED                                                           0
  MAMSTR WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MAMSTR MUTATED                                          0
  MAMSTR WILD-TYPE                                        3
D345V8, multiclass
                                                                   clus
vv                                                                  MAMSTR MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  MAMSTR WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D345V9, binary
                  cls
clus                 0   1
  MAMSTR MUTATED     0   4
  MAMSTR WILD-TYPE   5 280
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAMSTR MUTATED      0    4
  MAMSTR WILD-TYPE    5  280
     clus
vv    MAMSTR MUTATED MAMSTR WILD-TYPE
  NO               0                5
  YES              4              280
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MAMSTR MUTATED     3   0   0   1
  MAMSTR WILD-TYPE 224  10  10  23
D345V10, multiclass
    clus
vv   MAMSTR MUTATED MAMSTR WILD-TYPE
  R0              3              224
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D345V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAMSTR MUTATED       1                         0     3
  MAMSTR WILD-TYPE    75                         4   165
D345V12, multiclass
                           clus
vv                          MAMSTR MUTATED MAMSTR WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  3              165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(346) Variable = RING1 MUTATION ANALYSIS
D346V1, survival
                 sevent
clus2               0   1
  RING1 MUTATED     6   0
  RING1 WILD-TYPE 175  80
  RING1 MUTATED RING1 WILD-TYPE 
              6             255 
  RING1 MUTATED RING1 WILD-TYPE 
              0              80 
$`RING1 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-CD-5802 TCGA-CG-5721 TCGA-D7-A4YY TCGA-HU-A4H3 
       26.70        34.68         0.30         6.02        13.78        19.36 

$`RING1 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.18         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       16.44         5.92        15.16        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.25        10.19         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  RING1 MUTATED RING1 WILD-TYPE 
            0.3             0.0 
  RING1 MUTATED RING1 WILD-TYPE 
          34.68          105.07 
  RING1 MUTATED RING1 WILD-TYPE 
          16.57           12.59 
[1] "0.3 - 34.7 (16.6)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "2.6e+07"
D346V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RING1 MUTATED         0        0        0        1         1         1
  RING1 WILD-TYPE       1        9       27       25        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RING1 MUTATED           0          0          1          1        2
  RING1 WILD-TYPE         3         49         35         23       22
D346V3, multiclass
            clus
vv           RING1 MUTATED RING1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RING1 MUTATED     0   0   3   4
  RING1 WILD-TYPE  11  72 119  71
D346V4, multiclass
    clus
vv   RING1 MUTATED RING1 WILD-TYPE
  T1             0              11
  T2             0              72
  T3             3             119
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  RING1 MUTATED    3  1  1  2
  RING1 WILD-TYPE 90 80 49 51
D346V5, multiclass
    clus
vv   RING1 MUTATED RING1 WILD-TYPE
  N0             3              90
  N1             1              80
  N2             1              49
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D346V6, binary
                 cls
clus                0   1
  RING1 MUTATED     8   0
  RING1 WILD-TYPE 249  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RING1 MUTATED      8    0
  RING1 WILD-TYPE  249   18
   clus
vv  RING1 MUTATED RING1 WILD-TYPE
  0             8             249
  1             0              18
[1] 2 2
[1] FALSE
D346V7, binary
                 cls
clus                0   1
  RING1 MUTATED     5   3
  RING1 WILD-TYPE 105 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RING1 MUTATED      5    3
  RING1 WILD-TYPE  105  176
        clus
vv       RING1 MUTATED RING1 WILD-TYPE
  FEMALE             5             105
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RING1 MUTATED                                       2
  RING1 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RING1 MUTATED                                                        5
  RING1 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RING1 MUTATED                                                                   1
  RING1 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RING1 MUTATED                                                  0
  RING1 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RING1 MUTATED                                                          0
  RING1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RING1 MUTATED                                                           0
  RING1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RING1 MUTATED                                          0
  RING1 WILD-TYPE                                        3
D346V8, multiclass
                                                                   clus
vv                                                                  RING1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  RING1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D346V9, binary
                 cls
clus                0   1
  RING1 MUTATED     0   8
  RING1 WILD-TYPE   5 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RING1 MUTATED      0    8
  RING1 WILD-TYPE    5  276
     clus
vv    RING1 MUTATED RING1 WILD-TYPE
  NO              0               5
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RING1 MUTATED     5   0   0   2
  RING1 WILD-TYPE 222  10  10  22
D346V10, multiclass
    clus
vv   RING1 MUTATED RING1 WILD-TYPE
  R0             5             222
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D346V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RING1 MUTATED       2                         0     5
  RING1 WILD-TYPE    74                         4   163
D346V12, multiclass
                           clus
vv                          RING1 MUTATED RING1 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(347) Variable = ATM MUTATION ANALYSIS
D347V1, survival
               sevent
clus2             0   1
  ATM MUTATED    22   3
  ATM WILD-TYPE 159  77
  ATM MUTATED ATM WILD-TYPE 
           25           236 
  ATM MUTATED ATM WILD-TYPE 
            3            77 
$`ATM MUTATED`
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7851 
       34.68        32.78        30.90        23.93        18.15        12.43 
TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8591 
       20.55        19.50         0.26         4.31         1.12        13.45 
TCGA-BR-8680 TCGA-BR-A4CQ TCGA-BR-A4J7 TCGA-CD-5798 TCGA-CD-A4MI TCGA-CG-4301 
       15.81        22.26        19.36         2.83         0.10         3.02 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-8573 TCGA-D7-8575 TCGA-HU-8249 
        6.02       105.07        65.10        19.50        18.21        14.17 
TCGA-HU-A4GT 
        6.51 

$`ATM WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 
       31.20        32.94        12.82         9.21        24.76        15.42 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       28.01        15.32        28.73         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        7.40         6.18        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        15.81         9.34         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56        13.87         7.53         6.08         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       11.57         5.13         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
        6.58        12.20        12.62        20.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        1.02         0.99         0.99        12.03        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         0.10         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  ATM MUTATED ATM WILD-TYPE 
          0.1           0.0 
  ATM MUTATED ATM WILD-TYPE 
       105.07         79.07 
  ATM MUTATED ATM WILD-TYPE 
       18.150        12.395 
[1] "0.1 - 105.1 (18.1)" "0.0 - 79.1 (12.4)" 
[1] "hr=" "4"  
D347V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATM MUTATED         0        0        4        3         6         3
  ATM WILD-TYPE       1        9       23       23        25        41
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATM MUTATED           0          5          1          2        4
  ATM WILD-TYPE         3         44         35         22       20
D347V3, multiclass
            clus
vv           ATM MUTATED ATM WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             9
  STAGE IB             4            23
  STAGE II             3            23
  STAGE IIA            6            25
  STAGE IIB            3            41
  STAGE III            0             3
  STAGE IIIA           5            44
  STAGE IIIB           1            35
  STAGE IIIC           2            22
  STAGE IV             4            20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  ATM MUTATED     1   5  12  11
  ATM WILD-TYPE  10  67 110  64
D347V4, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  T1           1            10
  T2           5            67
  T3          12           110
  T4          11            64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  ATM MUTATED   15  6  5  1
  ATM WILD-TYPE 78 75 45 52
D347V5, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  N0          15            78
  N1           6            75
  N2           5            45
  N3           1            52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D347V6, binary
               cls
clus              0   1
  ATM MUTATED    28   2
  ATM WILD-TYPE 229  16
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     28    2
  ATM WILD-TYPE  229   16
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0          28           229
  1           2            16
[1] 2 2
[1] FALSE
D347V7, binary
               cls
clus              0   1
  ATM MUTATED    14  16
  ATM WILD-TYPE  96 163
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     14   16
  ATM WILD-TYPE   96  163
        clus
vv       ATM MUTATED ATM WILD-TYPE
  FEMALE          14            96
  MALE            16           163
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ATM MUTATED                                       1
  ATM WILD-TYPE                                    49
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ATM MUTATED                                                       19
  ATM WILD-TYPE                                                    116
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ATM MUTATED                                                                   3
  ATM WILD-TYPE                                                                37
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ATM MUTATED                                                  5
  ATM WILD-TYPE                                               33
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ATM MUTATED                                                          2
  ATM WILD-TYPE                                                       14
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ATM MUTATED                                                           0
  ATM WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ATM MUTATED                                          0
  ATM WILD-TYPE                                        3
D347V8, multiclass
                                                                   clus
vv                                                                  ATM MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                     19
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  ATM WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      116
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D347V9, binary
               cls
clus              0   1
  ATM MUTATED     0  30
  ATM WILD-TYPE   5 254
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      0   30
  ATM WILD-TYPE    5  254
     clus
vv    ATM MUTATED ATM WILD-TYPE
  NO            0             5
  YES          30           254
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  ATM MUTATED    24   0   1   3
  ATM WILD-TYPE 203  10   9  21
D347V10, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  R0          24           203
  R1           0            10
  R2           1             9
  RX           3            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D347V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATM MUTATED       7                         0    19
  ATM WILD-TYPE    69                         4   149
D347V12, multiclass
                           clus
vv                          ATM MUTATED ATM WILD-TYPE
  ASIAN                               7            69
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                              19           149
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(348) Variable = BRWD1 MUTATION ANALYSIS
D348V1, survival
                 sevent
clus2               0   1
  BRWD1 MUTATED    15   3
  BRWD1 WILD-TYPE 166  77
  BRWD1 MUTATED BRWD1 WILD-TYPE 
             18             243 
  BRWD1 MUTATED BRWD1 WILD-TYPE 
              3              77 
$`BRWD1 MUTATED`
TCGA-B7-5816 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8368 TCGA-BR-8372 
       26.70         9.57        34.68        24.76         4.31        19.17 
TCGA-BR-A452 TCGA-BR-A4QL TCGA-CG-4305 TCGA-CG-5721 TCGA-D7-6524 TCGA-D7-6818 
        7.53        11.57        15.95         6.02        17.85        10.55 
TCGA-D7-8572 TCGA-F1-A448 TCGA-FP-A4BE TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GX 
       16.80        21.27        11.08        29.98         0.10        10.19 

$`BRWD1 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       30.90         6.18         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 
       31.20        32.94        12.82         9.21        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       10.68        12.56        13.87         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6525 
       19.13        20.55        18.84        18.54        18.61        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 
       17.19        10.26        15.22        15.98        12.79        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.33        24.72        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 
       59.54         5.03        13.58         0.56         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GT 
        3.25        22.75        25.81        11.77         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  BRWD1 MUTATED BRWD1 WILD-TYPE 
            0.1             0.0 
  BRWD1 MUTATED BRWD1 WILD-TYPE 
          34.68          105.07 
  BRWD1 MUTATED BRWD1 WILD-TYPE 
          13.76           12.62 
[1] "0.1 - 34.7 (13.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.2"
D348V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BRWD1 MUTATED         1        1        1        3         3         2
  BRWD1 WILD-TYPE       0        8       26       23        28        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BRWD1 MUTATED           0          3          2          3        1
  BRWD1 WILD-TYPE         3         46         34         21       23
D348V3, multiclass
            clus
vv           BRWD1 MUTATED BRWD1 WILD-TYPE
  STAGE I                1               0
  STAGE IA               1               8
  STAGE IB               1              26
  STAGE II               3              23
  STAGE IIA              3              28
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             3              46
  STAGE IIIB             2              34
  STAGE IIIC             3              21
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BRWD1 MUTATED     2   8   5   6
  BRWD1 WILD-TYPE   9  64 117  69
D348V4, multiclass
    clus
vv   BRWD1 MUTATED BRWD1 WILD-TYPE
  T1             2               9
  T2             8              64
  T3             5             117
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  BRWD1 MUTATED    5  8  3  4
  BRWD1 WILD-TYPE 88 73 47 49
D348V5, multiclass
    clus
vv   BRWD1 MUTATED BRWD1 WILD-TYPE
  N0             5              88
  N1             8              73
  N2             3              47
  N3             4              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D348V6, binary
                 cls
clus                0   1
  BRWD1 MUTATED    20   0
  BRWD1 WILD-TYPE 237  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRWD1 MUTATED     20    0
  BRWD1 WILD-TYPE  237   18
   clus
vv  BRWD1 MUTATED BRWD1 WILD-TYPE
  0            20             237
  1             0              18
[1] 2 2
[1] FALSE
D348V7, binary
                 cls
clus                0   1
  BRWD1 MUTATED     6  15
  BRWD1 WILD-TYPE 104 164
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRWD1 MUTATED      6   15
  BRWD1 WILD-TYPE  104  164
        clus
vv       BRWD1 MUTATED BRWD1 WILD-TYPE
  FEMALE             6             104
  MALE              15             164
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  BRWD1 MUTATED                                       4
  BRWD1 WILD-TYPE                                    46
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BRWD1 MUTATED                                                       11
  BRWD1 WILD-TYPE                                                    124
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BRWD1 MUTATED                                                                   1
  BRWD1 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  BRWD1 MUTATED                                                  3
  BRWD1 WILD-TYPE                                               35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  BRWD1 MUTATED                                                          1
  BRWD1 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  BRWD1 MUTATED                                                           1
  BRWD1 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  BRWD1 MUTATED                                          0
  BRWD1 WILD-TYPE                                        3
D348V8, multiclass
                                                                   clus
vv                                                                  BRWD1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  BRWD1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D348V9, binary
                 cls
clus                0   1
  BRWD1 MUTATED     2  19
  BRWD1 WILD-TYPE   3 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRWD1 MUTATED      2   19
  BRWD1 WILD-TYPE    3  265
     clus
vv    BRWD1 MUTATED BRWD1 WILD-TYPE
  NO              2               3
  YES            19             265
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BRWD1 MUTATED    17   2   0   2
  BRWD1 WILD-TYPE 210   8  10  22
D348V10, multiclass
    clus
vv   BRWD1 MUTATED BRWD1 WILD-TYPE
  R0            17             210
  R1             2               8
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D348V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BRWD1 MUTATED       4                         2    12
  BRWD1 WILD-TYPE    72                         2   156
D348V12, multiclass
                           clus
vv                          BRWD1 MUTATED BRWD1 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             2               2
  WHITE                                12             156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(349) Variable = PFKP MUTATION ANALYSIS
D349V1, survival
                sevent
clus2              0   1
  PFKP MUTATED     7   3
  PFKP WILD-TYPE 174  77
  PFKP MUTATED PFKP WILD-TYPE 
            10            251 
  PFKP MUTATED PFKP WILD-TYPE 
             3             77 
$`PFKP MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6566 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-8078 
        6.97        30.90        32.78        28.73        12.43        12.26 
TCGA-BR-8591 TCGA-HU-A4G2 TCGA-HU-A4GU TCGA-HU-A4H8 
       13.45        24.30         6.25         8.88 

$`PFKP WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 
       15.42        28.01        18.15        15.32         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 
       12.76        18.71        17.49        14.43         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       15.81         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       12.10        10.62         0.76         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
       12.95        19.36        23.84        12.30         9.67        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  PFKP MUTATED PFKP WILD-TYPE 
          6.25           0.00 
  PFKP MUTATED PFKP WILD-TYPE 
         32.78         105.07 
  PFKP MUTATED PFKP WILD-TYPE 
         12.94          12.62 
[1] "6.2 - 32.8 (12.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D349V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PFKP MUTATED         0        0        1        0         1         4
  PFKP WILD-TYPE       1        9       26       26        30        40
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PFKP MUTATED           0          2          1          1        0
  PFKP WILD-TYPE         3         47         35         23       24
D349V3, multiclass
            clus
vv           PFKP MUTATED PFKP WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             1             30
  STAGE IIB             4             40
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            1             35
  STAGE IIIC            1             23
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PFKP MUTATED     2   1   5   4
  PFKP WILD-TYPE   9  71 117  71
D349V4, multiclass
    clus
vv   PFKP MUTATED PFKP WILD-TYPE
  T1            2              9
  T2            1             71
  T3            5            117
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  PFKP MUTATED    4  4  0  2
  PFKP WILD-TYPE 89 77 50 51
D349V5, multiclass
    clus
vv   PFKP MUTATED PFKP WILD-TYPE
  N0            4             89
  N1            4             77
  N2            0             50
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D349V6, binary
                cls
clus               0   1
  PFKP MUTATED    12   0
  PFKP WILD-TYPE 245  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFKP MUTATED     12    0
  PFKP WILD-TYPE  245   18
   clus
vv  PFKP MUTATED PFKP WILD-TYPE
  0           12            245
  1            0             18
[1] 2 2
[1] FALSE
D349V7, binary
                cls
clus               0   1
  PFKP MUTATED     6   7
  PFKP WILD-TYPE 104 172
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFKP MUTATED      6    7
  PFKP WILD-TYPE  104  172
        clus
vv       PFKP MUTATED PFKP WILD-TYPE
  FEMALE            6            104
  MALE              7            172
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PFKP MUTATED                                       2
  PFKP WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PFKP MUTATED                                                        9
  PFKP WILD-TYPE                                                    126
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PFKP MUTATED                                                                   1
  PFKP WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PFKP MUTATED                                                  1
  PFKP WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PFKP MUTATED                                                          0
  PFKP WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PFKP MUTATED                                                           0
  PFKP WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PFKP MUTATED                                          0
  PFKP WILD-TYPE                                        3
D349V8, multiclass
                                                                   clus
vv                                                                  PFKP MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  PFKP WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D349V9, binary
                cls
clus               0   1
  PFKP MUTATED     0  13
  PFKP WILD-TYPE   5 271
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFKP MUTATED      0   13
  PFKP WILD-TYPE    5  271
     clus
vv    PFKP MUTATED PFKP WILD-TYPE
  NO             0              5
  YES           13            271
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PFKP MUTATED     8   0   0   5
  PFKP WILD-TYPE 219  10  10  19
D349V10, multiclass
    clus
vv   PFKP MUTATED PFKP WILD-TYPE
  R0            8            219
  R1            0             10
  R2            0             10
  RX            5             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D349V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PFKP MUTATED       3                         0    10
  PFKP WILD-TYPE    73                         4   158
D349V12, multiclass
                           clus
vv                          PFKP MUTATED PFKP WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               10            158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(350) Variable = SAFB MUTATION ANALYSIS
D350V1, survival
                sevent
clus2              0   1
  SAFB MUTATED     5   2
  SAFB WILD-TYPE 176  78
  SAFB MUTATED SAFB WILD-TYPE 
             7            254 
  SAFB MUTATED SAFB WILD-TYPE 
             2             78 
$`SAFB MUTATED`
TCGA-BR-6456 TCGA-BR-8360 TCGA-BR-A4J2 TCGA-D7-A4YU TCGA-D7-A4YY TCGA-HU-8602 
       17.29         6.18        14.17        16.44        13.78        11.41 
TCGA-HU-A4GQ 
        0.10 

$`SAFB WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 
       13.51        12.89         8.98         0.72         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       14.27         5.92        15.16        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  SAFB MUTATED SAFB WILD-TYPE 
           0.1            0.0 
  SAFB MUTATED SAFB WILD-TYPE 
         17.29         105.07 
  SAFB MUTATED SAFB WILD-TYPE 
        13.780         12.605 
[1] "0.1 - 17.3 (13.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D350V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SAFB MUTATED         0        0        1        0         1         3
  SAFB WILD-TYPE       1        9       26       26        30        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SAFB MUTATED           0          0          2          1        0
  SAFB WILD-TYPE         3         49         34         23       24
D350V3, multiclass
            clus
vv           SAFB MUTATED SAFB WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             1             30
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            2             34
  STAGE IIIC            1             23
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SAFB MUTATED     0   1   4   3
  SAFB WILD-TYPE  11  71 118  72
D350V4, multiclass
    clus
vv   SAFB MUTATED SAFB WILD-TYPE
  T1            0             11
  T2            1             71
  T3            4            118
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  SAFB MUTATED    4  1  1  2
  SAFB WILD-TYPE 89 80 49 51
D350V5, multiclass
    clus
vv   SAFB MUTATED SAFB WILD-TYPE
  N0            4             89
  N1            1             80
  N2            1             49
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D350V6, binary
                cls
clus               0   1
  SAFB MUTATED     9   0
  SAFB WILD-TYPE 248  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAFB MUTATED      9    0
  SAFB WILD-TYPE  248   18
   clus
vv  SAFB MUTATED SAFB WILD-TYPE
  0            9            248
  1            0             18
[1] 2 2
[1] FALSE
D350V7, binary
                cls
clus               0   1
  SAFB MUTATED     3   6
  SAFB WILD-TYPE 107 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAFB MUTATED      3    6
  SAFB WILD-TYPE  107  173
        clus
vv       SAFB MUTATED SAFB WILD-TYPE
  FEMALE            3            107
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SAFB MUTATED                                       2
  SAFB WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SAFB MUTATED                                                        3
  SAFB WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SAFB MUTATED                                                                   2
  SAFB WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SAFB MUTATED                                                  2
  SAFB WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SAFB MUTATED                                                          0
  SAFB WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SAFB MUTATED                                                           0
  SAFB WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SAFB MUTATED                                          0
  SAFB WILD-TYPE                                        3
D350V8, multiclass
                                                                   clus
vv                                                                  SAFB MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  SAFB WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D350V9, binary
                cls
clus               0   1
  SAFB MUTATED     0   9
  SAFB WILD-TYPE   5 275
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAFB MUTATED      0    9
  SAFB WILD-TYPE    5  275
     clus
vv    SAFB MUTATED SAFB WILD-TYPE
  NO             0              5
  YES            9            275
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SAFB MUTATED     8   0   0   1
  SAFB WILD-TYPE 219  10  10  23
D350V10, multiclass
    clus
vv   SAFB MUTATED SAFB WILD-TYPE
  R0            8            219
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D350V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SAFB MUTATED       3                         0     5
  SAFB WILD-TYPE    73                         4   163
D350V12, multiclass
                           clus
vv                          SAFB MUTATED SAFB WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                5            163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(351) Variable = KCNH4 MUTATION ANALYSIS
D351V1, survival
                 sevent
clus2               0   1
  KCNH4 MUTATED     5   1
  KCNH4 WILD-TYPE 176  79
  KCNH4 MUTATED KCNH4 WILD-TYPE 
              6             255 
  KCNH4 MUTATED KCNH4 WILD-TYPE 
              1              79 
$`KCNH4 MUTATED`
TCGA-BR-6566 TCGA-BR-8081 TCGA-BR-8487 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-HU-A4GH 
       32.78        20.55         1.12        11.57         6.58        11.77 

$`KCNH4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       17.49        14.43         0.69        12.26         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  KCNH4 MUTATED KCNH4 WILD-TYPE 
           1.12            0.00 
  KCNH4 MUTATED KCNH4 WILD-TYPE 
          32.78          105.07 
  KCNH4 MUTATED KCNH4 WILD-TYPE 
          11.67           12.66 
[1] "1.1 - 32.8 (11.7)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.9"
D351V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCNH4 MUTATED         0        1        0        0         3         1
  KCNH4 WILD-TYPE       1        8       27       26        28        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCNH4 MUTATED           0          0          1          0        0
  KCNH4 WILD-TYPE         3         49         35         24       24
D351V3, multiclass
            clus
vv           KCNH4 MUTATED KCNH4 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              3              28
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCNH4 MUTATED     1   0   4   1
  KCNH4 WILD-TYPE  10  72 118  74
D351V4, multiclass
    clus
vv   KCNH4 MUTATED KCNH4 WILD-TYPE
  T1             1              10
  T2             0              72
  T3             4             118
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  KCNH4 MUTATED    5  0  0  1
  KCNH4 WILD-TYPE 88 81 50 52
D351V5, multiclass
    clus
vv   KCNH4 MUTATED KCNH4 WILD-TYPE
  N0             5              88
  N1             0              81
  N2             0              50
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D351V6, binary
                 cls
clus                0   1
  KCNH4 MUTATED     6   0
  KCNH4 WILD-TYPE 251  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH4 MUTATED      6    0
  KCNH4 WILD-TYPE  251   18
   clus
vv  KCNH4 MUTATED KCNH4 WILD-TYPE
  0             6             251
  1             0              18
[1] 2 2
[1] FALSE
D351V7, binary
                 cls
clus                0   1
  KCNH4 MUTATED     4   2
  KCNH4 WILD-TYPE 106 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH4 MUTATED      4    2
  KCNH4 WILD-TYPE  106  177
        clus
vv       KCNH4 MUTATED KCNH4 WILD-TYPE
  FEMALE             4             106
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KCNH4 MUTATED                                       1
  KCNH4 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KCNH4 MUTATED                                                        4
  KCNH4 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KCNH4 MUTATED                                                                   0
  KCNH4 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KCNH4 MUTATED                                                  1
  KCNH4 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KCNH4 MUTATED                                                          0
  KCNH4 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KCNH4 MUTATED                                                           0
  KCNH4 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KCNH4 MUTATED                                          0
  KCNH4 WILD-TYPE                                        3
D351V8, multiclass
                                                                   clus
vv                                                                  KCNH4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  KCNH4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D351V9, binary
                 cls
clus                0   1
  KCNH4 MUTATED     0   6
  KCNH4 WILD-TYPE   5 278
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH4 MUTATED      0    6
  KCNH4 WILD-TYPE    5  278
     clus
vv    KCNH4 MUTATED KCNH4 WILD-TYPE
  NO              0               5
  YES             6             278
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KCNH4 MUTATED     5   0   0   0
  KCNH4 WILD-TYPE 222  10  10  24
D351V10, multiclass
    clus
vv   KCNH4 MUTATED KCNH4 WILD-TYPE
  R0             5             222
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D351V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KCNH4 MUTATED       2                         0     4
  KCNH4 WILD-TYPE    74                         4   164
D351V12, multiclass
                           clus
vv                          KCNH4 MUTATED KCNH4 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(352) Variable = TMEM63A MUTATION ANALYSIS
D352V1, survival
                   sevent
clus2                 0   1
  TMEM63A MUTATED     6   3
  TMEM63A WILD-TYPE 175  77
  TMEM63A MUTATED TMEM63A WILD-TYPE 
                9               252 
  TMEM63A MUTATED TMEM63A WILD-TYPE 
                3                77 
$`TMEM63A MUTATED`
TCGA-BR-7851 TCGA-BR-8078 TCGA-BR-8382 TCGA-CD-8536 TCGA-CG-4305 TCGA-CG-5723 
       12.43        12.26        15.85         0.10        15.95       105.07 
TCGA-CG-5726 TCGA-CG-5733 TCGA-HU-A4GQ 
       28.96        21.07         0.10 

$`TMEM63A WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10         4.01        69.04         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  TMEM63A MUTATED TMEM63A WILD-TYPE 
              0.1               0.0 
  TMEM63A MUTATED TMEM63A WILD-TYPE 
           105.07             79.07 
  TMEM63A MUTATED TMEM63A WILD-TYPE 
           15.850            12.605 
[1] "0.1 - 105.1 (15.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.4"
D352V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEM63A MUTATED         0        1        0        3         0         2
  TMEM63A WILD-TYPE       1        8       27       23        31        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM63A MUTATED           0          1          0          2        1
  TMEM63A WILD-TYPE         3         48         36         22       23
D352V3, multiclass
            clus
vv           TMEM63A MUTATED TMEM63A WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 1                 8
  STAGE IB                 0                27
  STAGE II                 3                23
  STAGE IIA                0                31
  STAGE IIB                2                42
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               0                36
  STAGE IIIC               2                22
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM63A MUTATED     1   3   1   5
  TMEM63A WILD-TYPE  10  69 121  70
D352V4, multiclass
    clus
vv   TMEM63A MUTATED TMEM63A WILD-TYPE
  T1               1                10
  T2               3                69
  T3               1               121
  T4               5                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  TMEM63A MUTATED    4  3  3  1
  TMEM63A WILD-TYPE 89 78 47 52
D352V5, multiclass
    clus
vv   TMEM63A MUTATED TMEM63A WILD-TYPE
  N0               4                89
  N1               3                78
  N2               3                47
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D352V6, binary
                   cls
clus                  0   1
  TMEM63A MUTATED    11   0
  TMEM63A WILD-TYPE 246  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM63A MUTATED     11    0
  TMEM63A WILD-TYPE  246   18
   clus
vv  TMEM63A MUTATED TMEM63A WILD-TYPE
  0              11               246
  1               0                18
[1] 2 2
[1] FALSE
D352V7, binary
                   cls
clus                  0   1
  TMEM63A MUTATED     5   6
  TMEM63A WILD-TYPE 105 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM63A MUTATED      5    6
  TMEM63A WILD-TYPE  105  173
        clus
vv       TMEM63A MUTATED TMEM63A WILD-TYPE
  FEMALE               5               105
  MALE                 6               173
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TMEM63A MUTATED                                       0
  TMEM63A WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TMEM63A MUTATED                                                        7
  TMEM63A WILD-TYPE                                                    128
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TMEM63A MUTATED                                                                   3
  TMEM63A WILD-TYPE                                                                37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TMEM63A MUTATED                                                  1
  TMEM63A WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TMEM63A MUTATED                                                          0
  TMEM63A WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TMEM63A MUTATED                                                           0
  TMEM63A WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TMEM63A MUTATED                                          0
  TMEM63A WILD-TYPE                                        3
D352V8, multiclass
                                                                   clus
vv                                                                  TMEM63A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  TMEM63A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D352V9, binary
                   cls
clus                  0   1
  TMEM63A MUTATED     0  11
  TMEM63A WILD-TYPE   5 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM63A MUTATED      0   11
  TMEM63A WILD-TYPE    5  273
     clus
vv    TMEM63A MUTATED TMEM63A WILD-TYPE
  NO                0                 5
  YES              11               273
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TMEM63A MUTATED     9   0   0   2
  TMEM63A WILD-TYPE 218  10  10  22
D352V10, multiclass
    clus
vv   TMEM63A MUTATED TMEM63A WILD-TYPE
  R0               9               218
  R1               0                10
  R2               0                10
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D352V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMEM63A MUTATED       2                         0     5
  TMEM63A WILD-TYPE    74                         4   163
D352V12, multiclass
                           clus
vv                          TMEM63A MUTATED TMEM63A WILD-TYPE
  ASIAN                                   2                74
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   5               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(353) Variable = SOAT1 MUTATION ANALYSIS
D353V1, survival
                 sevent
clus2               0   1
  SOAT1 MUTATED     4   1
  SOAT1 WILD-TYPE 177  79
  SOAT1 MUTATED SOAT1 WILD-TYPE 
              5             256 
  SOAT1 MUTATED SOAT1 WILD-TYPE 
              1              79 
$`SOAT1 MUTATED`
TCGA-BR-7703 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CG-4465 
       24.76        15.81        13.45        11.57         9.01 

$`SOAT1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 
       25.18         9.21        20.22         1.12        12.79         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  SOAT1 MUTATED SOAT1 WILD-TYPE 
           9.01            0.00 
  SOAT1 MUTATED SOAT1 WILD-TYPE 
          24.76          105.07 
  SOAT1 MUTATED SOAT1 WILD-TYPE 
         13.450          12.605 
[1] "9.0 - 24.8 (13.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.5"
D353V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SOAT1 MUTATED         0        1        0        1         0         0
  SOAT1 WILD-TYPE       1        8       27       25        31        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SOAT1 MUTATED           0          0          2          1        1
  SOAT1 WILD-TYPE         3         49         34         23       23
D353V3, multiclass
            clus
vv           SOAT1 MUTATED SOAT1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              0              31
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             2              34
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SOAT1 MUTATED     1   1   1   3
  SOAT1 WILD-TYPE  10  71 121  72
D353V4, multiclass
    clus
vv   SOAT1 MUTATED SOAT1 WILD-TYPE
  T1             1              10
  T2             1              71
  T3             1             121
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  SOAT1 MUTATED    1  2  0  3
  SOAT1 WILD-TYPE 92 79 50 50
D353V5, multiclass
    clus
vv   SOAT1 MUTATED SOAT1 WILD-TYPE
  N0             1              92
  N1             2              79
  N2             0              50
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D353V6, binary
                 cls
clus                0   1
  SOAT1 MUTATED     5   1
  SOAT1 WILD-TYPE 252  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SOAT1 MUTATED      5    1
  SOAT1 WILD-TYPE  252   17
   clus
vv  SOAT1 MUTATED SOAT1 WILD-TYPE
  0             5             252
  1             1              17
[1] 2 2
[1] FALSE
D353V7, binary
                 cls
clus                0   1
  SOAT1 MUTATED     2   4
  SOAT1 WILD-TYPE 108 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SOAT1 MUTATED      2    4
  SOAT1 WILD-TYPE  108  175
        clus
vv       SOAT1 MUTATED SOAT1 WILD-TYPE
  FEMALE             2             108
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SOAT1 MUTATED                                       1
  SOAT1 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SOAT1 MUTATED                                                        3
  SOAT1 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SOAT1 MUTATED                                                                   0
  SOAT1 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SOAT1 MUTATED                                                  0
  SOAT1 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SOAT1 MUTATED                                                          1
  SOAT1 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SOAT1 MUTATED                                                           1
  SOAT1 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SOAT1 MUTATED                                          0
  SOAT1 WILD-TYPE                                        3
D353V8, multiclass
                                                                   clus
vv                                                                  SOAT1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  SOAT1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D353V9, binary
                 cls
clus                0   1
  SOAT1 MUTATED     1   5
  SOAT1 WILD-TYPE   4 279
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SOAT1 MUTATED      1    5
  SOAT1 WILD-TYPE    4  279
     clus
vv    SOAT1 MUTATED SOAT1 WILD-TYPE
  NO              1               4
  YES             5             279
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SOAT1 MUTATED     5   0   1   0
  SOAT1 WILD-TYPE 222  10   9  24
D353V10, multiclass
    clus
vv   SOAT1 MUTATED SOAT1 WILD-TYPE
  R0             5             222
  R1             0              10
  R2             1               9
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D353V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SOAT1 MUTATED       0                         0     4
  SOAT1 WILD-TYPE    76                         4   164
D353V12, multiclass
                           clus
vv                          SOAT1 MUTATED SOAT1 WILD-TYPE
  ASIAN                                 0              76
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(354) Variable = CTNNA1 MUTATION ANALYSIS
D354V1, survival
                  sevent
clus2                0   1
  CTNNA1 MUTATED     8   3
  CTNNA1 WILD-TYPE 173  77
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
              11              250 
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
               3               77 
$`CTNNA1 MUTATED`
TCGA-BR-8361 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 
       19.50        15.81        11.57         6.97         0.99         6.02 
TCGA-CG-5723 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-HU-8602 TCGA-HU-A4H3 
      105.07        14.27         5.92        11.41        19.36 

$`CTNNA1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
       30.97        36.00         1.02         0.99        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       21.14        20.91        16.44        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
            0.99             0.00 
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
          105.07            79.07 
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
           11.57            12.64 
[1] "1.0 - 105.1 (11.6)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.4"
D354V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CTNNA1 MUTATED         0        0        1        2         0         2
  CTNNA1 WILD-TYPE       1        9       26       24        31        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTNNA1 MUTATED           0          1          1          3        2
  CTNNA1 WILD-TYPE         3         48         35         21       22
D354V3, multiclass
            clus
vv           CTNNA1 MUTATED CTNNA1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                2               24
  STAGE IIA               0               31
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              3               21
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CTNNA1 MUTATED     0   4   2   6
  CTNNA1 WILD-TYPE  11  68 120  69
D354V4, multiclass
    clus
vv   CTNNA1 MUTATED CTNNA1 WILD-TYPE
  T1              0               11
  T2              4               68
  T3              2              120
  T4              6               69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CTNNA1 MUTATED    2  5  2  4
  CTNNA1 WILD-TYPE 91 76 48 49
D354V5, multiclass
    clus
vv   CTNNA1 MUTATED CTNNA1 WILD-TYPE
  N0              2               91
  N1              5               76
  N2              2               48
  N3              4               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D354V6, binary
                  cls
clus                 0   1
  CTNNA1 MUTATED    12   1
  CTNNA1 WILD-TYPE 245  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA1 MUTATED     12    1
  CTNNA1 WILD-TYPE  245   17
   clus
vv  CTNNA1 MUTATED CTNNA1 WILD-TYPE
  0             12              245
  1              1               17
[1] 2 2
[1] FALSE
D354V7, binary
                  cls
clus                 0   1
  CTNNA1 MUTATED     6   7
  CTNNA1 WILD-TYPE 104 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA1 MUTATED      6    7
  CTNNA1 WILD-TYPE  104  172
        clus
vv       CTNNA1 MUTATED CTNNA1 WILD-TYPE
  FEMALE              6              104
  MALE                7              172
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CTNNA1 MUTATED                                       2
  CTNNA1 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CTNNA1 MUTATED                                                        7
  CTNNA1 WILD-TYPE                                                    128
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CTNNA1 MUTATED                                                                   1
  CTNNA1 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CTNNA1 MUTATED                                                  3
  CTNNA1 WILD-TYPE                                               35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CTNNA1 MUTATED                                                          0
  CTNNA1 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CTNNA1 MUTATED                                                           0
  CTNNA1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CTNNA1 MUTATED                                          0
  CTNNA1 WILD-TYPE                                        3
D354V8, multiclass
                                                                   clus
vv                                                                  CTNNA1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  CTNNA1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D354V9, binary
                  cls
clus                 0   1
  CTNNA1 MUTATED     0  13
  CTNNA1 WILD-TYPE   5 271
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA1 MUTATED      0   13
  CTNNA1 WILD-TYPE    5  271
     clus
vv    CTNNA1 MUTATED CTNNA1 WILD-TYPE
  NO               0                5
  YES             13              271
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CTNNA1 MUTATED    11   1   0   1
  CTNNA1 WILD-TYPE 216   9  10  23
D354V10, multiclass
    clus
vv   CTNNA1 MUTATED CTNNA1 WILD-TYPE
  R0             11              216
  R1              1                9
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D354V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CTNNA1 MUTATED       3                         0     6
  CTNNA1 WILD-TYPE    73                         4   162
D354V12, multiclass
                           clus
vv                          CTNNA1 MUTATED CTNNA1 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(355) Variable = FAM55C MUTATION ANALYSIS
D355V1, survival
                  sevent
clus2                0   1
  FAM55C MUTATED    10   2
  FAM55C WILD-TYPE 171  78
  FAM55C MUTATED FAM55C WILD-TYPE 
              12              249 
  FAM55C MUTATED FAM55C WILD-TYPE 
               2               78 
$`FAM55C MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-8078 TCGA-BR-8680 
        6.97        34.68        28.73        12.43        12.26        15.81 
TCGA-BR-A4CQ TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-HU-A4G8 TCGA-HU-A4HD 
       22.26         6.02       105.07        65.10        11.84        27.42 

$`FAM55C WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 
       23.93        15.42        28.01        18.15        15.32         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        20.55         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       10.68        12.56        13.87         7.53         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        0.99         0.99        12.03        28.96        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-IN-7806 TCGA-IN-7808 
       23.84        12.30         9.67         8.88        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  FAM55C MUTATED FAM55C WILD-TYPE 
            6.02             0.00 
  FAM55C MUTATED FAM55C WILD-TYPE 
          105.07            79.07 
  FAM55C MUTATED FAM55C WILD-TYPE 
          19.035           12.590 
[1] "6.0 - 105.1 (19.0)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "3.8"
D355V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM55C MUTATED         0        0        1        2         1         3
  FAM55C WILD-TYPE       1        9       26       24        30        41
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM55C MUTATED           0          3          1          0        2
  FAM55C WILD-TYPE         3         46         35         24       22
D355V3, multiclass
            clus
vv           FAM55C MUTATED FAM55C WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                2               24
  STAGE IIA               1               30
  STAGE IIB               3               41
  STAGE III               0                3
  STAGE IIIA              3               46
  STAGE IIIB              1               35
  STAGE IIIC              0               24
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM55C MUTATED     0   3   5   5
  FAM55C WILD-TYPE  11  69 117  70
D355V4, multiclass
    clus
vv   FAM55C MUTATED FAM55C WILD-TYPE
  T1              0               11
  T2              3               69
  T3              5              117
  T4              5               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  FAM55C MUTATED    4  6  2  1
  FAM55C WILD-TYPE 89 75 48 52
D355V5, multiclass
    clus
vv   FAM55C MUTATED FAM55C WILD-TYPE
  N0              4               89
  N1              6               75
  N2              2               48
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D355V6, binary
                  cls
clus                 0   1
  FAM55C MUTATED    11   1
  FAM55C WILD-TYPE 246  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM55C MUTATED     11    1
  FAM55C WILD-TYPE  246   17
   clus
vv  FAM55C MUTATED FAM55C WILD-TYPE
  0             11              246
  1              1               17
[1] 2 2
[1] FALSE
D355V7, binary
                  cls
clus                 0   1
  FAM55C MUTATED     4   9
  FAM55C WILD-TYPE 106 170
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM55C MUTATED      4    9
  FAM55C WILD-TYPE  106  170
        clus
vv       FAM55C MUTATED FAM55C WILD-TYPE
  FEMALE              4              106
  MALE                9              170
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FAM55C MUTATED                                       1
  FAM55C WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAM55C MUTATED                                                        6
  FAM55C WILD-TYPE                                                    129
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAM55C MUTATED                                                                   3
  FAM55C WILD-TYPE                                                                37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FAM55C MUTATED                                                  2
  FAM55C WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FAM55C MUTATED                                                          1
  FAM55C WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FAM55C MUTATED                                                           0
  FAM55C WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FAM55C MUTATED                                          0
  FAM55C WILD-TYPE                                        3
D355V8, multiclass
                                                                   clus
vv                                                                  FAM55C MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  FAM55C WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D355V9, binary
                  cls
clus                 0   1
  FAM55C MUTATED     1  12
  FAM55C WILD-TYPE   4 272
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM55C MUTATED      1   12
  FAM55C WILD-TYPE    4  272
     clus
vv    FAM55C MUTATED FAM55C WILD-TYPE
  NO               1                4
  YES             12              272
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FAM55C MUTATED    11   0   0   1
  FAM55C WILD-TYPE 216  10  10  23
D355V10, multiclass
    clus
vv   FAM55C MUTATED FAM55C WILD-TYPE
  R0             11              216
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D355V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM55C MUTATED       3                         0     6
  FAM55C WILD-TYPE    73                         4   162
D355V12, multiclass
                           clus
vv                          FAM55C MUTATED FAM55C WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(356) Variable = SLC25A17 MUTATION ANALYSIS
D356V1, survival
                    sevent
clus2                  0   1
  SLC25A17 MUTATED     1   2
  SLC25A17 WILD-TYPE 180  78
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 3                258 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 2                 78 
$`SLC25A17 MUTATED`
TCGA-BR-7851 TCGA-CD-A4MG TCGA-CG-4306 
       12.43         6.58         1.02 

$`SLC25A17 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
              1.02               0.00 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
             12.43             105.07 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
              6.58              12.71 
[1] "1.0 - 12.4 (6.6)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "5.3"
D356V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC25A17 MUTATED         0        0        0        0         1         1
  SLC25A17 WILD-TYPE       1        9       27       26        30        43
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC25A17 MUTATED           0          0          0          0        1
  SLC25A17 WILD-TYPE         3         49         36         24       23
D356V3, multiclass
            clus
vv           SLC25A17 MUTATED SLC25A17 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  0                 27
  STAGE II                  0                 26
  STAGE IIA                 1                 30
  STAGE IIB                 1                 43
  STAGE III                 0                  3
  STAGE IIIA                0                 49
  STAGE IIIB                0                 36
  STAGE IIIC                0                 24
  STAGE IV                  1                 23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SLC25A17 MUTATED     0   0   2   1
  SLC25A17 WILD-TYPE  11  72 120  74
D356V4, multiclass
    clus
vv   SLC25A17 MUTATED SLC25A17 WILD-TYPE
  T1                0                 11
  T2                0                 72
  T3                2                120
  T4                1                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  SLC25A17 MUTATED    2  0  1  0
  SLC25A17 WILD-TYPE 91 81 49 53
D356V5, multiclass
    clus
vv   SLC25A17 MUTATED SLC25A17 WILD-TYPE
  N0                2                 91
  N1                0                 81
  N2                1                 49
  N3                0                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D356V6, binary
                    cls
clus                   0   1
  SLC25A17 MUTATED     3   1
  SLC25A17 WILD-TYPE 254  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A17 MUTATED      3    1
  SLC25A17 WILD-TYPE  254   17
   clus
vv  SLC25A17 MUTATED SLC25A17 WILD-TYPE
  0                3                254
  1                1                 17
[1] 2 2
[1] FALSE
D356V7, binary
                    cls
clus                   0   1
  SLC25A17 MUTATED     1   3
  SLC25A17 WILD-TYPE 109 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A17 MUTATED      1    3
  SLC25A17 WILD-TYPE  109  176
        clus
vv       SLC25A17 MUTATED SLC25A17 WILD-TYPE
  FEMALE                1                109
  MALE                  3                176
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SLC25A17 MUTATED                                       1
  SLC25A17 WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC25A17 MUTATED                                                        2
  SLC25A17 WILD-TYPE                                                    133
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC25A17 MUTATED                                                                   1
  SLC25A17 WILD-TYPE                                                                39
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SLC25A17 MUTATED                                                  0
  SLC25A17 WILD-TYPE                                               38
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SLC25A17 MUTATED                                                          0
  SLC25A17 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SLC25A17 MUTATED                                                           0
  SLC25A17 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SLC25A17 MUTATED                                          0
  SLC25A17 WILD-TYPE                                        3
D356V8, multiclass
                                                                   clus
vv                                                                  SLC25A17 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  SLC25A17 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D356V9, binary
                    cls
clus                   0   1
  SLC25A17 MUTATED     0   4
  SLC25A17 WILD-TYPE   5 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A17 MUTATED      0    4
  SLC25A17 WILD-TYPE    5  280
     clus
vv    SLC25A17 MUTATED SLC25A17 WILD-TYPE
  NO                 0                  5
  YES                4                280
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  SLC25A17 MUTATED     1   0   1   1
  SLC25A17 WILD-TYPE 226  10   9  23
D356V10, multiclass
    clus
vv   SLC25A17 MUTATED SLC25A17 WILD-TYPE
  R0                1                226
  R1                0                 10
  R2                1                  9
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D356V11, continuous
[1] "Remove cluster labels:" "SLC25A17 MUTATED"      
clus
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 1                250 
        TCGA-B7-5816         TCGA-BR-4183         TCGA-BR-4184 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-4188         TCGA-BR-4191         TCGA-BR-4253 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-4255         TCGA-BR-4256         TCGA-BR-4267 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-4279         TCGA-BR-4280         TCGA-BR-4361 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-4362         TCGA-BR-4368         TCGA-BR-6452 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-6453         TCGA-BR-6454         TCGA-BR-6455 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-6456         TCGA-BR-6457         TCGA-BR-6458 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6710         TCGA-BR-6801 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-6802         TCGA-BR-6803         TCGA-BR-6852 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-7196         TCGA-BR-7197         TCGA-BR-7703 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-7707         TCGA-BR-7715         TCGA-BR-7716 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-7717         TCGA-BR-7722         TCGA-BR-7723 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8058         TCGA-BR-8059 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8286 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8289         TCGA-BR-8291         TCGA-BR-8295 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8296         TCGA-BR-8297         TCGA-BR-8360 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8361         TCGA-BR-8363         TCGA-BR-8364 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8365         TCGA-BR-8366         TCGA-BR-8367 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8368         TCGA-BR-8369         TCGA-BR-8370 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8371         TCGA-BR-8372         TCGA-BR-8373 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8380         TCGA-BR-8381         TCGA-BR-8382 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8384         TCGA-BR-8483         TCGA-BR-8484 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8485         TCGA-BR-8486         TCGA-BR-8487 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8588         TCGA-BR-8589         TCGA-BR-8590 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8591         TCGA-BR-8592         TCGA-BR-8676 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8677         TCGA-BR-8678         TCGA-BR-8679 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8680         TCGA-BR-8682         TCGA-BR-8683 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8686         TCGA-BR-8687         TCGA-BR-8690 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-A44T         TCGA-BR-A44U         TCGA-BR-A452 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-A453         TCGA-BR-A4CQ         TCGA-BR-A4CR 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-A4CS         TCGA-BR-A4IU         TCGA-BR-A4IV 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J6 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-A4J8         TCGA-BR-A4PD         TCGA-BR-A4PE 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-A4QM         TCGA-CD-5804         TCGA-CD-8525 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CD-8526         TCGA-CD-8531         TCGA-CD-8535 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CD-A487         TCGA-CG-4301         TCGA-CG-4304 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4436         TCGA-CG-4437 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-4442         TCGA-CG-4443         TCGA-CG-4444 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4462 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4475         TCGA-CG-4476 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5717         TCGA-CG-5718 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-6822         TCGA-D7-8570         TCGA-D7-8572 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-8573         TCGA-D7-8574         TCGA-D7-8575 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-8576         TCGA-D7-8578         TCGA-D7-8579 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-A4YT         TCGA-D7-A4YU         TCGA-D7-A4YV 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-A4YX         TCGA-D7-A4YY         TCGA-D7-A4Z0 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-EQ-A4SO 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-F1-A448         TCGA-FP-7735         TCGA-FP-7829 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-FP-7916         TCGA-FP-7998         TCGA-FP-8099 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-FP-8209         TCGA-FP-8210         TCGA-FP-8211 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-FP-8631         TCGA-FP-A4BE         TCGA-FP-A4BF 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HF-7132         TCGA-HF-7133         TCGA-HF-7136 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HJ-7597         TCGA-HU-8243         TCGA-HU-8245 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-8249         TCGA-HU-8602         TCGA-HU-8604 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-8608         TCGA-HU-8610         TCGA-HU-A4G2 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-A4G3         TCGA-HU-A4G6         TCGA-HU-A4G8 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-A4G9         TCGA-HU-A4GC         TCGA-HU-A4GD 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-A4GF         TCGA-HU-A4GH         TCGA-HU-A4GN 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-A4GP         TCGA-HU-A4GQ         TCGA-HU-A4GT 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-A4GU         TCGA-HU-A4GX         TCGA-HU-A4GY 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-A4H0         TCGA-HU-A4H2         TCGA-HU-A4H3 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-A4H4         TCGA-HU-A4H5         TCGA-HU-A4H6 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-A4H8         TCGA-HU-A4HD         TCGA-IN-7806 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-IN-7808         TCGA-IN-8462         TCGA-IN-8663 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-IP-7968 
"SLC25A17 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC25A17 MUTATED       1                         0     2
  SLC25A17 WILD-TYPE    75                         4   166
D356V12, multiclass
                           clus
vv                          SLC25A17 MUTATED SLC25A17 WILD-TYPE
  ASIAN                                    1                 75
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    2                166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(357) Variable = ZNF626 MUTATION ANALYSIS
D357V1, survival
                  sevent
clus2                0   1
  ZNF626 MUTATED    11   3
  ZNF626 WILD-TYPE 170  77
  ZNF626 MUTATED ZNF626 WILD-TYPE 
              14              247 
  ZNF626 MUTATED ZNF626 WILD-TYPE 
               3               77 
$`ZNF626 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8360 
       26.70        34.68        30.90        12.26         8.05         6.18 
TCGA-BR-8683 TCGA-CD-8535 TCGA-CG-4477 TCGA-D7-8573 TCGA-D7-A4Z0 TCGA-FP-7916 
        9.86         0.13        30.97        19.50        14.76        14.07 
TCGA-HU-A4G9 TCGA-HU-A4H5 
       24.20        12.30 

$`ZNF626 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        0.69         9.60        20.55        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20        15.58         7.40        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        15.81        16.44        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-EQ-5647 TCGA-EQ-8122 
       16.44         5.92        15.16        13.78         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        11.84         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        23.84         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  ZNF626 MUTATED ZNF626 WILD-TYPE 
            0.13             0.00 
  ZNF626 MUTATED ZNF626 WILD-TYPE 
           34.68           105.07 
  ZNF626 MUTATED ZNF626 WILD-TYPE 
          14.415           12.590 
[1] "0.1 - 34.7 (14.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2"  
D357V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF626 MUTATED         0        1        2        0         3         3
  ZNF626 WILD-TYPE       1        8       25       26        28        41
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF626 MUTATED           0          2          1          2        0
  ZNF626 WILD-TYPE         3         47         35         22       24
D357V3, multiclass
            clus
vv           ZNF626 MUTATED ZNF626 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                2               25
  STAGE II                0               26
  STAGE IIA               3               28
  STAGE IIB               3               41
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              1               35
  STAGE IIIC              2               22
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF626 MUTATED     1   3   5   5
  ZNF626 WILD-TYPE  10  69 117  70
D357V4, multiclass
    clus
vv   ZNF626 MUTATED ZNF626 WILD-TYPE
  T1              1               10
  T2              3               69
  T3              5              117
  T4              5               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZNF626 MUTATED    8  2  3  2
  ZNF626 WILD-TYPE 85 79 47 51
D357V5, multiclass
    clus
vv   ZNF626 MUTATED ZNF626 WILD-TYPE
  N0              8               85
  N1              2               79
  N2              3               47
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D357V6, binary
                  cls
clus                 0   1
  ZNF626 MUTATED    14   0
  ZNF626 WILD-TYPE 243  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF626 MUTATED     14    0
  ZNF626 WILD-TYPE  243   18
   clus
vv  ZNF626 MUTATED ZNF626 WILD-TYPE
  0             14              243
  1              0               18
[1] 2 2
[1] FALSE
D357V7, binary
                  cls
clus                 0   1
  ZNF626 MUTATED     7   8
  ZNF626 WILD-TYPE 103 171
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF626 MUTATED      7    8
  ZNF626 WILD-TYPE  103  171
        clus
vv       ZNF626 MUTATED ZNF626 WILD-TYPE
  FEMALE              7              103
  MALE                8              171
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZNF626 MUTATED                                       2
  ZNF626 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF626 MUTATED                                                        5
  ZNF626 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF626 MUTATED                                                                   3
  ZNF626 WILD-TYPE                                                                37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZNF626 MUTATED                                                  3
  ZNF626 WILD-TYPE                                               35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZNF626 MUTATED                                                          1
  ZNF626 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZNF626 MUTATED                                                           1
  ZNF626 WILD-TYPE                                                         5
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZNF626 MUTATED                                          0
  ZNF626 WILD-TYPE                                        3
D357V8, multiclass
                                                                   clus
vv                                                                  ZNF626 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ZNF626 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D357V9, binary
                  cls
clus                 0   1
  ZNF626 MUTATED     0  15
  ZNF626 WILD-TYPE   5 269
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF626 MUTATED      0   15
  ZNF626 WILD-TYPE    5  269
     clus
vv    ZNF626 MUTATED ZNF626 WILD-TYPE
  NO               0                5
  YES             15              269
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF626 MUTATED    13   0   0   1
  ZNF626 WILD-TYPE 214  10  10  23
D357V10, multiclass
    clus
vv   ZNF626 MUTATED ZNF626 WILD-TYPE
  R0             13              214
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D357V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF626 MUTATED       5                         0     9
  ZNF626 WILD-TYPE    71                         4   159
D357V12, multiclass
                           clus
vv                          ZNF626 MUTATED ZNF626 WILD-TYPE
  ASIAN                                  5               71
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  9              159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(358) Variable = OPLAH MUTATION ANALYSIS
D358V1, survival
                 sevent
clus2               0   1
  OPLAH MUTATED     7   3
  OPLAH WILD-TYPE 174  77
  OPLAH MUTATED OPLAH WILD-TYPE 
             10             251 
  OPLAH MUTATED OPLAH WILD-TYPE 
              3              77 
$`OPLAH MUTATED`
TCGA-BR-7703 TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-A4J1 
       24.76        18.71        12.26         4.31        19.17         0.72 
TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-5721 TCGA-HU-A4GQ 
       11.57         6.58         6.02         0.10 

$`OPLAH WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       28.73        12.43         3.45         9.07        12.76        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  OPLAH MUTATED OPLAH WILD-TYPE 
            0.1             0.0 
  OPLAH MUTATED OPLAH WILD-TYPE 
          24.76          105.07 
  OPLAH MUTATED OPLAH WILD-TYPE 
          9.075          12.760 
[1] "0.1 - 24.8 (9.1)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.4"
D358V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OPLAH MUTATED         1        1        2        0         1         1
  OPLAH WILD-TYPE       0        8       25       26        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OPLAH MUTATED           0          3          1          2        1
  OPLAH WILD-TYPE         3         46         35         22       23
D358V3, multiclass
            clus
vv           OPLAH MUTATED OPLAH WILD-TYPE
  STAGE I                1               0
  STAGE IA               1               8
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             3              46
  STAGE IIIB             1              35
  STAGE IIIC             2              22
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OPLAH MUTATED     2   2   2   7
  OPLAH WILD-TYPE   9  70 120  68
D358V4, multiclass
    clus
vv   OPLAH MUTATED OPLAH WILD-TYPE
  T1             2               9
  T2             2              70
  T3             2             120
  T4             7              68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  OPLAH MUTATED    6  5  1  2
  OPLAH WILD-TYPE 87 76 49 51
D358V5, multiclass
    clus
vv   OPLAH MUTATED OPLAH WILD-TYPE
  N0             6              87
  N1             5              76
  N2             1              49
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D358V6, binary
                 cls
clus                0   1
  OPLAH MUTATED    13   0
  OPLAH WILD-TYPE 244  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPLAH MUTATED     13    0
  OPLAH WILD-TYPE  244   18
   clus
vv  OPLAH MUTATED OPLAH WILD-TYPE
  0            13             244
  1             0              18
[1] 2 2
[1] FALSE
D358V7, binary
                 cls
clus                0   1
  OPLAH MUTATED     5   9
  OPLAH WILD-TYPE 105 170
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPLAH MUTATED      5    9
  OPLAH WILD-TYPE  105  170
        clus
vv       OPLAH MUTATED OPLAH WILD-TYPE
  FEMALE             5             105
  MALE               9             170
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  OPLAH MUTATED                                       1
  OPLAH WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OPLAH MUTATED                                                        8
  OPLAH WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OPLAH MUTATED                                                                   2
  OPLAH WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  OPLAH MUTATED                                                  1
  OPLAH WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  OPLAH MUTATED                                                          1
  OPLAH WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  OPLAH MUTATED                                                           1
  OPLAH WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  OPLAH MUTATED                                          0
  OPLAH WILD-TYPE                                        3
D358V8, multiclass
                                                                   clus
vv                                                                  OPLAH MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  OPLAH WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D358V9, binary
                 cls
clus                0   1
  OPLAH MUTATED     0  14
  OPLAH WILD-TYPE   5 270
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPLAH MUTATED      0   14
  OPLAH WILD-TYPE    5  270
     clus
vv    OPLAH MUTATED OPLAH WILD-TYPE
  NO              0               5
  YES            14             270
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OPLAH MUTATED    11   0   0   2
  OPLAH WILD-TYPE 216  10  10  22
D358V10, multiclass
    clus
vv   OPLAH MUTATED OPLAH WILD-TYPE
  R0            11             216
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D358V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OPLAH MUTATED       3                         1     8
  OPLAH WILD-TYPE    73                         3   160
D358V12, multiclass
                           clus
vv                          OPLAH MUTATED OPLAH WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 8             160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(359) Variable = MYOCD MUTATION ANALYSIS
D359V1, survival
                 sevent
clus2               0   1
  MYOCD MUTATED     9   3
  MYOCD WILD-TYPE 172  77
  MYOCD MUTATED MYOCD WILD-TYPE 
             12             249 
  MYOCD MUTATED MYOCD WILD-TYPE 
              3              77 
$`MYOCD MUTATED`
TCGA-BR-4201 TCGA-BR-8363 TCGA-BR-8591 TCGA-BR-8686 TCGA-BR-A4J4 TCGA-BR-A4QL 
       30.90         0.26        13.45        15.68         0.53        11.57 
TCGA-CD-8529 TCGA-CG-5721 TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-F1-6874 TCGA-HU-A4GX 
        0.13         6.02         5.92        14.76        14.47        10.19 

$`MYOCD WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        19.50        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        9.86         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        8.98         0.72        14.17         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
        0.07         0.07         0.07         0.07         0.10         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-EQ-5647 
       20.91        14.27        16.44        15.16        13.78         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.99        16.24        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  MYOCD MUTATED MYOCD WILD-TYPE 
           0.13            0.00 
  MYOCD MUTATED MYOCD WILD-TYPE 
          30.90          105.07 
  MYOCD MUTATED MYOCD WILD-TYPE 
          10.88           12.66 
[1] "0.1 - 30.9 (10.9)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.1"
D359V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MYOCD MUTATED         1        0        2        0         0         2
  MYOCD WILD-TYPE       0        9       25       26        31        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MYOCD MUTATED           0          0          3          2        2
  MYOCD WILD-TYPE         3         49         33         22       22
D359V3, multiclass
            clus
vv           MYOCD MUTATED MYOCD WILD-TYPE
  STAGE I                1               0
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              0              31
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             3              33
  STAGE IIIC             2              22
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYOCD MUTATED     1   4   2   6
  MYOCD WILD-TYPE  10  68 120  69
D359V4, multiclass
    clus
vv   MYOCD MUTATED MYOCD WILD-TYPE
  T1             1              10
  T2             4              68
  T3             2             120
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  MYOCD MUTATED    3  4  3  2
  MYOCD WILD-TYPE 90 77 47 51
D359V5, multiclass
    clus
vv   MYOCD MUTATED MYOCD WILD-TYPE
  N0             3              90
  N1             4              77
  N2             3              47
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D359V6, binary
                 cls
clus                0   1
  MYOCD MUTATED    11   1
  MYOCD WILD-TYPE 246  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYOCD MUTATED     11    1
  MYOCD WILD-TYPE  246   17
   clus
vv  MYOCD MUTATED MYOCD WILD-TYPE
  0            11             246
  1             1              17
[1] 2 2
[1] FALSE
D359V7, binary
                 cls
clus                0   1
  MYOCD MUTATED     6   7
  MYOCD WILD-TYPE 104 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYOCD MUTATED      6    7
  MYOCD WILD-TYPE  104  172
        clus
vv       MYOCD MUTATED MYOCD WILD-TYPE
  FEMALE             6             104
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MYOCD MUTATED                                       1
  MYOCD WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MYOCD MUTATED                                                        6
  MYOCD WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MYOCD MUTATED                                                                   2
  MYOCD WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MYOCD MUTATED                                                  2
  MYOCD WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MYOCD MUTATED                                                          2
  MYOCD WILD-TYPE                                                       14
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MYOCD MUTATED                                                           0
  MYOCD WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MYOCD MUTATED                                          0
  MYOCD WILD-TYPE                                        3
D359V8, multiclass
                                                                   clus
vv                                                                  MYOCD MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  MYOCD WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D359V9, binary
                 cls
clus                0   1
  MYOCD MUTATED     0  13
  MYOCD WILD-TYPE   5 271
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYOCD MUTATED      0   13
  MYOCD WILD-TYPE    5  271
     clus
vv    MYOCD MUTATED MYOCD WILD-TYPE
  NO              0               5
  YES            13             271
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MYOCD MUTATED    12   0   0   1
  MYOCD WILD-TYPE 215  10  10  23
D359V10, multiclass
    clus
vv   MYOCD MUTATED MYOCD WILD-TYPE
  R0            12             215
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D359V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MYOCD MUTATED       4                         1     7
  MYOCD WILD-TYPE    72                         3   161
D359V12, multiclass
                           clus
vv                          MYOCD MUTATED MYOCD WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 7             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(360) Variable = NRAS MUTATION ANALYSIS
D360V1, survival
                sevent
clus2              0   1
  NRAS MUTATED     1   3
  NRAS WILD-TYPE 180  77
  NRAS MUTATED NRAS WILD-TYPE 
             4            257 
  NRAS MUTATED NRAS WILD-TYPE 
             3             77 
$`NRAS MUTATED`
TCGA-BR-6455 TCGA-CD-8536 TCGA-CD-A489 TCGA-HJ-7597 
       13.87         0.10        11.31        26.47 

$`NRAS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A 
        0.10         0.10         0.13         3.42         9.34        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 
        5.03        13.58         0.56        11.08         5.52         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  NRAS MUTATED NRAS WILD-TYPE 
           0.1            0.0 
  NRAS MUTATED NRAS WILD-TYPE 
         26.47         105.07 
  NRAS MUTATED NRAS WILD-TYPE 
         12.59          12.62 
[1] "0.1 - 26.5 (12.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.6"
D360V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NRAS MUTATED         0        0        1        1         1         1
  NRAS WILD-TYPE       1        9       26       25        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NRAS MUTATED           0          0          0          0        0
  NRAS WILD-TYPE         3         49         36         24       24
D360V3, multiclass
            clus
vv           NRAS MUTATED NRAS WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              1             25
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NRAS MUTATED     0   1   3   0
  NRAS WILD-TYPE  11  71 119  75
D360V4, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  T1            0             11
  T2            1             71
  T3            3            119
  T4            0             75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  NRAS MUTATED    3  1  0  0
  NRAS WILD-TYPE 90 80 50 53
D360V5, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  N0            3             90
  N1            1             80
  N2            0             50
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D360V6, binary
                cls
clus               0   1
  NRAS MUTATED     3   0
  NRAS WILD-TYPE 254  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      3    0
  NRAS WILD-TYPE  254   18
   clus
vv  NRAS MUTATED NRAS WILD-TYPE
  0            3            254
  1            0             18
[1] 2 2
[1] FALSE
D360V7, binary
                cls
clus               0   1
  NRAS MUTATED     1   3
  NRAS WILD-TYPE 109 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      1    3
  NRAS WILD-TYPE  109  176
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE            1            109
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NRAS MUTATED                                       1
  NRAS WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NRAS MUTATED                                                        2
  NRAS WILD-TYPE                                                    133
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NRAS MUTATED                                                                   0
  NRAS WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NRAS MUTATED                                                  0
  NRAS WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NRAS MUTATED                                                          0
  NRAS WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NRAS MUTATED                                                           0
  NRAS WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NRAS MUTATED                                          1
  NRAS WILD-TYPE                                        2
D360V8, multiclass
                                                                   clus
vv                                                                  NRAS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  NRAS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D360V9, binary
                cls
clus               0   1
  NRAS MUTATED     0   4
  NRAS WILD-TYPE   5 280
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0    4
  NRAS WILD-TYPE    5  280
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO             0              5
  YES            4            280
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NRAS MUTATED     3   0   0   0
  NRAS WILD-TYPE 224  10  10  24
D360V10, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  R0            3            224
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D360V11, continuous
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             2            249 
    TCGA-B7-5816     TCGA-BR-4183     TCGA-BR-4184     TCGA-BR-4188 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-4191     TCGA-BR-4253     TCGA-BR-4255     TCGA-BR-4256 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-4267     TCGA-BR-4279     TCGA-BR-4280     TCGA-BR-4361 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-4362     TCGA-BR-4368     TCGA-BR-6452     TCGA-BR-6453 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-6454     TCGA-BR-6456     TCGA-BR-6457     TCGA-BR-6458 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-6563     TCGA-BR-6564     TCGA-BR-6565     TCGA-BR-6566 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-6705     TCGA-BR-6706     TCGA-BR-6707     TCGA-BR-6710 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-6801     TCGA-BR-6802     TCGA-BR-6803     TCGA-BR-6852 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-7196     TCGA-BR-7197     TCGA-BR-7703     TCGA-BR-7707 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-7715     TCGA-BR-7716     TCGA-BR-7717     TCGA-BR-7722 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-7723     TCGA-BR-7851     TCGA-BR-7901     TCGA-BR-7957 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-7958     TCGA-BR-7959     TCGA-BR-8058     TCGA-BR-8059 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-8077     TCGA-BR-8078     TCGA-BR-8080     TCGA-BR-8081 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-8284     TCGA-BR-8286     TCGA-BR-8289     TCGA-BR-8291 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-8295     TCGA-BR-8296     TCGA-BR-8297     TCGA-BR-8360 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-8361     TCGA-BR-8363     TCGA-BR-8364     TCGA-BR-8365 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-8366     TCGA-BR-8367     TCGA-BR-8368     TCGA-BR-8369 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-8370     TCGA-BR-8371     TCGA-BR-8372     TCGA-BR-8373 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-8380     TCGA-BR-8381     TCGA-BR-8382     TCGA-BR-8384 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-8483     TCGA-BR-8484     TCGA-BR-8485     TCGA-BR-8486 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-8487     TCGA-BR-8588     TCGA-BR-8589     TCGA-BR-8590 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-8591     TCGA-BR-8592     TCGA-BR-8676     TCGA-BR-8677 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-8678     TCGA-BR-8679     TCGA-BR-8680     TCGA-BR-8682 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-8683     TCGA-BR-8686     TCGA-BR-8687     TCGA-BR-8690 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-A44T     TCGA-BR-A44U     TCGA-BR-A452     TCGA-BR-A453 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-A4CQ     TCGA-BR-A4CR     TCGA-BR-A4CS     TCGA-BR-A4IU 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-A4IV     TCGA-BR-A4IY     TCGA-BR-A4IZ     TCGA-BR-A4J1 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-A4J2     TCGA-BR-A4J4     TCGA-BR-A4J6     TCGA-BR-A4J8 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-A4PD     TCGA-BR-A4PE     TCGA-BR-A4PF     TCGA-BR-A4QI 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BR-A4QL     TCGA-BR-A4QM     TCGA-CD-5804     TCGA-CD-8525 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-CD-8526     TCGA-CD-8531     TCGA-CD-8535     TCGA-CD-A487 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-CG-4301     TCGA-CG-4304     TCGA-CG-4305     TCGA-CG-4436 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-CG-4437     TCGA-CG-4438     TCGA-CG-4440     TCGA-CG-4441 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-CG-4442     TCGA-CG-4443     TCGA-CG-4444     TCGA-CG-4449 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-CG-4455     TCGA-CG-4462     TCGA-CG-4465     TCGA-CG-4466 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-CG-4469     TCGA-CG-4474     TCGA-CG-4475     TCGA-CG-4476 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-CG-4477     TCGA-CG-5717     TCGA-CG-5718     TCGA-CG-5719 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-CG-5720     TCGA-CG-5721     TCGA-CG-5722     TCGA-CG-5723 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-CG-5724     TCGA-CG-5726     TCGA-CG-5727     TCGA-CG-5728 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-CG-5730     TCGA-CG-5732     TCGA-CG-5733     TCGA-CG-5734 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D7-5577     TCGA-D7-5578     TCGA-D7-5579     TCGA-D7-6518 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D7-6519     TCGA-D7-6520     TCGA-D7-6521     TCGA-D7-6522 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D7-6524     TCGA-D7-6525     TCGA-D7-6526     TCGA-D7-6527 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D7-6528     TCGA-D7-6815     TCGA-D7-6817     TCGA-D7-6818 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D7-6820     TCGA-D7-6822     TCGA-D7-8570     TCGA-D7-8572 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D7-8573     TCGA-D7-8574     TCGA-D7-8575     TCGA-D7-8576 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D7-8578     TCGA-D7-8579     TCGA-D7-A4YT     TCGA-D7-A4YU 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D7-A4YV     TCGA-D7-A4YX     TCGA-D7-A4YY     TCGA-D7-A4Z0 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-EQ-5647     TCGA-EQ-8122     TCGA-EQ-A4SO     TCGA-F1-6177 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-F1-6874     TCGA-F1-6875     TCGA-F1-A448     TCGA-FP-7735 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-FP-7829     TCGA-FP-7916     TCGA-FP-7998     TCGA-FP-8099 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-FP-8209     TCGA-FP-8210     TCGA-FP-8211     TCGA-FP-8631 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-FP-A4BE     TCGA-FP-A4BF     TCGA-HF-7132     TCGA-HF-7133 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-HF-7136     TCGA-HU-8243     TCGA-HU-8245     TCGA-HU-8249 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-HU-8602     TCGA-HU-8604     TCGA-HU-8608     TCGA-HU-8610 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-HU-A4G2     TCGA-HU-A4G3     TCGA-HU-A4G6     TCGA-HU-A4G8 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-HU-A4G9     TCGA-HU-A4GC     TCGA-HU-A4GD     TCGA-HU-A4GF 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-HU-A4GH     TCGA-HU-A4GN     TCGA-HU-A4GP     TCGA-HU-A4GQ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-HU-A4GT     TCGA-HU-A4GU     TCGA-HU-A4GX     TCGA-HU-A4GY 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-HU-A4H0     TCGA-HU-A4H2     TCGA-HU-A4H3     TCGA-HU-A4H4 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-HU-A4H5     TCGA-HU-A4H6     TCGA-HU-A4H8     TCGA-HU-A4HD 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-IN-7806     TCGA-IN-7808     TCGA-IN-8462     TCGA-IN-8663 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-IP-7968 
"NRAS WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NRAS MUTATED       2                         0     2
  NRAS WILD-TYPE    74                         4   166
D360V12, multiclass
                           clus
vv                          NRAS MUTATED NRAS WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                2            166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(361) Variable = SEC24C MUTATION ANALYSIS
D361V1, survival
                  sevent
clus2                0   1
  SEC24C MUTATED     5   3
  SEC24C WILD-TYPE 176  77
  SEC24C MUTATED SEC24C WILD-TYPE 
               8              253 
  SEC24C MUTATED SEC24C WILD-TYPE 
               3               77 
$`SEC24C MUTATED`
TCGA-BR-6566 TCGA-CG-5726 TCGA-EQ-5647 TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-A4G8 
       32.78        28.96         0.62        11.08        26.47        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GU 
       24.20         6.25 

$`SEC24C WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 
        0.99         6.02         0.99       105.07        12.03        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
       14.76         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 
        5.03        13.58         0.56         5.52         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
        5.59        12.30         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  SEC24C MUTATED SEC24C WILD-TYPE 
            0.62             0.00 
  SEC24C MUTATED SEC24C WILD-TYPE 
           32.78           105.07 
  SEC24C MUTATED SEC24C WILD-TYPE 
           18.02            12.62 
[1] "0.6 - 32.8 (18.0)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D361V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SEC24C MUTATED         1        2        1        0         2         2
  SEC24C WILD-TYPE       0        7       26       26        29        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SEC24C MUTATED           0          0          0          0        1
  SEC24C WILD-TYPE         3         49         36         24       23
D361V3, multiclass
            clus
vv           SEC24C MUTATED SEC24C WILD-TYPE
  STAGE I                 1                0
  STAGE IA                2                7
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               2               29
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SEC24C MUTATED     3   1   4   1
  SEC24C WILD-TYPE   8  71 118  74
D361V4, multiclass
    clus
vv   SEC24C MUTATED SEC24C WILD-TYPE
  T1              3                8
  T2              1               71
  T3              4              118
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  SEC24C MUTATED    5  3  0  1
  SEC24C WILD-TYPE 88 78 50 52
D361V5, multiclass
    clus
vv   SEC24C MUTATED SEC24C WILD-TYPE
  N0              5               88
  N1              3               78
  N2              0               50
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D361V6, binary
                  cls
clus                 0   1
  SEC24C MUTATED     7   1
  SEC24C WILD-TYPE 250  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC24C MUTATED      7    1
  SEC24C WILD-TYPE  250   17
   clus
vv  SEC24C MUTATED SEC24C WILD-TYPE
  0              7              250
  1              1               17
[1] 2 2
[1] FALSE
D361V7, binary
                  cls
clus                 0   1
  SEC24C MUTATED     6   4
  SEC24C WILD-TYPE 104 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC24C MUTATED      6    4
  SEC24C WILD-TYPE  104  175
        clus
vv       SEC24C MUTATED SEC24C WILD-TYPE
  FEMALE              6              104
  MALE                4              175
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SEC24C MUTATED                                       2
  SEC24C WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SEC24C MUTATED                                                        5
  SEC24C WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SEC24C MUTATED                                                                   1
  SEC24C WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SEC24C MUTATED                                                  1
  SEC24C WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SEC24C MUTATED                                                          0
  SEC24C WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SEC24C MUTATED                                                           0
  SEC24C WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SEC24C MUTATED                                          1
  SEC24C WILD-TYPE                                        2
D361V8, multiclass
                                                                   clus
vv                                                                  SEC24C MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       1
                                                                   clus
vv                                                                  SEC24C WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D361V9, binary
                  cls
clus                 0   1
  SEC24C MUTATED     0  10
  SEC24C WILD-TYPE   5 274
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC24C MUTATED      0   10
  SEC24C WILD-TYPE    5  274
     clus
vv    SEC24C MUTATED SEC24C WILD-TYPE
  NO               0                5
  YES             10              274
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SEC24C MUTATED     7   0   1   1
  SEC24C WILD-TYPE 220  10   9  23
D361V10, multiclass
    clus
vv   SEC24C MUTATED SEC24C WILD-TYPE
  R0              7              220
  R1              0               10
  R2              1                9
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D361V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SEC24C MUTATED       3                         2     4
  SEC24C WILD-TYPE    73                         2   164
D361V12, multiclass
                           clus
vv                          SEC24C MUTATED SEC24C WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              2                2
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(362) Variable = CEP57 MUTATION ANALYSIS
D362V1, survival
                 sevent
clus2               0   1
  CEP57 MUTATED     5   1
  CEP57 WILD-TYPE 176  79
  CEP57 MUTATED CEP57 WILD-TYPE 
              6             255 
  CEP57 MUTATED CEP57 WILD-TYPE 
              1              79 
$`CEP57 MUTATED`
TCGA-BR-4184 TCGA-BR-6566 TCGA-BR-8382 TCGA-CG-5721 TCGA-F1-6874 TCGA-HU-A4H3 
        6.97        32.78        15.85         6.02        14.47        19.36 

$`CEP57 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.99        16.24        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.25        10.19         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  CEP57 MUTATED CEP57 WILD-TYPE 
           6.02            0.00 
  CEP57 MUTATED CEP57 WILD-TYPE 
          32.78          105.07 
  CEP57 MUTATED CEP57 WILD-TYPE 
          15.16           12.59 
[1] "6.0 - 32.8 (15.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.2"
D362V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CEP57 MUTATED         0        0        1        0         1         0
  CEP57 WILD-TYPE       1        9       26       26        30        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEP57 MUTATED           0          2          0          2        1
  CEP57 WILD-TYPE         3         47         36         22       23
D362V3, multiclass
            clus
vv           CEP57 MUTATED CEP57 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             0              36
  STAGE IIIC             2              22
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CEP57 MUTATED     0   1   2   4
  CEP57 WILD-TYPE  11  71 120  71
D362V4, multiclass
    clus
vv   CEP57 MUTATED CEP57 WILD-TYPE
  T1             0              11
  T2             1              71
  T3             2             120
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CEP57 MUTATED    3  2  0  2
  CEP57 WILD-TYPE 90 79 50 51
D362V5, multiclass
    clus
vv   CEP57 MUTATED CEP57 WILD-TYPE
  N0             3              90
  N1             2              79
  N2             0              50
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D362V6, binary
                 cls
clus                0   1
  CEP57 MUTATED     6   0
  CEP57 WILD-TYPE 251  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEP57 MUTATED      6    0
  CEP57 WILD-TYPE  251   18
   clus
vv  CEP57 MUTATED CEP57 WILD-TYPE
  0             6             251
  1             0              18
[1] 2 2
[1] FALSE
D362V7, binary
                 cls
clus                0   1
  CEP57 MUTATED     4   3
  CEP57 WILD-TYPE 106 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEP57 MUTATED      4    3
  CEP57 WILD-TYPE  106  176
        clus
vv       CEP57 MUTATED CEP57 WILD-TYPE
  FEMALE             4             106
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CEP57 MUTATED                                       1
  CEP57 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CEP57 MUTATED                                                        4
  CEP57 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CEP57 MUTATED                                                                   2
  CEP57 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CEP57 MUTATED                                                  0
  CEP57 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CEP57 MUTATED                                                          0
  CEP57 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CEP57 MUTATED                                                           0
  CEP57 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CEP57 MUTATED                                          0
  CEP57 WILD-TYPE                                        3
D362V8, multiclass
                                                                   clus
vv                                                                  CEP57 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  CEP57 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D362V9, binary
                 cls
clus                0   1
  CEP57 MUTATED     0   7
  CEP57 WILD-TYPE   5 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEP57 MUTATED      0    7
  CEP57 WILD-TYPE    5  277
     clus
vv    CEP57 MUTATED CEP57 WILD-TYPE
  NO              0               5
  YES             7             277
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CEP57 MUTATED     5   0   0   2
  CEP57 WILD-TYPE 222  10  10  22
D362V10, multiclass
    clus
vv   CEP57 MUTATED CEP57 WILD-TYPE
  R0             5             222
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D362V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CEP57 MUTATED       1                         0     5
  CEP57 WILD-TYPE    75                         4   163
D362V12, multiclass
                           clus
vv                          CEP57 MUTATED CEP57 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(363) Variable = TMEM55A MUTATION ANALYSIS
D363V1, survival
                   sevent
clus2                 0   1
  TMEM55A MUTATED     2   0
  TMEM55A WILD-TYPE 179  80
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                2               259 
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                0                80 
$`TMEM55A MUTATED`
TCGA-BR-8361 TCGA-CD-A4MI 
        19.5          0.1 

$`TMEM55A WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  TMEM55A MUTATED TMEM55A WILD-TYPE 
              0.1               0.0 
  TMEM55A MUTATED TMEM55A WILD-TYPE 
            19.50            105.07 
  TMEM55A MUTATED TMEM55A WILD-TYPE 
             9.80             12.62 
[1] "0.1 - 19.5 (9.8)"   "0.0 - 105.1 (12.6)"
[1] "Remove cluster labels:" "TMEM55A MUTATED"       
D363V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEM55A MUTATED         0        0        0        0         0         0
  TMEM55A WILD-TYPE       1        9       27       26        31        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM55A MUTATED           0          0          1          1        0
  TMEM55A WILD-TYPE         3         49         35         23       24
D363V3, multiclass
[1] "Remove cluster labels:" "TMEM55A MUTATED"       
clus
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                2               272 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4267        TCGA-BR-4279 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4280        TCGA-BR-4361        TCGA-BR-4368        TCGA-BR-6452 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6710        TCGA-BR-6801        TCGA-BR-6802 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196        TCGA-BR-7197 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7703        TCGA-BR-7707        TCGA-BR-7715        TCGA-BR-7716 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7717        TCGA-BR-7722        TCGA-BR-7723        TCGA-BR-7851 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7901        TCGA-BR-7957        TCGA-BR-7958        TCGA-BR-7959 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8058        TCGA-BR-8059        TCGA-BR-8077        TCGA-BR-8078 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284        TCGA-BR-8286 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8289        TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8297        TCGA-BR-8360        TCGA-BR-8363        TCGA-BR-8364 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8365        TCGA-BR-8366        TCGA-BR-8367        TCGA-BR-8368 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8369        TCGA-BR-8370        TCGA-BR-8371        TCGA-BR-8372 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8373        TCGA-BR-8380        TCGA-BR-8381        TCGA-BR-8382 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8384        TCGA-BR-8483        TCGA-BR-8484        TCGA-BR-8485 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8486        TCGA-BR-8487        TCGA-BR-8588        TCGA-BR-8589 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8590        TCGA-BR-8591        TCGA-BR-8592        TCGA-BR-8676 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8677        TCGA-BR-8678        TCGA-BR-8679        TCGA-BR-8680 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8682        TCGA-BR-8683        TCGA-BR-8686        TCGA-BR-8687 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8690        TCGA-BR-A44T        TCGA-BR-A44U        TCGA-BR-A452 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A453        TCGA-BR-A4CQ        TCGA-BR-A4CR        TCGA-BR-A4CS 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY        TCGA-BR-A4IZ 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4        TCGA-BR-A4J6 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4J7        TCGA-BR-A4J8        TCGA-BR-A4PD        TCGA-BR-A4PE 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-BR-A4QM 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804        TCGA-CD-5813 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-8524        TCGA-CD-8525        TCGA-CD-8526        TCGA-CD-8527 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-8528        TCGA-CD-8529        TCGA-CD-8530        TCGA-CD-8531 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-8532        TCGA-CD-8534        TCGA-CD-8535        TCGA-CD-8536 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-A486        TCGA-CD-A487        TCGA-CD-A489        TCGA-CD-A48A 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-A48C        TCGA-CD-A4MG        TCGA-CD-A4MH        TCGA-CD-A4MJ 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4462 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4474 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4475        TCGA-CG-4476        TCGA-CG-4477        TCGA-CG-5717 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5726 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-8570        TCGA-D7-8572        TCGA-D7-8573        TCGA-D7-8574 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-8575        TCGA-D7-8576        TCGA-D7-8578        TCGA-D7-8579 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A4YT        TCGA-D7-A4YU        TCGA-D7-A4YV        TCGA-D7-A4YX 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A4YY        TCGA-D7-A4Z0        TCGA-EQ-5647        TCGA-EQ-8122 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-EQ-A4SO        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-F1-A448        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8210 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-8211        TCGA-FP-8631        TCGA-FP-A4BE        TCGA-FP-A4BF 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HF-7132        TCGA-HF-7133        TCGA-HF-7136        TCGA-HJ-7597 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-8243        TCGA-HU-8245        TCGA-HU-8249        TCGA-HU-8602 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-8604        TCGA-HU-8608        TCGA-HU-8610        TCGA-HU-A4G2 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4G3        TCGA-HU-A4G6        TCGA-HU-A4G8        TCGA-HU-A4G9 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GC        TCGA-HU-A4GD        TCGA-HU-A4GF        TCGA-HU-A4GH 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GN        TCGA-HU-A4GP        TCGA-HU-A4GQ        TCGA-HU-A4GT 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GU        TCGA-HU-A4GX        TCGA-HU-A4GY        TCGA-HU-A4H0 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4H2        TCGA-HU-A4H3        TCGA-HU-A4H4        TCGA-HU-A4H5 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4H6        TCGA-HU-A4H8        TCGA-HU-A4HD        TCGA-IN-7806 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IN-7808        TCGA-IN-8462        TCGA-IN-8663        TCGA-IP-7968 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
                   vv
clus                 T1  T2  T3  T4
  TMEM55A MUTATED     0   0   1   1
  TMEM55A WILD-TYPE  11  72 121  74
D363V4, multiclass
[1] "Remove cluster labels:" "TMEM55A MUTATED"       
clus
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                2               278 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4201        TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4267 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4294 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4363        TCGA-BR-4368 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4371        TCGA-BR-6452        TCGA-BR-6453        TCGA-BR-6454 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457        TCGA-BR-6458 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565        TCGA-BR-6566 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707        TCGA-BR-6710 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7196        TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7707 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8058        TCGA-BR-8059 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297        TCGA-BR-8360 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8363        TCGA-BR-8364        TCGA-BR-8365        TCGA-BR-8366 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8367        TCGA-BR-8368        TCGA-BR-8369        TCGA-BR-8370 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8371        TCGA-BR-8372        TCGA-BR-8373        TCGA-BR-8380 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8381        TCGA-BR-8382        TCGA-BR-8384        TCGA-BR-8483 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8484        TCGA-BR-8485        TCGA-BR-8486        TCGA-BR-8487 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8588        TCGA-BR-8589        TCGA-BR-8590        TCGA-BR-8591 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-8676        TCGA-BR-8677        TCGA-BR-8678 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8679        TCGA-BR-8680        TCGA-BR-8682        TCGA-BR-8683 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8686        TCGA-BR-8687        TCGA-BR-8690        TCGA-BR-A44T 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A44U        TCGA-BR-A452        TCGA-BR-A453        TCGA-BR-A4CQ 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4CR        TCGA-BR-A4CS        TCGA-BR-A4IU        TCGA-BR-A4IV 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4IY        TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4J4        TCGA-BR-A4J6        TCGA-BR-A4J7        TCGA-BR-A4J8 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4PD        TCGA-BR-A4PE        TCGA-BR-A4PF        TCGA-BR-A4QI 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4QL        TCGA-BR-A4QM        TCGA-CD-5798        TCGA-CD-5799 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-5804        TCGA-CD-5813        TCGA-CD-8524        TCGA-CD-8525 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-8526        TCGA-CD-8527        TCGA-CD-8528        TCGA-CD-8529 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-8530        TCGA-CD-8531        TCGA-CD-8532        TCGA-CD-8534 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-8535        TCGA-CD-8536        TCGA-CD-A486        TCGA-CD-A487 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-A489        TCGA-CD-A48A        TCGA-CD-A48C        TCGA-CD-A4MG 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-A4MH        TCGA-CD-A4MJ        TCGA-CG-4300        TCGA-CG-4301 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4442        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-D7-8570        TCGA-D7-8572 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-8573        TCGA-D7-8574        TCGA-D7-8575        TCGA-D7-8576 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-8578        TCGA-D7-8579        TCGA-D7-A4YT        TCGA-D7-A4YU 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A4YV        TCGA-D7-A4YX        TCGA-D7-A4YY        TCGA-D7-A4Z0 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-EQ-A4SO        TCGA-F1-6177 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-F1-A448        TCGA-FP-7735 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8211        TCGA-FP-8631 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-A4BE        TCGA-FP-A4BF        TCGA-HF-7132        TCGA-HF-7133 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HF-7136        TCGA-HJ-7597        TCGA-HU-8243        TCGA-HU-8245 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-8249        TCGA-HU-8602        TCGA-HU-8604        TCGA-HU-8608 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-8610        TCGA-HU-A4G2        TCGA-HU-A4G3        TCGA-HU-A4G6 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4G8        TCGA-HU-A4G9        TCGA-HU-A4GC        TCGA-HU-A4GD 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GF        TCGA-HU-A4GH        TCGA-HU-A4GN        TCGA-HU-A4GP 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GQ        TCGA-HU-A4GT        TCGA-HU-A4GU        TCGA-HU-A4GX 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GY        TCGA-HU-A4H0        TCGA-HU-A4H2        TCGA-HU-A4H3 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4H4        TCGA-HU-A4H5        TCGA-HU-A4H6        TCGA-HU-A4H8 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4HD        TCGA-IN-7806        TCGA-IN-7808        TCGA-IN-8462 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IN-8663        TCGA-IP-7968 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
                   vv
clus                N0 N1 N2 N3
  TMEM55A MUTATED    0  2  1  0
  TMEM55A WILD-TYPE 93 79 49 53
D363V5, multiclass
    clus
vv   TMEM55A MUTATED TMEM55A WILD-TYPE
  N0               0                93
  N1               2                79
  N2               1                49
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D363V6, binary
                   cls
clus                  0   1
  TMEM55A MUTATED     3   0
  TMEM55A WILD-TYPE 254  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM55A MUTATED      3    0
  TMEM55A WILD-TYPE  254   18
   clus
vv  TMEM55A MUTATED TMEM55A WILD-TYPE
  0               3               254
  1               0                18
[1] 2 2
[1] FALSE
D363V7, binary
                   cls
clus                  0   1
  TMEM55A MUTATED     2   1
  TMEM55A WILD-TYPE 108 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM55A MUTATED      2    1
  TMEM55A WILD-TYPE  108  178
        clus
vv       TMEM55A MUTATED TMEM55A WILD-TYPE
  FEMALE               2               108
  MALE                 1               178
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TMEM55A MUTATED                                       0
  TMEM55A WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TMEM55A MUTATED                                                        3
  TMEM55A WILD-TYPE                                                    132
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TMEM55A MUTATED                                                                   0
  TMEM55A WILD-TYPE                                                                40
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TMEM55A MUTATED                                                  0
  TMEM55A WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TMEM55A MUTATED                                                          0
  TMEM55A WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TMEM55A MUTATED                                                           0
  TMEM55A WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TMEM55A MUTATED                                          0
  TMEM55A WILD-TYPE                                        3
D363V8, multiclass
                                                                   clus
vv                                                                  TMEM55A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  TMEM55A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D363V9, binary
                   cls
clus                  0   1
  TMEM55A MUTATED     0   3
  TMEM55A WILD-TYPE   5 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM55A MUTATED      0    3
  TMEM55A WILD-TYPE    5  281
     clus
vv    TMEM55A MUTATED TMEM55A WILD-TYPE
  NO                0                 5
  YES               3               281
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TMEM55A MUTATED     1   0   0   1
  TMEM55A WILD-TYPE 226  10  10  23
D363V10, multiclass
[1] "Remove cluster labels:" "TMEM55A MUTATED"       
clus
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                2               269 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4187        TCGA-BR-4188        TCGA-BR-4191        TCGA-BR-4201 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4294        TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4363 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4366        TCGA-BR-4368        TCGA-BR-4369        TCGA-BR-4370 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4371        TCGA-BR-6452        TCGA-BR-6453        TCGA-BR-6454 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457        TCGA-BR-6458 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565        TCGA-BR-6566 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707        TCGA-BR-6710 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7196        TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7707 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8058        TCGA-BR-8059 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297        TCGA-BR-8360 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8363        TCGA-BR-8364        TCGA-BR-8365        TCGA-BR-8366 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8367        TCGA-BR-8368        TCGA-BR-8369        TCGA-BR-8370 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8371        TCGA-BR-8372        TCGA-BR-8373        TCGA-BR-8380 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8381        TCGA-BR-8382        TCGA-BR-8384        TCGA-BR-8483 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8484        TCGA-BR-8485        TCGA-BR-8486        TCGA-BR-8487 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8588        TCGA-BR-8589        TCGA-BR-8590        TCGA-BR-8591 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-8676        TCGA-BR-8677        TCGA-BR-8678 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8679        TCGA-BR-8680        TCGA-BR-8682        TCGA-BR-8683 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8686        TCGA-BR-8687        TCGA-BR-8690        TCGA-BR-A44T 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A44U        TCGA-BR-A452        TCGA-BR-A453        TCGA-BR-A4CQ 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4CR        TCGA-BR-A4CS        TCGA-BR-A4IU        TCGA-BR-A4IV 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4IY        TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4J4        TCGA-BR-A4J6        TCGA-BR-A4J7        TCGA-BR-A4J8 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4PD        TCGA-BR-A4PE        TCGA-BR-A4PF        TCGA-BR-A4QI 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4QL        TCGA-BR-A4QM        TCGA-CD-5800        TCGA-CD-5801 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-5804        TCGA-CD-8524        TCGA-CD-8525        TCGA-CD-8526 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-8527        TCGA-CD-8528        TCGA-CD-8529        TCGA-CD-8530 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-8531        TCGA-CD-8532        TCGA-CD-8534        TCGA-CD-8535 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-8536        TCGA-CD-A487        TCGA-CG-4300        TCGA-CG-4301 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4442        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-D7-8570        TCGA-D7-8572 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-8573        TCGA-D7-8574        TCGA-D7-8575        TCGA-D7-8576 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-8578        TCGA-D7-8579        TCGA-D7-A4YT        TCGA-D7-A4YU 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A4YV        TCGA-D7-A4YX        TCGA-D7-A4YY        TCGA-D7-A4Z0 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-A4SO        TCGA-F1-6177        TCGA-F1-6874 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-F1-6875        TCGA-F1-A448        TCGA-FP-7735        TCGA-FP-7829 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8211 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-8631        TCGA-FP-A4BE        TCGA-FP-A4BF        TCGA-HF-7132 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HF-7133        TCGA-HF-7136        TCGA-HJ-7597        TCGA-HU-8243 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-8245        TCGA-HU-8249        TCGA-HU-8602        TCGA-HU-8604 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-8608        TCGA-HU-8610        TCGA-HU-A4G2        TCGA-HU-A4G3 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4G6        TCGA-HU-A4G9        TCGA-HU-A4GC        TCGA-HU-A4GD 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GF        TCGA-HU-A4GH        TCGA-HU-A4GN        TCGA-HU-A4GP 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GQ        TCGA-HU-A4GT        TCGA-HU-A4GU        TCGA-HU-A4GX 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GY        TCGA-HU-A4H0        TCGA-HU-A4H2        TCGA-HU-A4H3 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4H4        TCGA-HU-A4H5        TCGA-HU-A4H6        TCGA-HU-A4H8 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4HD        TCGA-IN-7806        TCGA-IN-8462        TCGA-IN-8663 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IP-7968 
"TMEM55A WILD-TYPE" 
D363V11, continuous
[1] "Remove cluster labels:" "TMEM55A MUTATED"       
clus
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                2               249 
       TCGA-B7-5816        TCGA-BR-4183        TCGA-BR-4184        TCGA-BR-4188 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4191        TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4361 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4368        TCGA-BR-6452        TCGA-BR-6453        TCGA-BR-6454 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457        TCGA-BR-6458 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565        TCGA-BR-6566 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707        TCGA-BR-6710 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7196        TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7707 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8058        TCGA-BR-8059 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297        TCGA-BR-8360 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8363        TCGA-BR-8364        TCGA-BR-8365        TCGA-BR-8366 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8367        TCGA-BR-8368        TCGA-BR-8369        TCGA-BR-8370 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8371        TCGA-BR-8372        TCGA-BR-8373        TCGA-BR-8380 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8381        TCGA-BR-8382        TCGA-BR-8384        TCGA-BR-8483 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8484        TCGA-BR-8485        TCGA-BR-8486        TCGA-BR-8487 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8588        TCGA-BR-8589        TCGA-BR-8590        TCGA-BR-8591 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-8676        TCGA-BR-8677        TCGA-BR-8678 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8679        TCGA-BR-8680        TCGA-BR-8682        TCGA-BR-8683 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8686        TCGA-BR-8687        TCGA-BR-8690        TCGA-BR-A44T 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A44U        TCGA-BR-A452        TCGA-BR-A453        TCGA-BR-A4CQ 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4CR        TCGA-BR-A4CS        TCGA-BR-A4IU        TCGA-BR-A4IV 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4IY        TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4J4        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4PD 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4PE        TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4QM        TCGA-CD-5804        TCGA-CD-8525        TCGA-CD-8526 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-8531        TCGA-CD-8535        TCGA-CD-A487        TCGA-CG-4301 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4436        TCGA-CG-4437 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4442 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476        TCGA-CG-4477 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6822        TCGA-D7-8570        TCGA-D7-8572        TCGA-D7-8573 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-8574        TCGA-D7-8575        TCGA-D7-8576        TCGA-D7-8578 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-8579        TCGA-D7-A4YT        TCGA-D7-A4YU        TCGA-D7-A4YV 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A4YX        TCGA-D7-A4YY        TCGA-D7-A4Z0        TCGA-EQ-5647 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-EQ-8122        TCGA-EQ-A4SO        TCGA-F1-6177        TCGA-F1-6874 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-F1-6875        TCGA-F1-A448        TCGA-FP-7735        TCGA-FP-7829 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-8210        TCGA-FP-8211        TCGA-FP-8631        TCGA-FP-A4BE 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-A4BF        TCGA-HF-7132        TCGA-HF-7133        TCGA-HF-7136 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HJ-7597        TCGA-HU-8243        TCGA-HU-8245        TCGA-HU-8249 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-8602        TCGA-HU-8604        TCGA-HU-8608        TCGA-HU-8610 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4G2        TCGA-HU-A4G3        TCGA-HU-A4G6        TCGA-HU-A4G8 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4G9        TCGA-HU-A4GC        TCGA-HU-A4GD        TCGA-HU-A4GF 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GH        TCGA-HU-A4GN        TCGA-HU-A4GP        TCGA-HU-A4GQ 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GT        TCGA-HU-A4GU        TCGA-HU-A4GX        TCGA-HU-A4GY 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4H0        TCGA-HU-A4H2        TCGA-HU-A4H3        TCGA-HU-A4H4 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4H5        TCGA-HU-A4H6        TCGA-HU-A4H8        TCGA-HU-A4HD 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IN-8462        TCGA-IN-8663 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IP-7968 
"TMEM55A WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMEM55A MUTATED       1                         0     2
  TMEM55A WILD-TYPE    75                         4   166
D363V12, multiclass
                           clus
vv                          TMEM55A MUTATED TMEM55A WILD-TYPE
  ASIAN                                   1                75
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   2               166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(364) Variable = CASD1 MUTATION ANALYSIS
D364V1, survival
                 sevent
clus2               0   1
  CASD1 MUTATED     7   3
  CASD1 WILD-TYPE 174  77
  CASD1 MUTATED CASD1 WILD-TYPE 
             10             251 
  CASD1 MUTATED CASD1 WILD-TYPE 
              3              77 
$`CASD1 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-4438 TCGA-CG-4477 
       30.90        34.68         6.58        15.95        54.08        30.97 
TCGA-CG-5733 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4H3 
       21.07        11.41        11.84        19.36 

$`CASD1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       18.35         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 
        3.02        27.02         1.02         7.99         8.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        22.98         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       28.96        79.07        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        5.52        26.47         5.92        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       12.95        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  CASD1 MUTATED CASD1 WILD-TYPE 
           6.58            0.00 
  CASD1 MUTATED CASD1 WILD-TYPE 
          54.08          105.07 
  CASD1 MUTATED CASD1 WILD-TYPE 
         20.215          12.560 
[1] "6.6 - 54.1 (20.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.8"
D364V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CASD1 MUTATED         1        0        1        1         2         2
  CASD1 WILD-TYPE       0        9       26       25        29        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CASD1 MUTATED           0          1          0          1        1
  CASD1 WILD-TYPE         3         48         36         23       23
D364V3, multiclass
            clus
vv           CASD1 MUTATED CASD1 WILD-TYPE
  STAGE I                1               0
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              2              29
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CASD1 MUTATED     1   4   3   3
  CASD1 WILD-TYPE  10  68 119  72
D364V4, multiclass
    clus
vv   CASD1 MUTATED CASD1 WILD-TYPE
  T1             1              10
  T2             4              68
  T3             3             119
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CASD1 MUTATED    4  3  2  1
  CASD1 WILD-TYPE 89 78 48 52
D364V5, multiclass
    clus
vv   CASD1 MUTATED CASD1 WILD-TYPE
  N0             4              89
  N1             3              78
  N2             2              48
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D364V6, binary
                 cls
clus                0   1
  CASD1 MUTATED    10   0
  CASD1 WILD-TYPE 247  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASD1 MUTATED     10    0
  CASD1 WILD-TYPE  247   18
   clus
vv  CASD1 MUTATED CASD1 WILD-TYPE
  0            10             247
  1             0              18
[1] 2 2
[1] FALSE
D364V7, binary
                 cls
clus                0   1
  CASD1 MUTATED     7   4
  CASD1 WILD-TYPE 103 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASD1 MUTATED      7    4
  CASD1 WILD-TYPE  103  175
        clus
vv       CASD1 MUTATED CASD1 WILD-TYPE
  FEMALE             7             103
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CASD1 MUTATED                                       4
  CASD1 WILD-TYPE                                    46
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CASD1 MUTATED                                                        4
  CASD1 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CASD1 MUTATED                                                                   3
  CASD1 WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CASD1 MUTATED                                                  0
  CASD1 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CASD1 MUTATED                                                          0
  CASD1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CASD1 MUTATED                                                           0
  CASD1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CASD1 MUTATED                                          0
  CASD1 WILD-TYPE                                        3
D364V8, multiclass
                                                                   clus
vv                                                                  CASD1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  CASD1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D364V9, binary
                 cls
clus                0   1
  CASD1 MUTATED     0  11
  CASD1 WILD-TYPE   5 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASD1 MUTATED      0   11
  CASD1 WILD-TYPE    5  273
     clus
vv    CASD1 MUTATED CASD1 WILD-TYPE
  NO              0               5
  YES            11             273
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CASD1 MUTATED     8   0   0   1
  CASD1 WILD-TYPE 219  10  10  23
D364V10, multiclass
    clus
vv   CASD1 MUTATED CASD1 WILD-TYPE
  R0             8             219
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D364V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CASD1 MUTATED       4                         1     2
  CASD1 WILD-TYPE    72                         3   166
D364V12, multiclass
                           clus
vv                          CASD1 MUTATED CASD1 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 2             166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(365) Variable = CADPS2 MUTATION ANALYSIS
D365V1, survival
                  sevent
clus2                0   1
  CADPS2 MUTATED     8   3
  CADPS2 WILD-TYPE 173  77
  CADPS2 MUTATED CADPS2 WILD-TYPE 
              11              250 
  CADPS2 MUTATED CADPS2 WILD-TYPE 
               3               77 
$`CADPS2 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8361 TCGA-CD-A4MG 
        6.97        34.68        23.93        12.26        19.50         6.58 
TCGA-F1-6874 TCGA-FP-A4BE TCGA-HU-A4GF TCGA-HU-A4GQ TCGA-HU-A4H2 
       14.47        11.08        25.81         0.10        12.95 

$`CADPS2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
       16.31         2.20        15.58         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        22.75        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 
        6.51         6.25        10.19         0.26         2.10        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  CADPS2 MUTATED CADPS2 WILD-TYPE 
             0.1              0.0 
  CADPS2 MUTATED CADPS2 WILD-TYPE 
           34.68           105.07 
  CADPS2 MUTATED CADPS2 WILD-TYPE 
          12.950           12.605 
[1] "0.1 - 34.7 (12.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D365V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CADPS2 MUTATED         0        0        2        0         4         1
  CADPS2 WILD-TYPE       1        9       25       26        27        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CADPS2 MUTATED           0          1          1          2        0
  CADPS2 WILD-TYPE         3         48         35         22       24
D365V3, multiclass
            clus
vv           CADPS2 MUTATED CADPS2 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                2               25
  STAGE II                0               26
  STAGE IIA               4               27
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              2               22
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CADPS2 MUTATED     0   2   6   3
  CADPS2 WILD-TYPE  11  70 116  72
D365V4, multiclass
    clus
vv   CADPS2 MUTATED CADPS2 WILD-TYPE
  T1              0               11
  T2              2               70
  T3              6              116
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CADPS2 MUTATED    7  1  2  1
  CADPS2 WILD-TYPE 86 80 48 52
D365V5, multiclass
    clus
vv   CADPS2 MUTATED CADPS2 WILD-TYPE
  N0              7               86
  N1              1               80
  N2              2               48
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D365V6, binary
                  cls
clus                 0   1
  CADPS2 MUTATED    10   0
  CADPS2 WILD-TYPE 247  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CADPS2 MUTATED     10    0
  CADPS2 WILD-TYPE  247   18
   clus
vv  CADPS2 MUTATED CADPS2 WILD-TYPE
  0             10              247
  1              0               18
[1] 2 2
[1] FALSE
D365V7, binary
                  cls
clus                 0   1
  CADPS2 MUTATED     5   6
  CADPS2 WILD-TYPE 105 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CADPS2 MUTATED      5    6
  CADPS2 WILD-TYPE  105  173
        clus
vv       CADPS2 MUTATED CADPS2 WILD-TYPE
  FEMALE              5              105
  MALE                6              173
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CADPS2 MUTATED                                       1
  CADPS2 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CADPS2 MUTATED                                                        6
  CADPS2 WILD-TYPE                                                    129
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CADPS2 MUTATED                                                                   1
  CADPS2 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CADPS2 MUTATED                                                  3
  CADPS2 WILD-TYPE                                               35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CADPS2 MUTATED                                                          0
  CADPS2 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CADPS2 MUTATED                                                           0
  CADPS2 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CADPS2 MUTATED                                          0
  CADPS2 WILD-TYPE                                        3
D365V8, multiclass
                                                                   clus
vv                                                                  CADPS2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  CADPS2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D365V9, binary
                  cls
clus                 0   1
  CADPS2 MUTATED     0  11
  CADPS2 WILD-TYPE   5 273
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CADPS2 MUTATED      0   11
  CADPS2 WILD-TYPE    5  273
     clus
vv    CADPS2 MUTATED CADPS2 WILD-TYPE
  NO               0                5
  YES             11              273
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CADPS2 MUTATED     9   0   0   1
  CADPS2 WILD-TYPE 218  10  10  23
D365V10, multiclass
    clus
vv   CADPS2 MUTATED CADPS2 WILD-TYPE
  R0              9              218
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D365V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CADPS2 MUTATED       4                         1     6
  CADPS2 WILD-TYPE    72                         3   162
D365V12, multiclass
                           clus
vv                          CADPS2 MUTATED CADPS2 WILD-TYPE
  ASIAN                                  4               72
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(366) Variable = MASTL MUTATION ANALYSIS
D366V1, survival
                 sevent
clus2               0   1
  MASTL MUTATED     5   5
  MASTL WILD-TYPE 176  75
  MASTL MUTATED MASTL WILD-TYPE 
             10             251 
  MASTL MUTATED MASTL WILD-TYPE 
              5              75 
$`MASTL MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8059 TCGA-BR-8363 TCGA-BR-8680 TCGA-CD-5801 
       34.68        32.94        14.43         0.26        15.81        13.18 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5728 TCGA-IN-8663 
        6.58         6.02        65.10         3.39 

$`MASTL WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       19.50        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        2.83         3.25        13.15         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         2.53 

  MASTL MUTATED MASTL WILD-TYPE 
           0.26            0.00 
  MASTL MUTATED MASTL WILD-TYPE 
          65.10          105.07 
  MASTL MUTATED MASTL WILD-TYPE 
         13.805          12.590 
[1] "0.3 - 65.1 (13.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D366V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MASTL MUTATED         0        0        2        0         3         1
  MASTL WILD-TYPE       1        9       25       26        28        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MASTL MUTATED           1          1          0          0        2
  MASTL WILD-TYPE         2         48         36         24       22
D366V3, multiclass
            clus
vv           MASTL MUTATED MASTL WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              3              28
  STAGE IIB              1              43
  STAGE III              1               2
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MASTL MUTATED     1   3   4   3
  MASTL WILD-TYPE  10  69 118  72
D366V4, multiclass
    clus
vv   MASTL MUTATED MASTL WILD-TYPE
  T1             1              10
  T2             3              69
  T3             4             118
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  MASTL MUTATED    5  3  2  0
  MASTL WILD-TYPE 88 78 48 53
D366V5, multiclass
    clus
vv   MASTL MUTATED MASTL WILD-TYPE
  N0             5              88
  N1             3              78
  N2             2              48
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D366V6, binary
                 cls
clus                0   1
  MASTL MUTATED    10   1
  MASTL WILD-TYPE 247  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MASTL MUTATED     10    1
  MASTL WILD-TYPE  247   17
   clus
vv  MASTL MUTATED MASTL WILD-TYPE
  0            10             247
  1             1              17
[1] 2 2
[1] FALSE
D366V7, binary
                 cls
clus                0   1
  MASTL MUTATED     5   6
  MASTL WILD-TYPE 105 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MASTL MUTATED      5    6
  MASTL WILD-TYPE  105  173
        clus
vv       MASTL MUTATED MASTL WILD-TYPE
  FEMALE             5             105
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MASTL MUTATED                                       1
  MASTL WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MASTL MUTATED                                                        6
  MASTL WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MASTL MUTATED                                                                   3
  MASTL WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MASTL MUTATED                                                  1
  MASTL WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MASTL MUTATED                                                          0
  MASTL WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MASTL MUTATED                                                           0
  MASTL WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MASTL MUTATED                                          0
  MASTL WILD-TYPE                                        3
D366V8, multiclass
                                                                   clus
vv                                                                  MASTL MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  MASTL WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D366V9, binary
                 cls
clus                0   1
  MASTL MUTATED     0  11
  MASTL WILD-TYPE   5 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MASTL MUTATED      0   11
  MASTL WILD-TYPE    5  273
     clus
vv    MASTL MUTATED MASTL WILD-TYPE
  NO              0               5
  YES            11             273
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MASTL MUTATED     9   0   0   1
  MASTL WILD-TYPE 218  10  10  23
D366V10, multiclass
    clus
vv   MASTL MUTATED MASTL WILD-TYPE
  R0             9             218
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D366V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MASTL MUTATED       3                         0     6
  MASTL WILD-TYPE    73                         4   162
D366V12, multiclass
                           clus
vv                          MASTL MUTATED MASTL WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(367) Variable = MRI1 MUTATION ANALYSIS
D367V1, survival
                sevent
clus2              0   1
  MRI1 MUTATED     4   0
  MRI1 WILD-TYPE 177  80
  MRI1 MUTATED MRI1 WILD-TYPE 
             4            257 
  MRI1 MUTATED MRI1 WILD-TYPE 
             0             80 
$`MRI1 MUTATED`
TCGA-BR-8487 TCGA-CD-A4MJ TCGA-CG-5721 TCGA-HU-A4GU 
        1.12        12.62         6.02         6.25 

$`MRI1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  MRI1 MUTATED MRI1 WILD-TYPE 
          1.12           0.00 
  MRI1 MUTATED MRI1 WILD-TYPE 
         12.62         105.07 
  MRI1 MUTATED MRI1 WILD-TYPE 
         6.135         12.760 
[1] "1.1 - 12.6 (6.1)"   "0.0 - 105.1 (12.8)"
[1] "hr="     "3300000"
D367V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MRI1 MUTATED         0        0        1        0         1         1
  MRI1 WILD-TYPE       1        9       26       26        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRI1 MUTATED           0          0          0          0        1
  MRI1 WILD-TYPE         3         49         36         24       23
D367V3, multiclass
            clus
vv           MRI1 MUTATED MRI1 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MRI1 MUTATED     0   1   2   1
  MRI1 WILD-TYPE  11  71 120  74
D367V4, multiclass
    clus
vv   MRI1 MUTATED MRI1 WILD-TYPE
  T1            0             11
  T2            1             71
  T3            2            120
  T4            1             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  MRI1 MUTATED    2  2  0  0
  MRI1 WILD-TYPE 91 79 50 53
D367V5, multiclass
    clus
vv   MRI1 MUTATED MRI1 WILD-TYPE
  N0            2             91
  N1            2             79
  N2            0             50
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D367V6, binary
                cls
clus               0   1
  MRI1 MUTATED     4   0
  MRI1 WILD-TYPE 253  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  MRI1 MUTATED      4    0
  MRI1 WILD-TYPE  253   18
   clus
vv  MRI1 MUTATED MRI1 WILD-TYPE
  0            4            253
  1            0             18
[1] 2 2
[1] FALSE
D367V7, binary
                cls
clus               0   1
  MRI1 MUTATED     1   3
  MRI1 WILD-TYPE 109 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  MRI1 MUTATED      1    3
  MRI1 WILD-TYPE  109  176
        clus
vv       MRI1 MUTATED MRI1 WILD-TYPE
  FEMALE            1            109
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MRI1 MUTATED                                       1
  MRI1 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MRI1 MUTATED                                                        2
  MRI1 WILD-TYPE                                                    133
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MRI1 MUTATED                                                                   1
  MRI1 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MRI1 MUTATED                                                  0
  MRI1 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MRI1 MUTATED                                                          0
  MRI1 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MRI1 MUTATED                                                           0
  MRI1 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MRI1 MUTATED                                          0
  MRI1 WILD-TYPE                                        3
D367V8, multiclass
                                                                   clus
vv                                                                  MRI1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  MRI1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D367V9, binary
                cls
clus               0   1
  MRI1 MUTATED     0   4
  MRI1 WILD-TYPE   5 280
[1] "tbl2"
                cls
clus             [,1] [,2]
  MRI1 MUTATED      0    4
  MRI1 WILD-TYPE    5  280
     clus
vv    MRI1 MUTATED MRI1 WILD-TYPE
  NO             0              5
  YES            4            280
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MRI1 MUTATED     3   0   0   0
  MRI1 WILD-TYPE 224  10  10  24
D367V10, multiclass
    clus
vv   MRI1 MUTATED MRI1 WILD-TYPE
  R0            3            224
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D367V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MRI1 MUTATED       2                         0     1
  MRI1 WILD-TYPE    74                         4   167
D367V12, multiclass
                           clus
vv                          MRI1 MUTATED MRI1 WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                1            167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(368) Variable = KBTBD6 MUTATION ANALYSIS
D368V1, survival
                  sevent
clus2                0   1
  KBTBD6 MUTATED     5   4
  KBTBD6 WILD-TYPE 176  76
  KBTBD6 MUTATED KBTBD6 WILD-TYPE 
               9              252 
  KBTBD6 MUTATED KBTBD6 WILD-TYPE 
               4               76 
$`KBTBD6 MUTATED`
TCGA-BR-4184 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-4440 TCGA-CG-5723 TCGA-D7-6518 
        6.97        15.81         6.58         4.01       105.07        19.13 
TCGA-HJ-7597 TCGA-HU-8608 TCGA-HU-A4GN 
       26.47        10.62        29.98 

$`KBTBD6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
       54.08        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 
       21.07         7.99        12.36        12.66        11.93        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       11.08         5.52         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       12.10         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       24.20         3.25        22.75        25.81        11.77         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  KBTBD6 MUTATED KBTBD6 WILD-TYPE 
            4.01             0.00 
  KBTBD6 MUTATED KBTBD6 WILD-TYPE 
          105.07            79.07 
  KBTBD6 MUTATED KBTBD6 WILD-TYPE 
          15.810           12.605 
[1] "4.0 - 105.1 (15.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.1"
D368V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KBTBD6 MUTATED         0        0        2        1         2         0
  KBTBD6 WILD-TYPE       1        9       25       25        29        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KBTBD6 MUTATED           0          3          1          0        2
  KBTBD6 WILD-TYPE         3         46         35         24       22
D368V3, multiclass
            clus
vv           KBTBD6 MUTATED KBTBD6 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                2               25
  STAGE II                1               25
  STAGE IIA               2               29
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              3               46
  STAGE IIIB              1               35
  STAGE IIIC              0               24
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KBTBD6 MUTATED     0   5   3   3
  KBTBD6 WILD-TYPE  11  67 119  72
D368V4, multiclass
    clus
vv   KBTBD6 MUTATED KBTBD6 WILD-TYPE
  T1              0               11
  T2              5               67
  T3              3              119
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  KBTBD6 MUTATED    4  5  2  2
  KBTBD6 WILD-TYPE 89 76 48 51
D368V5, multiclass
    clus
vv   KBTBD6 MUTATED KBTBD6 WILD-TYPE
  N0              4               89
  N1              5               76
  N2              2               48
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D368V6, binary
                  cls
clus                 0   1
  KBTBD6 MUTATED     9   2
  KBTBD6 WILD-TYPE 248  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KBTBD6 MUTATED      9    2
  KBTBD6 WILD-TYPE  248   16
   clus
vv  KBTBD6 MUTATED KBTBD6 WILD-TYPE
  0              9              248
  1              2               16
[1] 2 2
[1] FALSE
D368V7, binary
                  cls
clus                 0   1
  KBTBD6 MUTATED     4   9
  KBTBD6 WILD-TYPE 106 170
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KBTBD6 MUTATED      4    9
  KBTBD6 WILD-TYPE  106  170
        clus
vv       KBTBD6 MUTATED KBTBD6 WILD-TYPE
  FEMALE              4              106
  MALE                9              170
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KBTBD6 MUTATED                                       3
  KBTBD6 WILD-TYPE                                    47
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KBTBD6 MUTATED                                                        5
  KBTBD6 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KBTBD6 MUTATED                                                                   2
  KBTBD6 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KBTBD6 MUTATED                                                  2
  KBTBD6 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KBTBD6 MUTATED                                                          0
  KBTBD6 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KBTBD6 MUTATED                                                           0
  KBTBD6 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KBTBD6 MUTATED                                          1
  KBTBD6 WILD-TYPE                                        2
D368V8, multiclass
                                                                   clus
vv                                                                  KBTBD6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       1
                                                                   clus
vv                                                                  KBTBD6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D368V9, binary
                  cls
clus                 0   1
  KBTBD6 MUTATED     0  13
  KBTBD6 WILD-TYPE   5 271
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KBTBD6 MUTATED      0   13
  KBTBD6 WILD-TYPE    5  271
     clus
vv    KBTBD6 MUTATED KBTBD6 WILD-TYPE
  NO               0                5
  YES             13              271
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  KBTBD6 MUTATED     6   1   1   4
  KBTBD6 WILD-TYPE 221   9   9  20
D368V10, multiclass
    clus
vv   KBTBD6 MUTATED KBTBD6 WILD-TYPE
  R0              6              221
  R1              1                9
  R2              1                9
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D368V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KBTBD6 MUTATED       4                         0     6
  KBTBD6 WILD-TYPE    72                         4   162
D368V12, multiclass
                           clus
vv                          KBTBD6 MUTATED KBTBD6 WILD-TYPE
  ASIAN                                  4               72
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(369) Variable = PLA2G15 MUTATION ANALYSIS
D369V1, survival
                   sevent
clus2                 0   1
  PLA2G15 MUTATED     4   3
  PLA2G15 WILD-TYPE 177  77
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
                7               254 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
                3                77 
$`PLA2G15 MUTATED`
TCGA-BR-4280 TCGA-BR-6802 TCGA-BR-8360 TCGA-CD-A4MJ TCGA-CG-5726 TCGA-HU-A4GH 
        6.61        30.90         6.18        12.62        28.96        11.77 
TCGA-HU-A4GQ 
        0.10 

$`PLA2G15 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       25.81        29.98         8.98         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
              0.1               0.0 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
            30.90            105.07 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
            11.77             12.71 
[1] "0.1 - 30.9 (11.8)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.3"
D369V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLA2G15 MUTATED         0        2        2        1         1         0
  PLA2G15 WILD-TYPE       1        7       25       25        30        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLA2G15 MUTATED           1          1          0          1        0
  PLA2G15 WILD-TYPE         2         48         36         23       24
D369V3, multiclass
            clus
vv           PLA2G15 MUTATED PLA2G15 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 2                 7
  STAGE IB                 2                25
  STAGE II                 1                25
  STAGE IIA                1                30
  STAGE IIB                0                44
  STAGE III                1                 2
  STAGE IIIA               1                48
  STAGE IIIB               0                36
  STAGE IIIC               1                23
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLA2G15 MUTATED     2   4   2   1
  PLA2G15 WILD-TYPE   9  68 120  74
D369V4, multiclass
    clus
vv   PLA2G15 MUTATED PLA2G15 WILD-TYPE
  T1               2                 9
  T2               4                68
  T3               2               120
  T4               1                74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  PLA2G15 MUTATED    5  2  2  0
  PLA2G15 WILD-TYPE 88 79 48 53
D369V5, multiclass
    clus
vv   PLA2G15 MUTATED PLA2G15 WILD-TYPE
  N0               5                88
  N1               2                79
  N2               2                48
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D369V6, binary
                   cls
clus                  0   1
  PLA2G15 MUTATED     9   0
  PLA2G15 WILD-TYPE 248  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G15 MUTATED      9    0
  PLA2G15 WILD-TYPE  248   18
   clus
vv  PLA2G15 MUTATED PLA2G15 WILD-TYPE
  0               9               248
  1               0                18
[1] 2 2
[1] FALSE
D369V7, binary
                   cls
clus                  0   1
  PLA2G15 MUTATED     1   8
  PLA2G15 WILD-TYPE 109 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G15 MUTATED      1    8
  PLA2G15 WILD-TYPE  109  171
        clus
vv       PLA2G15 MUTATED PLA2G15 WILD-TYPE
  FEMALE               1               109
  MALE                 8               171
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PLA2G15 MUTATED                                       0
  PLA2G15 WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLA2G15 MUTATED                                                        3
  PLA2G15 WILD-TYPE                                                    132
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLA2G15 MUTATED                                                                   3
  PLA2G15 WILD-TYPE                                                                37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PLA2G15 MUTATED                                                  2
  PLA2G15 WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PLA2G15 MUTATED                                                          1
  PLA2G15 WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PLA2G15 MUTATED                                                           0
  PLA2G15 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PLA2G15 MUTATED                                          0
  PLA2G15 WILD-TYPE                                        3
D369V8, multiclass
                                                                   clus
vv                                                                  PLA2G15 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  PLA2G15 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D369V9, binary
                   cls
clus                  0   1
  PLA2G15 MUTATED     1   8
  PLA2G15 WILD-TYPE   4 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G15 MUTATED      1    8
  PLA2G15 WILD-TYPE    4  276
     clus
vv    PLA2G15 MUTATED PLA2G15 WILD-TYPE
  NO                1                 4
  YES               8               276
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PLA2G15 MUTATED     7   0   0   1
  PLA2G15 WILD-TYPE 220  10  10  23
D369V10, multiclass
    clus
vv   PLA2G15 MUTATED PLA2G15 WILD-TYPE
  R0               7               220
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D369V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLA2G15 MUTATED       3                         0     3
  PLA2G15 WILD-TYPE    73                         4   165
D369V12, multiclass
                           clus
vv                          PLA2G15 MUTATED PLA2G15 WILD-TYPE
  ASIAN                                   3                73
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   3               165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(370) Variable = JHDM1D MUTATION ANALYSIS
D370V1, survival
                  sevent
clus2                0   1
  JHDM1D MUTATED     6   3
  JHDM1D WILD-TYPE 175  77
  JHDM1D MUTATED JHDM1D WILD-TYPE 
               9              252 
  JHDM1D MUTATED JHDM1D WILD-TYPE 
               3               77 
$`JHDM1D MUTATED`
TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8368 TCGA-CD-8535 TCGA-CD-A4MG TCGA-CG-4305 
       34.68        23.93         4.31         0.13         6.58        15.95 
TCGA-CG-5726 TCGA-D7-A4YV TCGA-F1-6874 
       28.96         5.92        14.47 

$`JHDM1D WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 
       14.76         0.62         7.99        16.24        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  JHDM1D MUTATED JHDM1D WILD-TYPE 
            0.13             0.00 
  JHDM1D MUTATED JHDM1D WILD-TYPE 
           34.68           105.07 
  JHDM1D MUTATED JHDM1D WILD-TYPE 
          14.470           12.605 
[1] "0.1 - 34.7 (14.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1"  
D370V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  JHDM1D MUTATED         0        1        4        1         2         1
  JHDM1D WILD-TYPE       1        8       23       25        29        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  JHDM1D MUTATED           0          1          0          0        0
  JHDM1D WILD-TYPE         3         48         36         24       24
D370V3, multiclass
            clus
vv           JHDM1D MUTATED JHDM1D WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                4               23
  STAGE II                1               25
  STAGE IIA               2               29
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  JHDM1D MUTATED     1   5   4   0
  JHDM1D WILD-TYPE  10  67 118  75
D370V4, multiclass
    clus
vv   JHDM1D MUTATED JHDM1D WILD-TYPE
  T1              1               10
  T2              5               67
  T3              4              118
  T4              0               75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  JHDM1D MUTATED    7  3  0  0
  JHDM1D WILD-TYPE 86 78 50 53
D370V5, multiclass
    clus
vv   JHDM1D MUTATED JHDM1D WILD-TYPE
  N0              7               86
  N1              3               78
  N2              0               50
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D370V6, binary
                  cls
clus                 0   1
  JHDM1D MUTATED    10   0
  JHDM1D WILD-TYPE 247  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JHDM1D MUTATED     10    0
  JHDM1D WILD-TYPE  247   18
   clus
vv  JHDM1D MUTATED JHDM1D WILD-TYPE
  0             10              247
  1              0               18
[1] 2 2
[1] FALSE
D370V7, binary
                  cls
clus                 0   1
  JHDM1D MUTATED     4   6
  JHDM1D WILD-TYPE 106 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JHDM1D MUTATED      4    6
  JHDM1D WILD-TYPE  106  173
        clus
vv       JHDM1D MUTATED JHDM1D WILD-TYPE
  FEMALE              4              106
  MALE                6              173
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  JHDM1D MUTATED                                       1
  JHDM1D WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  JHDM1D MUTATED                                                        5
  JHDM1D WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  JHDM1D MUTATED                                                                   3
  JHDM1D WILD-TYPE                                                                37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  JHDM1D MUTATED                                                  1
  JHDM1D WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  JHDM1D MUTATED                                                          0
  JHDM1D WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  JHDM1D MUTATED                                                           0
  JHDM1D WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  JHDM1D MUTATED                                          0
  JHDM1D WILD-TYPE                                        3
D370V8, multiclass
                                                                   clus
vv                                                                  JHDM1D MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  JHDM1D WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D370V9, binary
                  cls
clus                 0   1
  JHDM1D MUTATED     0  10
  JHDM1D WILD-TYPE   5 274
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JHDM1D MUTATED      0   10
  JHDM1D WILD-TYPE    5  274
     clus
vv    JHDM1D MUTATED JHDM1D WILD-TYPE
  NO               0                5
  YES             10              274
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  JHDM1D MUTATED     9   0   0   0
  JHDM1D WILD-TYPE 218  10  10  24
D370V10, multiclass
    clus
vv   JHDM1D MUTATED JHDM1D WILD-TYPE
  R0              9              218
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D370V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  JHDM1D MUTATED       2                         0     5
  JHDM1D WILD-TYPE    74                         4   163
D370V12, multiclass
                           clus
vv                          JHDM1D MUTATED JHDM1D WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  5              163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(371) Variable = NUFIP2 MUTATION ANALYSIS
D371V1, survival
                  sevent
clus2                0   1
  NUFIP2 MUTATED     3   2
  NUFIP2 WILD-TYPE 178  78
  NUFIP2 MUTATED NUFIP2 WILD-TYPE 
               5              256 
  NUFIP2 MUTATED NUFIP2 WILD-TYPE 
               2               78 
$`NUFIP2 MUTATED`
TCGA-BR-8372 TCGA-D7-5578 TCGA-D7-8570 TCGA-D7-A4YV TCGA-HU-A4GQ 
       19.17        12.66        24.72         5.92         0.10 

$`NUFIP2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.36        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       15.98        12.79        10.55        11.31        12.33        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       14.27        16.44        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        11.77        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  NUFIP2 MUTATED NUFIP2 WILD-TYPE 
             0.1              0.0 
  NUFIP2 MUTATED NUFIP2 WILD-TYPE 
           24.72           105.07 
  NUFIP2 MUTATED NUFIP2 WILD-TYPE 
          12.660           12.605 
[1] "0.1 - 24.7 (12.7)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.6"
D371V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NUFIP2 MUTATED         0        0        0        1         0         1
  NUFIP2 WILD-TYPE       1        9       27       25        31        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUFIP2 MUTATED           0          1          1          2        0
  NUFIP2 WILD-TYPE         3         48         35         22       24
D371V3, multiclass
            clus
vv           NUFIP2 MUTATED NUFIP2 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                1               25
  STAGE IIA               0               31
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              2               22
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NUFIP2 MUTATED     0   1   3   2
  NUFIP2 WILD-TYPE  11  71 119  73
D371V4, multiclass
    clus
vv   NUFIP2 MUTATED NUFIP2 WILD-TYPE
  T1              0               11
  T2              1               71
  T3              3              119
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  NUFIP2 MUTATED    0  2  2  2
  NUFIP2 WILD-TYPE 93 79 48 51
D371V5, multiclass
    clus
vv   NUFIP2 MUTATED NUFIP2 WILD-TYPE
  N0              0               93
  N1              2               79
  N2              2               48
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D371V6, binary
                  cls
clus                 0   1
  NUFIP2 MUTATED     7   0
  NUFIP2 WILD-TYPE 250  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP2 MUTATED      7    0
  NUFIP2 WILD-TYPE  250   18
   clus
vv  NUFIP2 MUTATED NUFIP2 WILD-TYPE
  0              7              250
  1              0               18
[1] 2 2
[1] FALSE
D371V7, binary
                  cls
clus                 0   1
  NUFIP2 MUTATED     2   5
  NUFIP2 WILD-TYPE 108 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP2 MUTATED      2    5
  NUFIP2 WILD-TYPE  108  174
        clus
vv       NUFIP2 MUTATED NUFIP2 WILD-TYPE
  FEMALE              2              108
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NUFIP2 MUTATED                                       0
  NUFIP2 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NUFIP2 MUTATED                                                        2
  NUFIP2 WILD-TYPE                                                    133
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NUFIP2 MUTATED                                                                   0
  NUFIP2 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NUFIP2 MUTATED                                                  4
  NUFIP2 WILD-TYPE                                               34
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NUFIP2 MUTATED                                                          1
  NUFIP2 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NUFIP2 MUTATED                                                           0
  NUFIP2 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NUFIP2 MUTATED                                          0
  NUFIP2 WILD-TYPE                                        3
D371V8, multiclass
                                                                   clus
vv                                                                  NUFIP2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  NUFIP2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D371V9, binary
                  cls
clus                 0   1
  NUFIP2 MUTATED     1   6
  NUFIP2 WILD-TYPE   4 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP2 MUTATED      1    6
  NUFIP2 WILD-TYPE    4  278
     clus
vv    NUFIP2 MUTATED NUFIP2 WILD-TYPE
  NO               1                4
  YES              6              278
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NUFIP2 MUTATED     6   0   0   1
  NUFIP2 WILD-TYPE 221  10  10  23
D371V10, multiclass
    clus
vv   NUFIP2 MUTATED NUFIP2 WILD-TYPE
  R0              6              221
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D371V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NUFIP2 MUTATED       1                         0     5
  NUFIP2 WILD-TYPE    75                         4   163
D371V12, multiclass
                           clus
vv                          NUFIP2 MUTATED NUFIP2 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  5              163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(372) Variable = KCNJ10 MUTATION ANALYSIS
D372V1, survival
                  sevent
clus2                0   1
  KCNJ10 MUTATED     5   3
  KCNJ10 WILD-TYPE 176  77
  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
               8              253 
  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
               3               77 
$`KCNJ10 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CG-5733 
       26.70         6.97        34.68         1.12         6.58        21.07 
TCGA-HU-8602 TCGA-HU-A4GT 
       11.41         6.51 

$`KCNJ10 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
            1.12             0.00 
  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
           34.68           105.07 
  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
            9.19            12.66 
[1] "1.1 - 34.7 (9.2)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.2"
D372V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCNJ10 MUTATED         1        0        0        0         4         2
  KCNJ10 WILD-TYPE       0        9       27       26        27        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCNJ10 MUTATED           0          3          0          0        0
  KCNJ10 WILD-TYPE         3         46         36         24       24
D372V3, multiclass
            clus
vv           KCNJ10 MUTATED KCNJ10 WILD-TYPE
  STAGE I                 1                0
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               4               27
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              3               46
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KCNJ10 MUTATED     1   1   5   3
  KCNJ10 WILD-TYPE  10  71 117  72
D372V4, multiclass
    clus
vv   KCNJ10 MUTATED KCNJ10 WILD-TYPE
  T1              1               10
  T2              1               71
  T3              5              117
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  KCNJ10 MUTATED    7  3  1  0
  KCNJ10 WILD-TYPE 86 78 49 53
D372V5, multiclass
    clus
vv   KCNJ10 MUTATED KCNJ10 WILD-TYPE
  N0              7               86
  N1              3               78
  N2              1               49
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D372V6, binary
                  cls
clus                 0   1
  KCNJ10 MUTATED     9   0
  KCNJ10 WILD-TYPE 248  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNJ10 MUTATED      9    0
  KCNJ10 WILD-TYPE  248   18
   clus
vv  KCNJ10 MUTATED KCNJ10 WILD-TYPE
  0              9              248
  1              0               18
[1] 2 2
[1] FALSE
D372V7, binary
                  cls
clus                 0   1
  KCNJ10 MUTATED     8   3
  KCNJ10 WILD-TYPE 102 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNJ10 MUTATED      8    3
  KCNJ10 WILD-TYPE  102  176
        clus
vv       KCNJ10 MUTATED KCNJ10 WILD-TYPE
  FEMALE              8              102
  MALE                3              176
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KCNJ10 MUTATED                                       3
  KCNJ10 WILD-TYPE                                    47
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KCNJ10 MUTATED                                                        6
  KCNJ10 WILD-TYPE                                                    129
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KCNJ10 MUTATED                                                                   1
  KCNJ10 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KCNJ10 MUTATED                                                  1
  KCNJ10 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KCNJ10 MUTATED                                                          0
  KCNJ10 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KCNJ10 MUTATED                                                           0
  KCNJ10 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KCNJ10 MUTATED                                          0
  KCNJ10 WILD-TYPE                                        3
D372V8, multiclass
                                                                   clus
vv                                                                  KCNJ10 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  KCNJ10 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D372V9, binary
                  cls
clus                 0   1
  KCNJ10 MUTATED     0  11
  KCNJ10 WILD-TYPE   5 273
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNJ10 MUTATED      0   11
  KCNJ10 WILD-TYPE    5  273
     clus
vv    KCNJ10 MUTATED KCNJ10 WILD-TYPE
  NO               0                5
  YES             11              273
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  KCNJ10 MUTATED     7   0   0   3
  KCNJ10 WILD-TYPE 220  10  10  21
D372V10, multiclass
    clus
vv   KCNJ10 MUTATED KCNJ10 WILD-TYPE
  R0              7              220
  R1              0               10
  R2              0               10
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D372V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KCNJ10 MUTATED       3                         1     6
  KCNJ10 WILD-TYPE    73                         3   162
D372V12, multiclass
                           clus
vv                          KCNJ10 MUTATED KCNJ10 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(373) Variable = TRUB1 MUTATION ANALYSIS
D373V1, survival
                 sevent
clus2               0   1
  TRUB1 MUTATED     8   0
  TRUB1 WILD-TYPE 173  80
  TRUB1 MUTATED TRUB1 WILD-TYPE 
              8             253 
  TRUB1 MUTATED TRUB1 WILD-TYPE 
              0              80 
$`TRUB1 MUTATED`
TCGA-BR-6802 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-8536 
       30.90        19.17         1.12        13.45        15.81         0.10 
TCGA-CG-5721 TCGA-F1-6874 
        6.02        14.47 

$`TRUB1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
        9.21        20.22        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 
        0.13         0.16         0.10         0.10         0.13         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
       13.78        14.76         0.62         7.99        16.24        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  TRUB1 MUTATED TRUB1 WILD-TYPE 
            0.1             0.0 
  TRUB1 MUTATED TRUB1 WILD-TYPE 
          30.90          105.07 
  TRUB1 MUTATED TRUB1 WILD-TYPE 
          13.96           12.59 
[1] "0.1 - 30.9 (14.0)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "2.5e+07"
D373V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRUB1 MUTATED         0        0        1        1         1         0
  TRUB1 WILD-TYPE       1        9       26       25        30        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRUB1 MUTATED           0          1          0          2        2
  TRUB1 WILD-TYPE         3         48         36         22       22
D373V3, multiclass
            clus
vv           TRUB1 MUTATED TRUB1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             2              22
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRUB1 MUTATED     0   1   4   4
  TRUB1 WILD-TYPE  11  71 118  71
D373V4, multiclass
    clus
vv   TRUB1 MUTATED TRUB1 WILD-TYPE
  T1             0              11
  T2             1              71
  T3             4             118
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  TRUB1 MUTATED    3  1  2  2
  TRUB1 WILD-TYPE 90 80 48 51
D373V5, multiclass
    clus
vv   TRUB1 MUTATED TRUB1 WILD-TYPE
  N0             3              90
  N1             1              80
  N2             2              48
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D373V6, binary
                 cls
clus                0   1
  TRUB1 MUTATED     7   1
  TRUB1 WILD-TYPE 250  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRUB1 MUTATED      7    1
  TRUB1 WILD-TYPE  250   17
   clus
vv  TRUB1 MUTATED TRUB1 WILD-TYPE
  0             7             250
  1             1              17
[1] 2 2
[1] FALSE
D373V7, binary
                 cls
clus                0   1
  TRUB1 MUTATED     1   8
  TRUB1 WILD-TYPE 109 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRUB1 MUTATED      1    8
  TRUB1 WILD-TYPE  109  171
        clus
vv       TRUB1 MUTATED TRUB1 WILD-TYPE
  FEMALE             1             109
  MALE               8             171
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TRUB1 MUTATED                                       0
  TRUB1 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TRUB1 MUTATED                                                        6
  TRUB1 WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TRUB1 MUTATED                                                                   2
  TRUB1 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TRUB1 MUTATED                                                  1
  TRUB1 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TRUB1 MUTATED                                                          0
  TRUB1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TRUB1 MUTATED                                                           0
  TRUB1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TRUB1 MUTATED                                          0
  TRUB1 WILD-TYPE                                        3
D373V8, multiclass
                                                                   clus
vv                                                                  TRUB1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  TRUB1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D373V9, binary
                 cls
clus                0   1
  TRUB1 MUTATED     0   9
  TRUB1 WILD-TYPE   5 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRUB1 MUTATED      0    9
  TRUB1 WILD-TYPE    5  275
     clus
vv    TRUB1 MUTATED TRUB1 WILD-TYPE
  NO              0               5
  YES             9             275
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TRUB1 MUTATED     8   0   0   1
  TRUB1 WILD-TYPE 219  10  10  23
D373V10, multiclass
    clus
vv   TRUB1 MUTATED TRUB1 WILD-TYPE
  R0             8             219
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D373V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TRUB1 MUTATED       2                         0     6
  TRUB1 WILD-TYPE    74                         4   162
D373V12, multiclass
                           clus
vv                          TRUB1 MUTATED TRUB1 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(374) Variable = AGBL5 MUTATION ANALYSIS
D374V1, survival
                 sevent
clus2               0   1
  AGBL5 MUTATED     8   3
  AGBL5 WILD-TYPE 173  77
  AGBL5 MUTATED AGBL5 WILD-TYPE 
             11             250 
  AGBL5 MUTATED AGBL5 WILD-TYPE 
              3              77 
$`AGBL5 MUTATED`
TCGA-BR-7707 TCGA-BR-8361 TCGA-BR-8680 TCGA-CD-5813 TCGA-CG-5720 TCGA-CG-5723 
       23.93        19.50        15.81         0.39         0.99       105.07 
TCGA-CG-5728 TCGA-D7-5579 TCGA-HJ-7597 TCGA-HU-A4GQ TCGA-HU-A4GU 
       65.10        11.93        26.47         0.10         6.25 

$`AGBL5 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.30         0.07         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
        6.97        36.00         1.02         6.02         0.99        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.36        12.66        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  AGBL5 MUTATED AGBL5 WILD-TYPE 
            0.1             0.0 
  AGBL5 MUTATED AGBL5 WILD-TYPE 
         105.07           79.07 
  AGBL5 MUTATED AGBL5 WILD-TYPE 
         15.810          12.605 
[1] "0.1 - 105.1 (15.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.8"
D374V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AGBL5 MUTATED         0        0        4        2         0         1
  AGBL5 WILD-TYPE       1        9       23       24        31        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AGBL5 MUTATED           0          2          0          2        1
  AGBL5 WILD-TYPE         3         47         36         22       23
D374V3, multiclass
            clus
vv           AGBL5 MUTATED AGBL5 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               4              23
  STAGE II               2              24
  STAGE IIA              0              31
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             0              36
  STAGE IIIC             2              22
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AGBL5 MUTATED     0   5   3   4
  AGBL5 WILD-TYPE  11  67 119  71
D374V4, multiclass
    clus
vv   AGBL5 MUTATED AGBL5 WILD-TYPE
  T1             0              11
  T2             5              67
  T3             3             119
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  AGBL5 MUTATED    6  2  4  0
  AGBL5 WILD-TYPE 87 79 46 53
D374V5, multiclass
    clus
vv   AGBL5 MUTATED AGBL5 WILD-TYPE
  N0             6              87
  N1             2              79
  N2             4              46
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D374V6, binary
                 cls
clus                0   1
  AGBL5 MUTATED    10   1
  AGBL5 WILD-TYPE 247  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL5 MUTATED     10    1
  AGBL5 WILD-TYPE  247   17
   clus
vv  AGBL5 MUTATED AGBL5 WILD-TYPE
  0            10             247
  1             1              17
[1] 2 2
[1] FALSE
D374V7, binary
                 cls
clus                0   1
  AGBL5 MUTATED     5   7
  AGBL5 WILD-TYPE 105 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL5 MUTATED      5    7
  AGBL5 WILD-TYPE  105  172
        clus
vv       AGBL5 MUTATED AGBL5 WILD-TYPE
  FEMALE             5             105
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AGBL5 MUTATED                                       1
  AGBL5 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AGBL5 MUTATED                                                        5
  AGBL5 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AGBL5 MUTATED                                                                   1
  AGBL5 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AGBL5 MUTATED                                                  2
  AGBL5 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AGBL5 MUTATED                                                          2
  AGBL5 WILD-TYPE                                                       14
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AGBL5 MUTATED                                                           0
  AGBL5 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AGBL5 MUTATED                                          1
  AGBL5 WILD-TYPE                                        2
D374V8, multiclass
                                                                   clus
vv                                                                  AGBL5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  AGBL5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D374V9, binary
                 cls
clus                0   1
  AGBL5 MUTATED     0  12
  AGBL5 WILD-TYPE   5 272
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL5 MUTATED      0   12
  AGBL5 WILD-TYPE    5  272
     clus
vv    AGBL5 MUTATED AGBL5 WILD-TYPE
  NO              0               5
  YES            12             272
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AGBL5 MUTATED     9   1   0   1
  AGBL5 WILD-TYPE 218   9  10  23
D374V10, multiclass
    clus
vv   AGBL5 MUTATED AGBL5 WILD-TYPE
  R0             9             218
  R1             1               9
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D374V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AGBL5 MUTATED       4                         0     5
  AGBL5 WILD-TYPE    72                         4   163
D374V12, multiclass
                           clus
vv                          AGBL5 MUTATED AGBL5 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(375) Variable = PLAG1 MUTATION ANALYSIS
D375V1, survival
                 sevent
clus2               0   1
  PLAG1 MUTATED     5   4
  PLAG1 WILD-TYPE 176  76
  PLAG1 MUTATED PLAG1 WILD-TYPE 
              9             252 
  PLAG1 MUTATED PLAG1 WILD-TYPE 
              4              76 
$`PLAG1 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8592 TCGA-CG-4465 
        6.97        34.68         4.31         1.12         6.28         9.01 
TCGA-CG-5721 TCGA-CG-5726 TCGA-HU-A4H8 
        6.02        28.96         8.88 

$`PLAG1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 
       20.22        12.79        15.81         9.34        13.45         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 
        1.02         0.99         0.99       105.07        12.03        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  PLAG1 MUTATED PLAG1 WILD-TYPE 
           1.12            0.00 
  PLAG1 MUTATED PLAG1 WILD-TYPE 
          34.68          105.07 
  PLAG1 MUTATED PLAG1 WILD-TYPE 
          6.970          12.775 
[1] "1.1 - 34.7 (7.0)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.7"
D375V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLAG1 MUTATED         0        1        2        0         2         0
  PLAG1 WILD-TYPE       1        8       25       26        29        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLAG1 MUTATED           0          2          1          0        3
  PLAG1 WILD-TYPE         3         47         35         24       21
D375V3, multiclass
            clus
vv           PLAG1 MUTATED PLAG1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               3              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PLAG1 MUTATED     2   1   3   5
  PLAG1 WILD-TYPE   9  71 119  70
D375V4, multiclass
    clus
vv   PLAG1 MUTATED PLAG1 WILD-TYPE
  T1             2               9
  T2             1              71
  T3             3             119
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PLAG1 MUTATED    5  4  1  1
  PLAG1 WILD-TYPE 88 77 49 52
D375V5, multiclass
    clus
vv   PLAG1 MUTATED PLAG1 WILD-TYPE
  N0             5              88
  N1             4              77
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D375V6, binary
                 cls
clus                0   1
  PLAG1 MUTATED     9   1
  PLAG1 WILD-TYPE 248  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLAG1 MUTATED      9    1
  PLAG1 WILD-TYPE  248   17
   clus
vv  PLAG1 MUTATED PLAG1 WILD-TYPE
  0             9             248
  1             1              17
[1] 2 2
[1] FALSE
D375V7, binary
                 cls
clus                0   1
  PLAG1 MUTATED     7   4
  PLAG1 WILD-TYPE 103 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLAG1 MUTATED      7    4
  PLAG1 WILD-TYPE  103  175
        clus
vv       PLAG1 MUTATED PLAG1 WILD-TYPE
  FEMALE             7             103
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PLAG1 MUTATED                                       2
  PLAG1 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLAG1 MUTATED                                                        6
  PLAG1 WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLAG1 MUTATED                                                                   2
  PLAG1 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PLAG1 MUTATED                                                  1
  PLAG1 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PLAG1 MUTATED                                                          0
  PLAG1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PLAG1 MUTATED                                                           0
  PLAG1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PLAG1 MUTATED                                          0
  PLAG1 WILD-TYPE                                        3
D375V8, multiclass
                                                                   clus
vv                                                                  PLAG1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  PLAG1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D375V9, binary
                 cls
clus                0   1
  PLAG1 MUTATED     0  11
  PLAG1 WILD-TYPE   5 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLAG1 MUTATED      0   11
  PLAG1 WILD-TYPE    5  273
     clus
vv    PLAG1 MUTATED PLAG1 WILD-TYPE
  NO              0               5
  YES            11             273
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PLAG1 MUTATED     7   0   1   3
  PLAG1 WILD-TYPE 220  10   9  21
D375V10, multiclass
    clus
vv   PLAG1 MUTATED PLAG1 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             1               9
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D375V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLAG1 MUTATED       1                         0     7
  PLAG1 WILD-TYPE    75                         4   161
D375V12, multiclass
                           clus
vv                          PLAG1 MUTATED PLAG1 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 7             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(376) Variable = HEPACAM2 MUTATION ANALYSIS
D376V1, survival
                    sevent
clus2                  0   1
  HEPACAM2 MUTATED     3   3
  HEPACAM2 WILD-TYPE 178  77
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                 6                255 
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                 3                 77 
$`HEPACAM2 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-7851 TCGA-BR-8368 TCGA-CD-A4MG TCGA-D7-5578 
        6.97        30.90        12.43         4.31         6.58        12.66 

$`HEPACAM2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        12.36        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
              4.31               0.00 
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
             30.90             105.07 
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
              9.70              12.76 
[1] "4.3 - 30.9 (9.7)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.9"
D376V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HEPACAM2 MUTATED         0        0        1        0         1         1
  HEPACAM2 WILD-TYPE       1        9       26       26        30        43
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HEPACAM2 MUTATED           0          2          0          1        0
  HEPACAM2 WILD-TYPE         3         47         36         23       24
D376V3, multiclass
            clus
vv           HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  1                 26
  STAGE II                  0                 26
  STAGE IIA                 1                 30
  STAGE IIB                 1                 43
  STAGE III                 0                  3
  STAGE IIIA                2                 47
  STAGE IIIB                0                 36
  STAGE IIIC                1                 23
  STAGE IV                  0                 24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HEPACAM2 MUTATED     0   2   3   2
  HEPACAM2 WILD-TYPE  11  70 119  73
D376V4, multiclass
    clus
vv   HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  T1                0                 11
  T2                2                 70
  T3                3                119
  T4                2                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  HEPACAM2 MUTATED    3  2  1  1
  HEPACAM2 WILD-TYPE 90 79 49 52
D376V5, multiclass
    clus
vv   HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  N0                3                 90
  N1                2                 79
  N2                1                 49
  N3                1                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D376V6, binary
                    cls
clus                   0   1
  HEPACAM2 MUTATED     7   0
  HEPACAM2 WILD-TYPE 250  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HEPACAM2 MUTATED      7    0
  HEPACAM2 WILD-TYPE  250   18
   clus
vv  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  0                7                250
  1                0                 18
[1] 2 2
[1] FALSE
D376V7, binary
                    cls
clus                   0   1
  HEPACAM2 MUTATED     3   5
  HEPACAM2 WILD-TYPE 107 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HEPACAM2 MUTATED      3    5
  HEPACAM2 WILD-TYPE  107  174
        clus
vv       HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  FEMALE                3                107
  MALE                  5                174
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  HEPACAM2 MUTATED                                       1
  HEPACAM2 WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HEPACAM2 MUTATED                                                        5
  HEPACAM2 WILD-TYPE                                                    130
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HEPACAM2 MUTATED                                                                   1
  HEPACAM2 WILD-TYPE                                                                39
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  HEPACAM2 MUTATED                                                  1
  HEPACAM2 WILD-TYPE                                               37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  HEPACAM2 MUTATED                                                          0
  HEPACAM2 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  HEPACAM2 MUTATED                                                           0
  HEPACAM2 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  HEPACAM2 MUTATED                                          0
  HEPACAM2 WILD-TYPE                                        3
D376V8, multiclass
                                                                   clus
vv                                                                  HEPACAM2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  HEPACAM2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D376V9, binary
                    cls
clus                   0   1
  HEPACAM2 MUTATED     0   8
  HEPACAM2 WILD-TYPE   5 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HEPACAM2 MUTATED      0    8
  HEPACAM2 WILD-TYPE    5  276
     clus
vv    HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  NO                 0                  5
  YES                8                276
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  HEPACAM2 MUTATED     3   1   0   3
  HEPACAM2 WILD-TYPE 224   9  10  21
D376V10, multiclass
    clus
vv   HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  R0                3                224
  R1                1                  9
  R2                0                 10
  RX                3                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D376V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HEPACAM2 MUTATED       1                         0     7
  HEPACAM2 WILD-TYPE    75                         4   161
D376V12, multiclass
                           clus
vv                          HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  ASIAN                                    1                 75
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    7                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(377) Variable = CSF3R MUTATION ANALYSIS
D377V1, survival
                 sevent
clus2               0   1
  CSF3R MUTATED     7   3
  CSF3R WILD-TYPE 174  77
  CSF3R MUTATED CSF3R WILD-TYPE 
             10             251 
  CSF3R MUTATED CSF3R WILD-TYPE 
              3              77 
$`CSF3R MUTATED`
TCGA-BR-6452 TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8368 TCGA-CD-A4MG TCGA-CG-4305 
       34.68        18.71        12.26         4.31         6.58        15.95 
TCGA-CG-4437 TCGA-CG-5726 TCGA-D7-A4YV TCGA-F1-6874 
        8.05        28.96         5.92        14.47 

$`CSF3R WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       28.73        12.43         3.45         9.07        12.76        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 
        0.99         6.02         0.99       105.07        12.03        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        0.62         7.99        16.24        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  CSF3R MUTATED CSF3R WILD-TYPE 
           4.31            0.00 
  CSF3R MUTATED CSF3R WILD-TYPE 
          34.68          105.07 
  CSF3R MUTATED CSF3R WILD-TYPE 
         13.365          12.620 
[1] "4.3 - 34.7 (13.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D377V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CSF3R MUTATED         0        1        3        2         2         2
  CSF3R WILD-TYPE       1        8       24       24        29        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSF3R MUTATED           0          2          0          0        0
  CSF3R WILD-TYPE         3         47         36         24       24
D377V3, multiclass
            clus
vv           CSF3R MUTATED CSF3R WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               3              24
  STAGE II               2              24
  STAGE IIA              2              29
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CSF3R MUTATED     1   5   3   3
  CSF3R WILD-TYPE  10  67 119  72
D377V4, multiclass
    clus
vv   CSF3R MUTATED CSF3R WILD-TYPE
  T1             1              10
  T2             5              67
  T3             3             119
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CSF3R MUTATED    8  4  0  0
  CSF3R WILD-TYPE 85 77 50 53
D377V5, multiclass
    clus
vv   CSF3R MUTATED CSF3R WILD-TYPE
  N0             8              85
  N1             4              77
  N2             0              50
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D377V6, binary
                 cls
clus                0   1
  CSF3R MUTATED    12   0
  CSF3R WILD-TYPE 245  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSF3R MUTATED     12    0
  CSF3R WILD-TYPE  245   18
   clus
vv  CSF3R MUTATED CSF3R WILD-TYPE
  0            12             245
  1             0              18
[1] 2 2
[1] FALSE
D377V7, binary
                 cls
clus                0   1
  CSF3R MUTATED     5   7
  CSF3R WILD-TYPE 105 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSF3R MUTATED      5    7
  CSF3R WILD-TYPE  105  172
        clus
vv       CSF3R MUTATED CSF3R WILD-TYPE
  FEMALE             5             105
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CSF3R MUTATED                                       1
  CSF3R WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CSF3R MUTATED                                                        5
  CSF3R WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CSF3R MUTATED                                                                   4
  CSF3R WILD-TYPE                                                                36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CSF3R MUTATED                                                  1
  CSF3R WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CSF3R MUTATED                                                          1
  CSF3R WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CSF3R MUTATED                                                           0
  CSF3R WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CSF3R MUTATED                                          0
  CSF3R WILD-TYPE                                        3
D377V8, multiclass
                                                                   clus
vv                                                                  CSF3R MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  CSF3R WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D377V9, binary
                 cls
clus                0   1
  CSF3R MUTATED     0  12
  CSF3R WILD-TYPE   5 272
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSF3R MUTATED      0   12
  CSF3R WILD-TYPE    5  272
     clus
vv    CSF3R MUTATED CSF3R WILD-TYPE
  NO              0               5
  YES            12             272
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CSF3R MUTATED    10   0   0   1
  CSF3R WILD-TYPE 217  10  10  23
D377V10, multiclass
    clus
vv   CSF3R MUTATED CSF3R WILD-TYPE
  R0            10             217
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D377V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CSF3R MUTATED       1                         0     7
  CSF3R WILD-TYPE    75                         4   161
D377V12, multiclass
                           clus
vv                          CSF3R MUTATED CSF3R WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 7             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(378) Variable = RPGR MUTATION ANALYSIS
D378V1, survival
                sevent
clus2              0   1
  RPGR MUTATED     7   0
  RPGR WILD-TYPE 174  80
  RPGR MUTATED RPGR WILD-TYPE 
             7            254 
  RPGR MUTATED RPGR WILD-TYPE 
             0             80 
$`RPGR MUTATED`
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 TCGA-CG-5728 TCGA-HU-A4GU 
        1.12        15.81        13.45        15.81        65.10         6.25 
TCGA-HU-A4H3 
       19.36 

$`RPGR WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 
        5.39        25.18         9.21        20.22        12.79         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        28.96        79.07         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  RPGR MUTATED RPGR WILD-TYPE 
          1.12           0.00 
  RPGR MUTATED RPGR WILD-TYPE 
         65.10         105.07 
  RPGR MUTATED RPGR WILD-TYPE 
        15.810         12.575 
[1] "1.1 - 65.1 (15.8)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "2.6e+07"
D378V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RPGR MUTATED         0        0        1        0         1         1
  RPGR WILD-TYPE       1        9       26       26        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RPGR MUTATED           0          1          1          2        1
  RPGR WILD-TYPE         3         48         35         22       23
D378V3, multiclass
            clus
vv           RPGR MUTATED RPGR WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            2             22
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RPGR MUTATED     0   1   2   5
  RPGR WILD-TYPE  11  71 120  70
D378V4, multiclass
    clus
vv   RPGR MUTATED RPGR WILD-TYPE
  T1            0             11
  T2            1             71
  T3            2            120
  T4            5             70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  RPGR MUTATED    3  2  1  2
  RPGR WILD-TYPE 90 79 49 51
D378V5, multiclass
    clus
vv   RPGR MUTATED RPGR WILD-TYPE
  N0            3             90
  N1            2             79
  N2            1             49
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D378V6, binary
                cls
clus               0   1
  RPGR MUTATED     7   1
  RPGR WILD-TYPE 250  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPGR MUTATED      7    1
  RPGR WILD-TYPE  250   17
   clus
vv  RPGR MUTATED RPGR WILD-TYPE
  0            7            250
  1            1             17
[1] 2 2
[1] FALSE
D378V7, binary
                cls
clus               0   1
  RPGR MUTATED     4   4
  RPGR WILD-TYPE 106 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPGR MUTATED      4    4
  RPGR WILD-TYPE  106  175
        clus
vv       RPGR MUTATED RPGR WILD-TYPE
  FEMALE            4            106
  MALE              4            175
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RPGR MUTATED                                       2
  RPGR WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RPGR MUTATED                                                        4
  RPGR WILD-TYPE                                                    131
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RPGR MUTATED                                                                   1
  RPGR WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RPGR MUTATED                                                  1
  RPGR WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RPGR MUTATED                                                          0
  RPGR WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RPGR MUTATED                                                           0
  RPGR WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RPGR MUTATED                                          0
  RPGR WILD-TYPE                                        3
D378V8, multiclass
                                                                   clus
vv                                                                  RPGR MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  RPGR WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D378V9, binary
                cls
clus               0   1
  RPGR MUTATED     0   8
  RPGR WILD-TYPE   5 276
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPGR MUTATED      0    8
  RPGR WILD-TYPE    5  276
     clus
vv    RPGR MUTATED RPGR WILD-TYPE
  NO             0              5
  YES            8            276
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RPGR MUTATED     7   0   0   1
  RPGR WILD-TYPE 220  10  10  23
D378V10, multiclass
    clus
vv   RPGR MUTATED RPGR WILD-TYPE
  R0            7            220
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D378V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RPGR MUTATED       3                         0     4
  RPGR WILD-TYPE    73                         4   164
D378V12, multiclass
                           clus
vv                          RPGR MUTATED RPGR WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                4            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(379) Variable = EPB49 MUTATION ANALYSIS
D379V1, survival
                 sevent
clus2               0   1
  EPB49 MUTATED     4   2
  EPB49 WILD-TYPE 177  78
  EPB49 MUTATED EPB49 WILD-TYPE 
              6             255 
  EPB49 MUTATED EPB49 WILD-TYPE 
              2              78 
$`EPB49 MUTATED`
TCGA-BR-4201 TCGA-BR-8368 TCGA-BR-8487 TCGA-CG-5723 TCGA-FP-7916 TCGA-HU-A4H4 
       30.90         4.31         1.12       105.07        14.07        23.84 

$`EPB49 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  EPB49 MUTATED EPB49 WILD-TYPE 
           1.12            0.00 
  EPB49 MUTATED EPB49 WILD-TYPE 
         105.07           79.07 
  EPB49 MUTATED EPB49 WILD-TYPE 
         18.955          12.590 
[1] "1.1 - 105.1 (19.0)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.8"
D379V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPB49 MUTATED         0        0        1        1         1         1
  EPB49 WILD-TYPE       1        9       26       25        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EPB49 MUTATED           0          1          0          1        0
  EPB49 WILD-TYPE         3         48         36         23       24
D379V3, multiclass
            clus
vv           EPB49 MUTATED EPB49 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EPB49 MUTATED     0   4   1   2
  EPB49 WILD-TYPE  11  68 121  73
D379V4, multiclass
    clus
vv   EPB49 MUTATED EPB49 WILD-TYPE
  T1             0              11
  T2             4              68
  T3             1             121
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  EPB49 MUTATED    3  2  1  1
  EPB49 WILD-TYPE 90 79 49 52
D379V5, multiclass
    clus
vv   EPB49 MUTATED EPB49 WILD-TYPE
  N0             3              90
  N1             2              79
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D379V6, binary
                 cls
clus                0   1
  EPB49 MUTATED     7   0
  EPB49 WILD-TYPE 250  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPB49 MUTATED      7    0
  EPB49 WILD-TYPE  250   18
   clus
vv  EPB49 MUTATED EPB49 WILD-TYPE
  0             7             250
  1             0              18
[1] 2 2
[1] FALSE
D379V7, binary
                 cls
clus                0   1
  EPB49 MUTATED     6   2
  EPB49 WILD-TYPE 104 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPB49 MUTATED      6    2
  EPB49 WILD-TYPE  104  177
        clus
vv       EPB49 MUTATED EPB49 WILD-TYPE
  FEMALE             6             104
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  EPB49 MUTATED                                       1
  EPB49 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EPB49 MUTATED                                                        6
  EPB49 WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EPB49 MUTATED                                                                   0
  EPB49 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  EPB49 MUTATED                                                  1
  EPB49 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  EPB49 MUTATED                                                          0
  EPB49 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  EPB49 MUTATED                                                           0
  EPB49 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  EPB49 MUTATED                                          0
  EPB49 WILD-TYPE                                        3
D379V8, multiclass
                                                                   clus
vv                                                                  EPB49 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  EPB49 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D379V9, binary
                 cls
clus                0   1
  EPB49 MUTATED     0   8
  EPB49 WILD-TYPE   5 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPB49 MUTATED      0    8
  EPB49 WILD-TYPE    5  276
     clus
vv    EPB49 MUTATED EPB49 WILD-TYPE
  NO              0               5
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EPB49 MUTATED     4   0   0   3
  EPB49 WILD-TYPE 223  10  10  21
D379V10, multiclass
    clus
vv   EPB49 MUTATED EPB49 WILD-TYPE
  R0             4             223
  R1             0              10
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D379V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EPB49 MUTATED       2                         0     5
  EPB49 WILD-TYPE    74                         4   163
D379V12, multiclass
                           clus
vv                          EPB49 MUTATED EPB49 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(380) Variable = LRFN3 MUTATION ANALYSIS
D380V1, survival
                 sevent
clus2               0   1
  LRFN3 MUTATED    13   3
  LRFN3 WILD-TYPE 168  77
  LRFN3 MUTATED LRFN3 WILD-TYPE 
             16             245 
  LRFN3 MUTATED LRFN3 WILD-TYPE 
              3              77 
$`LRFN3 MUTATED`
TCGA-BR-6852 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8487 TCGA-CD-8529 TCGA-CD-8535 
       32.94         6.18        19.50         1.12         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-5726 TCGA-HU-8602 
        0.10         6.58         0.10         1.02        28.96        11.41 
TCGA-HU-8610 TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H8 
        0.76         2.10        19.36         8.88 

$`LRFN3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        30.90        31.20        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        7.40         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.16         0.10         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       11.31        12.43        11.61        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       14.17        12.10        10.62        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
        0.26        12.95        23.84        12.30         9.67        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  LRFN3 MUTATED LRFN3 WILD-TYPE 
            0.1             0.0 
  LRFN3 MUTATED LRFN3 WILD-TYPE 
          32.94          105.07 
  LRFN3 MUTATED LRFN3 WILD-TYPE 
           4.14           12.79 
[1] "0.1 - 32.9 (4.1)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.1"
D380V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LRFN3 MUTATED         0        2        1        1         4         1
  LRFN3 WILD-TYPE       1        7       26       25        27        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRFN3 MUTATED           0          1          1          3        2
  LRFN3 WILD-TYPE         3         48         35         21       22
D380V3, multiclass
            clus
vv           LRFN3 MUTATED LRFN3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               2               7
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              4              27
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             3              21
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LRFN3 MUTATED     3   0   9   5
  LRFN3 WILD-TYPE   8  72 113  70
D380V4, multiclass
    clus
vv   LRFN3 MUTATED LRFN3 WILD-TYPE
  T1             3               8
  T2             0              72
  T3             9             113
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  LRFN3 MUTATED    9  3  2  2
  LRFN3 WILD-TYPE 84 78 48 51
D380V5, multiclass
    clus
vv   LRFN3 MUTATED LRFN3 WILD-TYPE
  N0             9              84
  N1             3              78
  N2             2              48
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D380V6, binary
                 cls
clus                0   1
  LRFN3 MUTATED    15   2
  LRFN3 WILD-TYPE 242  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRFN3 MUTATED     15    2
  LRFN3 WILD-TYPE  242   16
   clus
vv  LRFN3 MUTATED LRFN3 WILD-TYPE
  0            15             242
  1             2              16
[1] 2 2
[1] FALSE
D380V7, binary
                 cls
clus                0   1
  LRFN3 MUTATED     7  11
  LRFN3 WILD-TYPE 103 168
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRFN3 MUTATED      7   11
  LRFN3 WILD-TYPE  103  168
        clus
vv       LRFN3 MUTATED LRFN3 WILD-TYPE
  FEMALE             7             103
  MALE              11             168
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  LRFN3 MUTATED                                       4
  LRFN3 WILD-TYPE                                    46
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LRFN3 MUTATED                                                        9
  LRFN3 WILD-TYPE                                                    126
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LRFN3 MUTATED                                                                   2
  LRFN3 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  LRFN3 MUTATED                                                  2
  LRFN3 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  LRFN3 MUTATED                                                          1
  LRFN3 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  LRFN3 MUTATED                                                           0
  LRFN3 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  LRFN3 MUTATED                                          0
  LRFN3 WILD-TYPE                                        3
D380V8, multiclass
                                                                   clus
vv                                                                  LRFN3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  LRFN3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D380V9, binary
                 cls
clus                0   1
  LRFN3 MUTATED     0  18
  LRFN3 WILD-TYPE   5 266
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRFN3 MUTATED      0   18
  LRFN3 WILD-TYPE    5  266
     clus
vv    LRFN3 MUTATED LRFN3 WILD-TYPE
  NO              0               5
  YES            18             266
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LRFN3 MUTATED    13   0   1   2
  LRFN3 WILD-TYPE 214  10   9  22
D380V10, multiclass
    clus
vv   LRFN3 MUTATED LRFN3 WILD-TYPE
  R0            13             214
  R1             0              10
  R2             1               9
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D380V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LRFN3 MUTATED      10                         0     6
  LRFN3 WILD-TYPE    66                         4   162
D380V12, multiclass
                           clus
vv                          LRFN3 MUTATED LRFN3 WILD-TYPE
  ASIAN                                10              66
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(381) Variable = GRK4 MUTATION ANALYSIS
D381V1, survival
                sevent
clus2              0   1
  GRK4 MUTATED     4   0
  GRK4 WILD-TYPE 177  80
  GRK4 MUTATED GRK4 WILD-TYPE 
             4            257 
  GRK4 MUTATED GRK4 WILD-TYPE 
             0             80 
$`GRK4 MUTATED`
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8487 TCGA-FP-A4BE 
        6.18        19.50         1.12        11.08 

$`GRK4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       15.58         7.40         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
        5.03        13.58         0.56         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  GRK4 MUTATED GRK4 WILD-TYPE 
          1.12           0.00 
  GRK4 MUTATED GRK4 WILD-TYPE 
         19.50         105.07 
  GRK4 MUTATED GRK4 WILD-TYPE 
          8.63          12.66 
[1] "1.1 - 19.5 (8.6)"   "0.0 - 105.1 (12.7)"
[1] "hr="     "9100000"
D381V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GRK4 MUTATED         0        0        0        0         3         0
  GRK4 WILD-TYPE       1        9       27       26        28        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GRK4 MUTATED           0          0          0          1        0
  GRK4 WILD-TYPE         3         49         36         23       24
D381V3, multiclass
            clus
vv           GRK4 MUTATED GRK4 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              0             26
  STAGE IIA             3             28
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            1             23
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GRK4 MUTATED     0   0   3   1
  GRK4 WILD-TYPE  11  72 119  74
D381V4, multiclass
    clus
vv   GRK4 MUTATED GRK4 WILD-TYPE
  T1            0             11
  T2            0             72
  T3            3            119
  T4            1             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  GRK4 MUTATED    3  0  1  0
  GRK4 WILD-TYPE 90 81 49 53
D381V5, multiclass
    clus
vv   GRK4 MUTATED GRK4 WILD-TYPE
  N0            3             90
  N1            0             81
  N2            1             49
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D381V6, binary
                cls
clus               0   1
  GRK4 MUTATED     4   0
  GRK4 WILD-TYPE 253  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRK4 MUTATED      4    0
  GRK4 WILD-TYPE  253   18
   clus
vv  GRK4 MUTATED GRK4 WILD-TYPE
  0            4            253
  1            0             18
[1] 2 2
[1] FALSE
D381V7, binary
                cls
clus               0   1
  GRK4 MUTATED     2   2
  GRK4 WILD-TYPE 108 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRK4 MUTATED      2    2
  GRK4 WILD-TYPE  108  177
        clus
vv       GRK4 MUTATED GRK4 WILD-TYPE
  FEMALE            2            108
  MALE              2            177
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GRK4 MUTATED                                       0
  GRK4 WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GRK4 MUTATED                                                        3
  GRK4 WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GRK4 MUTATED                                                                   1
  GRK4 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GRK4 MUTATED                                                  0
  GRK4 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GRK4 MUTATED                                                          0
  GRK4 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GRK4 MUTATED                                                           0
  GRK4 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GRK4 MUTATED                                          0
  GRK4 WILD-TYPE                                        3
D381V8, multiclass
                                                                   clus
vv                                                                  GRK4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  GRK4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D381V9, binary
                cls
clus               0   1
  GRK4 MUTATED     0   4
  GRK4 WILD-TYPE   5 280
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRK4 MUTATED      0    4
  GRK4 WILD-TYPE    5  280
     clus
vv    GRK4 MUTATED GRK4 WILD-TYPE
  NO             0              5
  YES            4            280
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GRK4 MUTATED     4   0   0   0
  GRK4 WILD-TYPE 223  10  10  24
D381V10, multiclass
    clus
vv   GRK4 MUTATED GRK4 WILD-TYPE
  R0            4            223
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D381V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GRK4 MUTATED       0                         1     3
  GRK4 WILD-TYPE    76                         3   165
D381V12, multiclass
                           clus
vv                          GRK4 MUTATED GRK4 WILD-TYPE
  ASIAN                                0             76
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                                3            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(382) Variable = ZNF23 MUTATION ANALYSIS
D382V1, survival
                 sevent
clus2               0   1
  ZNF23 MUTATED     2   0
  ZNF23 WILD-TYPE 179  80
  ZNF23 MUTATED ZNF23 WILD-TYPE 
              2             259 
  ZNF23 MUTATED ZNF23 WILD-TYPE 
              0              80 
$`ZNF23 MUTATED`
TCGA-BR-8372 TCGA-FP-A4BE 
       19.17        11.08 

$`ZNF23 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  ZNF23 MUTATED ZNF23 WILD-TYPE 
          11.08            0.00 
  ZNF23 MUTATED ZNF23 WILD-TYPE 
          19.17          105.07 
  ZNF23 MUTATED ZNF23 WILD-TYPE 
         15.125          12.620 
[1] "11.1 - 19.2 (15.1)" "0.0 - 105.1 (12.6)"
[1] "Remove cluster labels:" "ZNF23 MUTATED"         
D382V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF23 MUTATED         0        0        0        0         1         0
  ZNF23 WILD-TYPE       1        9       27       26        30        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF23 MUTATED           0          0          0          1        0
  ZNF23 WILD-TYPE         3         49         36         23       24
D382V3, multiclass
[1] "Remove cluster labels:" "ZNF23 MUTATED"         
clus
  ZNF23 MUTATED ZNF23 WILD-TYPE 
              2             272 
     TCGA-B7-5816      TCGA-B7-5818      TCGA-BR-4183      TCGA-BR-4184 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4267      TCGA-BR-4279 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-4280      TCGA-BR-4361      TCGA-BR-4368      TCGA-BR-6452 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-6453      TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-6457      TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-6565      TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-6707      TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-6803      TCGA-BR-6852      TCGA-BR-7196      TCGA-BR-7197 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-7703      TCGA-BR-7707      TCGA-BR-7715      TCGA-BR-7716 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-7717      TCGA-BR-7722      TCGA-BR-7723      TCGA-BR-7851 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-7901      TCGA-BR-7957      TCGA-BR-7958      TCGA-BR-7959 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8058      TCGA-BR-8059      TCGA-BR-8077      TCGA-BR-8078 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8080      TCGA-BR-8081      TCGA-BR-8284      TCGA-BR-8286 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8289      TCGA-BR-8291      TCGA-BR-8295      TCGA-BR-8296 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8297      TCGA-BR-8360      TCGA-BR-8361      TCGA-BR-8363 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8364      TCGA-BR-8365      TCGA-BR-8366      TCGA-BR-8367 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8368      TCGA-BR-8369      TCGA-BR-8370      TCGA-BR-8371 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8373      TCGA-BR-8380      TCGA-BR-8381      TCGA-BR-8382 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8384      TCGA-BR-8483      TCGA-BR-8484      TCGA-BR-8485 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8486      TCGA-BR-8487      TCGA-BR-8588      TCGA-BR-8589 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8590      TCGA-BR-8591      TCGA-BR-8592      TCGA-BR-8676 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8677      TCGA-BR-8678      TCGA-BR-8679      TCGA-BR-8680 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8682      TCGA-BR-8683      TCGA-BR-8686      TCGA-BR-8687 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8690      TCGA-BR-A44T      TCGA-BR-A44U      TCGA-BR-A452 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A453      TCGA-BR-A4CQ      TCGA-BR-A4CR      TCGA-BR-A4CS 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A4IU      TCGA-BR-A4IV      TCGA-BR-A4IY      TCGA-BR-A4IZ 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A4J1      TCGA-BR-A4J2      TCGA-BR-A4J4      TCGA-BR-A4J6 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A4J7      TCGA-BR-A4J8      TCGA-BR-A4PD      TCGA-BR-A4PE 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A4PF      TCGA-BR-A4QI      TCGA-BR-A4QL      TCGA-BR-A4QM 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-5798      TCGA-CD-5799      TCGA-CD-5800      TCGA-CD-5801 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-5802      TCGA-CD-5803      TCGA-CD-5804      TCGA-CD-5813 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-8524      TCGA-CD-8525      TCGA-CD-8526      TCGA-CD-8527 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-8528      TCGA-CD-8529      TCGA-CD-8530      TCGA-CD-8531 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-8532      TCGA-CD-8534      TCGA-CD-8535      TCGA-CD-8536 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-A486      TCGA-CD-A487      TCGA-CD-A489      TCGA-CD-A48A 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-A48C      TCGA-CD-A4MG      TCGA-CD-A4MH      TCGA-CD-A4MI 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-A4MJ      TCGA-CG-4300      TCGA-CG-4301      TCGA-CG-4304 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-4305      TCGA-CG-4306      TCGA-CG-4436      TCGA-CG-4437 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-4438      TCGA-CG-4440      TCGA-CG-4441      TCGA-CG-4442 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-4443      TCGA-CG-4444      TCGA-CG-4449      TCGA-CG-4455 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-4462      TCGA-CG-4465      TCGA-CG-4466      TCGA-CG-4469 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-4474      TCGA-CG-4475      TCGA-CG-4476      TCGA-CG-4477 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-5717      TCGA-CG-5718      TCGA-CG-5719      TCGA-CG-5720 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-5721      TCGA-CG-5722      TCGA-CG-5723      TCGA-CG-5724 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-5726      TCGA-CG-5727      TCGA-CG-5728      TCGA-CG-5730 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-5732      TCGA-CG-5733      TCGA-CG-5734      TCGA-D7-5577 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-5578      TCGA-D7-5579      TCGA-D7-6518      TCGA-D7-6519 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-6520      TCGA-D7-6521      TCGA-D7-6522      TCGA-D7-6524 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-6525      TCGA-D7-6526      TCGA-D7-6527      TCGA-D7-6528 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-6815      TCGA-D7-6817      TCGA-D7-6818      TCGA-D7-6820 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-6822      TCGA-D7-8570      TCGA-D7-8572      TCGA-D7-8573 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-8574      TCGA-D7-8575      TCGA-D7-8576      TCGA-D7-8578 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-8579      TCGA-D7-A4YT      TCGA-D7-A4YU      TCGA-D7-A4YV 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-A4YX      TCGA-D7-A4YY      TCGA-D7-A4Z0      TCGA-EQ-5647 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-EQ-8122      TCGA-EQ-A4SO      TCGA-F1-6177      TCGA-F1-6874 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-F1-6875      TCGA-F1-A448      TCGA-FP-7735      TCGA-FP-7829 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-FP-7916      TCGA-FP-7998      TCGA-FP-8099      TCGA-FP-8209 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-FP-8210      TCGA-FP-8211      TCGA-FP-8631      TCGA-FP-A4BF 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HF-7132      TCGA-HF-7133      TCGA-HF-7136      TCGA-HJ-7597 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-8243      TCGA-HU-8245      TCGA-HU-8249      TCGA-HU-8602 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-8604      TCGA-HU-8608      TCGA-HU-8610      TCGA-HU-A4G2 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4G3      TCGA-HU-A4G6      TCGA-HU-A4G8      TCGA-HU-A4G9 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4GC      TCGA-HU-A4GD      TCGA-HU-A4GF      TCGA-HU-A4GH 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4GN      TCGA-HU-A4GP      TCGA-HU-A4GQ      TCGA-HU-A4GT 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4GU      TCGA-HU-A4GX      TCGA-HU-A4GY      TCGA-HU-A4H0 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4H2      TCGA-HU-A4H3      TCGA-HU-A4H4      TCGA-HU-A4H5 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4H6      TCGA-HU-A4H8      TCGA-HU-A4HD      TCGA-IN-7806 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-IN-7808      TCGA-IN-8462      TCGA-IN-8663      TCGA-IP-7968 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
                 vv
clus               T1  T2  T3  T4
  ZNF23 MUTATED     0   0   1   1
  ZNF23 WILD-TYPE  11  72 121  74
D382V4, multiclass
[1] "Remove cluster labels:" "ZNF23 MUTATED"         
clus
  ZNF23 MUTATED ZNF23 WILD-TYPE 
              2             278 
     TCGA-B7-5816      TCGA-B7-5818      TCGA-BR-4183      TCGA-BR-4184 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-4201      TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4267 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4292      TCGA-BR-4294 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-4357      TCGA-BR-4361      TCGA-BR-4363      TCGA-BR-4368 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-4371      TCGA-BR-6452      TCGA-BR-6453      TCGA-BR-6454 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457      TCGA-BR-6458 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565      TCGA-BR-6566 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707      TCGA-BR-6710 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803      TCGA-BR-6852 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703      TCGA-BR-7707 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-7715      TCGA-BR-7716      TCGA-BR-7717      TCGA-BR-7722 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-7723      TCGA-BR-7851      TCGA-BR-7901      TCGA-BR-7957 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-7958      TCGA-BR-7959      TCGA-BR-8058      TCGA-BR-8059 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8077      TCGA-BR-8078      TCGA-BR-8080      TCGA-BR-8081 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8284      TCGA-BR-8286      TCGA-BR-8289      TCGA-BR-8291 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8295      TCGA-BR-8296      TCGA-BR-8297      TCGA-BR-8360 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8361      TCGA-BR-8363      TCGA-BR-8364      TCGA-BR-8365 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8366      TCGA-BR-8367      TCGA-BR-8368      TCGA-BR-8369 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8370      TCGA-BR-8371      TCGA-BR-8373      TCGA-BR-8380 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8381      TCGA-BR-8382      TCGA-BR-8384      TCGA-BR-8483 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8484      TCGA-BR-8485      TCGA-BR-8486      TCGA-BR-8487 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8588      TCGA-BR-8589      TCGA-BR-8590      TCGA-BR-8591 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8592      TCGA-BR-8676      TCGA-BR-8677      TCGA-BR-8678 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8679      TCGA-BR-8680      TCGA-BR-8682      TCGA-BR-8683 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8686      TCGA-BR-8687      TCGA-BR-8690      TCGA-BR-A44T 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A44U      TCGA-BR-A452      TCGA-BR-A453      TCGA-BR-A4CQ 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A4CR      TCGA-BR-A4CS      TCGA-BR-A4IU      TCGA-BR-A4IV 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A4IY      TCGA-BR-A4IZ      TCGA-BR-A4J1      TCGA-BR-A4J2 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A4J4      TCGA-BR-A4J6      TCGA-BR-A4J7      TCGA-BR-A4J8 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A4PD      TCGA-BR-A4PE      TCGA-BR-A4PF      TCGA-BR-A4QI 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A4QL      TCGA-BR-A4QM      TCGA-CD-5798      TCGA-CD-5799 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-5800      TCGA-CD-5801      TCGA-CD-5802      TCGA-CD-5803 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-5804      TCGA-CD-5813      TCGA-CD-8524      TCGA-CD-8525 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-8526      TCGA-CD-8527      TCGA-CD-8528      TCGA-CD-8529 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-8530      TCGA-CD-8531      TCGA-CD-8532      TCGA-CD-8534 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-8535      TCGA-CD-8536      TCGA-CD-A486      TCGA-CD-A487 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-A489      TCGA-CD-A48A      TCGA-CD-A48C      TCGA-CD-A4MG 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-A4MH      TCGA-CD-A4MI      TCGA-CD-A4MJ      TCGA-CG-4300 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-4301      TCGA-CG-4304      TCGA-CG-4305      TCGA-CG-4306 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-4436      TCGA-CG-4437      TCGA-CG-4438      TCGA-CG-4440 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-4441      TCGA-CG-4442      TCGA-CG-4443      TCGA-CG-4444 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-4449      TCGA-CG-4455      TCGA-CG-4462      TCGA-CG-4465 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-4466      TCGA-CG-4469      TCGA-CG-4474      TCGA-CG-4475 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-4476      TCGA-CG-4477      TCGA-CG-5717      TCGA-CG-5718 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-5719      TCGA-CG-5720      TCGA-CG-5721      TCGA-CG-5722 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-5723      TCGA-CG-5724      TCGA-CG-5726      TCGA-CG-5727 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-5728      TCGA-CG-5730      TCGA-CG-5732      TCGA-CG-5733 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-5734      TCGA-D7-5577      TCGA-D7-5578      TCGA-D7-5579 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-6518      TCGA-D7-6519      TCGA-D7-6520      TCGA-D7-6521 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-6522      TCGA-D7-6524      TCGA-D7-6525      TCGA-D7-6526 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-6527      TCGA-D7-6528      TCGA-D7-6815      TCGA-D7-6817 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-6818      TCGA-D7-6820      TCGA-D7-6822      TCGA-D7-8570 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-8572      TCGA-D7-8573      TCGA-D7-8574      TCGA-D7-8575 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-8576      TCGA-D7-8578      TCGA-D7-8579      TCGA-D7-A4YT 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-A4YU      TCGA-D7-A4YV      TCGA-D7-A4YX      TCGA-D7-A4YY 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-A4Z0      TCGA-EQ-5647      TCGA-EQ-8122      TCGA-EQ-A4SO 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-F1-6177      TCGA-F1-6874      TCGA-F1-6875      TCGA-F1-A448 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-FP-7735      TCGA-FP-7829      TCGA-FP-7916      TCGA-FP-7998 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-FP-8099      TCGA-FP-8209      TCGA-FP-8210      TCGA-FP-8211 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-FP-8631      TCGA-FP-A4BF      TCGA-HF-7132      TCGA-HF-7133 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HF-7136      TCGA-HJ-7597      TCGA-HU-8243      TCGA-HU-8245 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-8249      TCGA-HU-8602      TCGA-HU-8604      TCGA-HU-8608 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-8610      TCGA-HU-A4G2      TCGA-HU-A4G3      TCGA-HU-A4G6 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4G8      TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4GF      TCGA-HU-A4GH      TCGA-HU-A4GN      TCGA-HU-A4GP 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4GQ      TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4GY      TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4H4      TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4HD      TCGA-IN-7806      TCGA-IN-7808      TCGA-IN-8462 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-IN-8663      TCGA-IP-7968 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
                 vv
clus              N0 N1 N2 N3
  ZNF23 MUTATED    1  1  0  1
  ZNF23 WILD-TYPE 92 80 50 52
D382V5, multiclass
    clus
vv   ZNF23 MUTATED ZNF23 WILD-TYPE
  N0             1              92
  N1             1              80
  N2             0              50
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D382V6, binary
                 cls
clus                0   1
  ZNF23 MUTATED     3   0
  ZNF23 WILD-TYPE 254  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF23 MUTATED      3    0
  ZNF23 WILD-TYPE  254   18
   clus
vv  ZNF23 MUTATED ZNF23 WILD-TYPE
  0             3             254
  1             0              18
[1] 2 2
[1] FALSE
D382V7, binary
                 cls
clus                0   1
  ZNF23 MUTATED     0   3
  ZNF23 WILD-TYPE 110 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF23 MUTATED      0    3
  ZNF23 WILD-TYPE  110  176
        clus
vv       ZNF23 MUTATED ZNF23 WILD-TYPE
  FEMALE             0             110
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZNF23 MUTATED                                       0
  ZNF23 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF23 MUTATED                                                        3
  ZNF23 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF23 MUTATED                                                                   0
  ZNF23 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZNF23 MUTATED                                                  0
  ZNF23 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZNF23 MUTATED                                                          0
  ZNF23 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZNF23 MUTATED                                                           0
  ZNF23 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZNF23 MUTATED                                          0
  ZNF23 WILD-TYPE                                        3
D382V8, multiclass
                                                                   clus
vv                                                                  ZNF23 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ZNF23 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D382V9, binary
                 cls
clus                0   1
  ZNF23 MUTATED     0   3
  ZNF23 WILD-TYPE   5 281
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF23 MUTATED      0    3
  ZNF23 WILD-TYPE    5  281
     clus
vv    ZNF23 MUTATED ZNF23 WILD-TYPE
  NO              0               5
  YES             3             281
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ZNF23 MUTATED     2   0   0   1
  ZNF23 WILD-TYPE 225  10  10  23
D382V10, multiclass
    clus
vv   ZNF23 MUTATED ZNF23 WILD-TYPE
  R0             2             225
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D382V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF23 MUTATED       0                         1     2
  ZNF23 WILD-TYPE    76                         3   166
D382V12, multiclass
                           clus
vv                          ZNF23 MUTATED ZNF23 WILD-TYPE
  ASIAN                                 0              76
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 2             166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(383) Variable = SERPINB8 MUTATION ANALYSIS
D383V1, survival
                    sevent
clus2                  0   1
  SERPINB8 MUTATED     6   1
  SERPINB8 WILD-TYPE 175  79
  SERPINB8 MUTATED SERPINB8 WILD-TYPE 
                 7                254 
  SERPINB8 MUTATED SERPINB8 WILD-TYPE 
                 1                 79 
$`SERPINB8 MUTATED`
TCGA-BR-7703 TCGA-BR-7707 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5732 TCGA-HU-A4H3 
       24.76        23.93       105.07        65.10        69.04        19.36 
TCGA-HU-A4H8 
        8.88 

$`SERPINB8 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
        9.21        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        6.02         0.99        12.03        28.96        79.07         4.01 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.25        10.19         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       12.30         9.67        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  SERPINB8 MUTATED SERPINB8 WILD-TYPE 
              8.88               0.00 
  SERPINB8 MUTATED SERPINB8 WILD-TYPE 
            105.07              79.07 
  SERPINB8 MUTATED SERPINB8 WILD-TYPE 
            24.760             12.495 
[1] "8.9 - 105.1 (24.8)" "0.0 - 79.1 (12.5)" 
[1] "hr=" "7"  
D383V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SERPINB8 MUTATED         0        1        4        1         0         0
  SERPINB8 WILD-TYPE       1        8       23       25        31        44
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINB8 MUTATED           0          0          0          1        1
  SERPINB8 WILD-TYPE         3         49         36         23       23
D383V3, multiclass
            clus
vv           SERPINB8 MUTATED SERPINB8 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  1                  8
  STAGE IB                  4                 23
  STAGE II                  1                 25
  STAGE IIA                 0                 31
  STAGE IIB                 0                 44
  STAGE III                 0                  3
  STAGE IIIA                0                 49
  STAGE IIIB                0                 36
  STAGE IIIC                1                 23
  STAGE IV                  1                 23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SERPINB8 MUTATED     2   5   0   1
  SERPINB8 WILD-TYPE   9  67 122  74
D383V4, multiclass
    clus
vv   SERPINB8 MUTATED SERPINB8 WILD-TYPE
  T1                2                  9
  T2                5                 67
  T3                0                122
  T4                1                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  SERPINB8 MUTATED    4  2  0  2
  SERPINB8 WILD-TYPE 89 79 50 51
D383V5, multiclass
    clus
vv   SERPINB8 MUTATED SERPINB8 WILD-TYPE
  N0                4                 89
  N1                2                 79
  N2                0                 50
  N3                2                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D383V6, binary
                    cls
clus                   0   1
  SERPINB8 MUTATED     8   0
  SERPINB8 WILD-TYPE 249  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB8 MUTATED      8    0
  SERPINB8 WILD-TYPE  249   18
   clus
vv  SERPINB8 MUTATED SERPINB8 WILD-TYPE
  0                8                249
  1                0                 18
[1] 2 2
[1] FALSE
D383V7, binary
                    cls
clus                   0   1
  SERPINB8 MUTATED     3   5
  SERPINB8 WILD-TYPE 107 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB8 MUTATED      3    5
  SERPINB8 WILD-TYPE  107  174
        clus
vv       SERPINB8 MUTATED SERPINB8 WILD-TYPE
  FEMALE                3                107
  MALE                  5                174
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SERPINB8 MUTATED                                       1
  SERPINB8 WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SERPINB8 MUTATED                                                        2
  SERPINB8 WILD-TYPE                                                    133
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SERPINB8 MUTATED                                                                   3
  SERPINB8 WILD-TYPE                                                                37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SERPINB8 MUTATED                                                  1
  SERPINB8 WILD-TYPE                                               37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SERPINB8 MUTATED                                                          0
  SERPINB8 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SERPINB8 MUTATED                                                           1
  SERPINB8 WILD-TYPE                                                         5
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SERPINB8 MUTATED                                          0
  SERPINB8 WILD-TYPE                                        3
D383V8, multiclass
                                                                   clus
vv                                                                  SERPINB8 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  SERPINB8 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D383V9, binary
                    cls
clus                   0   1
  SERPINB8 MUTATED     0   8
  SERPINB8 WILD-TYPE   5 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB8 MUTATED      0    8
  SERPINB8 WILD-TYPE    5  276
     clus
vv    SERPINB8 MUTATED SERPINB8 WILD-TYPE
  NO                 0                  5
  YES                8                276
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  SERPINB8 MUTATED     8   0   0   0
  SERPINB8 WILD-TYPE 219  10  10  24
D383V10, multiclass
    clus
vv   SERPINB8 MUTATED SERPINB8 WILD-TYPE
  R0                8                219
  R1                0                 10
  R2                0                 10
  RX                0                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D383V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SERPINB8 MUTATED       2                         0     2
  SERPINB8 WILD-TYPE    74                         4   166
D383V12, multiclass
                           clus
vv                          SERPINB8 MUTATED SERPINB8 WILD-TYPE
  ASIAN                                    2                 74
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    2                166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(384) Variable = ERBB4 MUTATION ANALYSIS
D384V1, survival
                 sevent
clus2               0   1
  ERBB4 MUTATED    24  11
  ERBB4 WILD-TYPE 157  69
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             35             226 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             11              69 
$`ERBB4 MUTATED`
TCGA-B7-5816 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6705 TCGA-BR-7197 TCGA-BR-7703 
       26.70         6.61        34.68        25.61         9.21        24.76 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8295 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8370 
        3.45        12.76         2.20        19.50         0.26         3.32 
TCGA-BR-8372 TCGA-BR-8485 TCGA-BR-8590 TCGA-BR-8680 TCGA-BR-A4J8 TCGA-BR-A4PD 
       19.17         9.21         9.34        15.81        13.51        20.65 
TCGA-CD-5801 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8536 TCGA-CD-A48A TCGA-CD-A4MG 
       13.18         0.39         0.07         0.10        12.43         6.58 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4469 TCGA-CG-5721 TCGA-D7-6820 TCGA-D7-A4YV 
        1.02         7.99         7.07         6.02        11.31         5.92 
TCGA-D7-A4Z0 TCGA-F1-6874 TCGA-HU-A4GT TCGA-HU-A4H8 TCGA-IN-8462 
       14.76        14.47         6.51         8.88        18.81 

$`ERBB4 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       30.90         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       32.94        12.82        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 
       15.32        28.73        12.43         9.07        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       12.95         2.66        16.31        15.58         7.40         6.18 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 
       25.18        20.22         1.12        12.79        15.81        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 
        3.25        13.15         0.30         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH 
        0.13         3.42         9.34        11.31        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 
       19.07        12.03         0.00         9.01        18.97        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.55        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
       15.16        13.78         0.62         7.99        16.24        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
       12.95        19.36        23.84        12.30         9.67        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45         3.39         2.53 

  ERBB4 MUTATED ERBB4 WILD-TYPE 
           0.07            0.00 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
          34.68          105.07 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
          9.210          12.805 
[1] "0.1 - 34.7 (9.2)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.4"
D384V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ERBB4 MUTATED         0        1        5        4         4         8
  ERBB4 WILD-TYPE       1        8       22       22        27        36
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ERBB4 MUTATED           1          1          4          4        4
  ERBB4 WILD-TYPE         2         48         32         20       20
D384V3, multiclass
            clus
vv           ERBB4 MUTATED ERBB4 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               5              22
  STAGE II               4              22
  STAGE IIA              4              27
  STAGE IIB              8              36
  STAGE III              1               2
  STAGE IIIA             1              48
  STAGE IIIB             4              32
  STAGE IIIC             4              20
  STAGE IV               4              20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ERBB4 MUTATED     3   8  16  10
  ERBB4 WILD-TYPE   8  64 106  65
D384V4, multiclass
    clus
vv   ERBB4 MUTATED ERBB4 WILD-TYPE
  T1             3               8
  T2             8              64
  T3            16             106
  T4            10              65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ERBB4 MUTATED   17  9  5  6
  ERBB4 WILD-TYPE 76 72 45 47
D384V5, multiclass
    clus
vv   ERBB4 MUTATED ERBB4 WILD-TYPE
  N0            17              76
  N1             9              72
  N2             5              45
  N3             6              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D384V6, binary
                 cls
clus                0   1
  ERBB4 MUTATED    37   2
  ERBB4 WILD-TYPE 220  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED     37    2
  ERBB4 WILD-TYPE  220   16
   clus
vv  ERBB4 MUTATED ERBB4 WILD-TYPE
  0            37             220
  1             2              16
[1] 2 2
[1] FALSE
D384V7, binary
                 cls
clus                0   1
  ERBB4 MUTATED    17  22
  ERBB4 WILD-TYPE  93 157
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED     17   22
  ERBB4 WILD-TYPE   93  157
        clus
vv       ERBB4 MUTATED ERBB4 WILD-TYPE
  FEMALE            17              93
  MALE              22             157
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ERBB4 MUTATED                                       3
  ERBB4 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ERBB4 MUTATED                                                       23
  ERBB4 WILD-TYPE                                                    112
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ERBB4 MUTATED                                                                   5
  ERBB4 WILD-TYPE                                                                35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ERBB4 MUTATED                                                  5
  ERBB4 WILD-TYPE                                               33
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ERBB4 MUTATED                                                          2
  ERBB4 WILD-TYPE                                                       14
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ERBB4 MUTATED                                                           1
  ERBB4 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ERBB4 MUTATED                                          0
  ERBB4 WILD-TYPE                                        3
D384V8, multiclass
                                                                   clus
vv                                                                  ERBB4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ERBB4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        112
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D384V9, binary
                 cls
clus                0   1
  ERBB4 MUTATED     0  39
  ERBB4 WILD-TYPE   5 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED      0   39
  ERBB4 WILD-TYPE    5  245
     clus
vv    ERBB4 MUTATED ERBB4 WILD-TYPE
  NO              0               5
  YES            39             245
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ERBB4 MUTATED    30   1   1   4
  ERBB4 WILD-TYPE 197   9   9  20
D384V10, multiclass
    clus
vv   ERBB4 MUTATED ERBB4 WILD-TYPE
  R0            30             197
  R1             1               9
  R2             1               9
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D384V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERBB4 MUTATED       9                         0    26
  ERBB4 WILD-TYPE    67                         4   142
D384V12, multiclass
                           clus
vv                          ERBB4 MUTATED ERBB4 WILD-TYPE
  ASIAN                                 9              67
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                26             142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(385) Variable = WDR59 MUTATION ANALYSIS
D385V1, survival
                 sevent
clus2               0   1
  WDR59 MUTATED     7   3
  WDR59 WILD-TYPE 174  77
  WDR59 MUTATED WDR59 WILD-TYPE 
             10             251 
  WDR59 MUTATED WDR59 WILD-TYPE 
              3              77 
$`WDR59 MUTATED`
TCGA-BR-4280 TCGA-CD-A4MI TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4444 TCGA-EQ-8122 
        6.61         0.10        15.95         1.02        47.05         7.99 
TCGA-FP-A4BE TCGA-HU-A4GX TCGA-HU-A4H8 TCGA-IP-7968 
       11.08        10.19         8.88         2.53 

$`WDR59 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       20.02         3.02        27.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-A4SO 
        5.92        15.16        13.78        14.76         0.62        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51         6.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       27.42        21.21         3.45        18.81         3.39 

  WDR59 MUTATED WDR59 WILD-TYPE 
            0.1             0.0 
  WDR59 MUTATED WDR59 WILD-TYPE 
          47.05          105.07 
  WDR59 MUTATED WDR59 WILD-TYPE 
          8.435          12.790 
[1] "0.1 - 47.0 (8.4)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.4"
D385V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WDR59 MUTATED         1        0        1        1         1         1
  WDR59 WILD-TYPE       0        9       26       25        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WDR59 MUTATED           1          1          2          1        1
  WDR59 WILD-TYPE         2         48         34         23       23
D385V3, multiclass
            clus
vv           WDR59 MUTATED WDR59 WILD-TYPE
  STAGE I                1               0
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              1               2
  STAGE IIIA             1              48
  STAGE IIIB             2              34
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WDR59 MUTATED     2   3   5   1
  WDR59 WILD-TYPE   9  69 117  74
D385V4, multiclass
    clus
vv   WDR59 MUTATED WDR59 WILD-TYPE
  T1             2               9
  T2             3              69
  T3             5             117
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  WDR59 MUTATED    1  6  4  0
  WDR59 WILD-TYPE 92 75 46 53
D385V5, multiclass
    clus
vv   WDR59 MUTATED WDR59 WILD-TYPE
  N0             1              92
  N1             6              75
  N2             4              46
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D385V6, binary
                 cls
clus                0   1
  WDR59 MUTATED     7   1
  WDR59 WILD-TYPE 250  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR59 MUTATED      7    1
  WDR59 WILD-TYPE  250   17
   clus
vv  WDR59 MUTATED WDR59 WILD-TYPE
  0             7             250
  1             1              17
[1] 2 2
[1] FALSE
D385V7, binary
                 cls
clus                0   1
  WDR59 MUTATED     3   8
  WDR59 WILD-TYPE 107 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR59 MUTATED      3    8
  WDR59 WILD-TYPE  107  171
        clus
vv       WDR59 MUTATED WDR59 WILD-TYPE
  FEMALE             3             107
  MALE               8             171
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  WDR59 MUTATED                                       2
  WDR59 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WDR59 MUTATED                                                        7
  WDR59 WILD-TYPE                                                    128
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WDR59 MUTATED                                                                   1
  WDR59 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  WDR59 MUTATED                                                  1
  WDR59 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  WDR59 MUTATED                                                          0
  WDR59 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  WDR59 MUTATED                                                           0
  WDR59 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  WDR59 MUTATED                                          0
  WDR59 WILD-TYPE                                        3
D385V8, multiclass
                                                                   clus
vv                                                                  WDR59 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  WDR59 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D385V9, binary
                 cls
clus                0   1
  WDR59 MUTATED     0  11
  WDR59 WILD-TYPE   5 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR59 MUTATED      0   11
  WDR59 WILD-TYPE    5  273
     clus
vv    WDR59 MUTATED WDR59 WILD-TYPE
  NO              0               5
  YES            11             273
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  WDR59 MUTATED     7   0   1   1
  WDR59 WILD-TYPE 220  10   9  23
D385V10, multiclass
    clus
vv   WDR59 MUTATED WDR59 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             1               9
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D385V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WDR59 MUTATED       3                         2     3
  WDR59 WILD-TYPE    73                         2   165
D385V12, multiclass
                           clus
vv                          WDR59 MUTATED WDR59 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             2               2
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(386) Variable = SPHK2 MUTATION ANALYSIS
D386V1, survival
                 sevent
clus2               0   1
  SPHK2 MUTATED     2   0
  SPHK2 WILD-TYPE 179  80
  SPHK2 MUTATED SPHK2 WILD-TYPE 
              2             259 
  SPHK2 MUTATED SPHK2 WILD-TYPE 
              0              80 
$`SPHK2 MUTATED`
TCGA-BR-A4QL TCGA-HU-A4G8 
       11.57        11.84 

$`SPHK2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  SPHK2 MUTATED SPHK2 WILD-TYPE 
          11.57            0.00 
  SPHK2 MUTATED SPHK2 WILD-TYPE 
          11.84          105.07 
  SPHK2 MUTATED SPHK2 WILD-TYPE 
         11.705          12.660 
[1] "11.6 - 11.8 (11.7)" "0.0 - 105.1 (12.7)"
[1] "Remove cluster labels:" "SPHK2 MUTATED"         
D386V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPHK2 MUTATED         0        0        1        0         0         1
  SPHK2 WILD-TYPE       1        9       26       26        31        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPHK2 MUTATED           0          0          1          0        0
  SPHK2 WILD-TYPE         3         49         35         24       24
D386V3, multiclass
            clus
vv           SPHK2 MUTATED SPHK2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              0              31
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SPHK2 MUTATED     0   1   2   0
  SPHK2 WILD-TYPE  11  71 120  75
D386V4, multiclass
    clus
vv   SPHK2 MUTATED SPHK2 WILD-TYPE
  T1             0              11
  T2             1              71
  T3             2             120
  T4             0              75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  SPHK2 MUTATED    1  1  0  1
  SPHK2 WILD-TYPE 92 80 50 52
D386V5, multiclass
    clus
vv   SPHK2 MUTATED SPHK2 WILD-TYPE
  N0             1              92
  N1             1              80
  N2             0              50
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D386V6, binary
                 cls
clus                0   1
  SPHK2 MUTATED     3   0
  SPHK2 WILD-TYPE 254  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPHK2 MUTATED      3    0
  SPHK2 WILD-TYPE  254   18
   clus
vv  SPHK2 MUTATED SPHK2 WILD-TYPE
  0             3             254
  1             0              18
[1] 2 2
[1] FALSE
D386V7, binary
                 cls
clus                0   1
  SPHK2 MUTATED     2   1
  SPHK2 WILD-TYPE 108 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPHK2 MUTATED      2    1
  SPHK2 WILD-TYPE  108  178
        clus
vv       SPHK2 MUTATED SPHK2 WILD-TYPE
  FEMALE             2             108
  MALE               1             178
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SPHK2 MUTATED                                       1
  SPHK2 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SPHK2 MUTATED                                                        1
  SPHK2 WILD-TYPE                                                    134
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SPHK2 MUTATED                                                                   1
  SPHK2 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SPHK2 MUTATED                                                  0
  SPHK2 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SPHK2 MUTATED                                                          0
  SPHK2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SPHK2 MUTATED                                                           0
  SPHK2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SPHK2 MUTATED                                          0
  SPHK2 WILD-TYPE                                        3
D386V8, multiclass
                                                                   clus
vv                                                                  SPHK2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        1
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  SPHK2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D386V9, binary
                 cls
clus                0   1
  SPHK2 MUTATED     0   3
  SPHK2 WILD-TYPE   5 281
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPHK2 MUTATED      0    3
  SPHK2 WILD-TYPE    5  281
     clus
vv    SPHK2 MUTATED SPHK2 WILD-TYPE
  NO              0               5
  YES             3             281
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SPHK2 MUTATED     2   0   0   0
  SPHK2 WILD-TYPE 225  10  10  24
D386V10, multiclass
[1] "Remove cluster labels:" "SPHK2 MUTATED"         
clus
  SPHK2 MUTATED SPHK2 WILD-TYPE 
              2             269 
     TCGA-B7-5816      TCGA-B7-5818      TCGA-BR-4183      TCGA-BR-4184 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-4187      TCGA-BR-4188      TCGA-BR-4191      TCGA-BR-4201 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256      TCGA-BR-4257 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4292 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-4294      TCGA-BR-4357      TCGA-BR-4361      TCGA-BR-4362 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-4363      TCGA-BR-4366      TCGA-BR-4368      TCGA-BR-4369 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-4370      TCGA-BR-4371      TCGA-BR-6452      TCGA-BR-6453 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-6852      TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-7707      TCGA-BR-7715      TCGA-BR-7716      TCGA-BR-7717 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-7722      TCGA-BR-7723      TCGA-BR-7851      TCGA-BR-7901 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-7957      TCGA-BR-7958      TCGA-BR-7959      TCGA-BR-8058 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8059      TCGA-BR-8077      TCGA-BR-8078      TCGA-BR-8080 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8081      TCGA-BR-8284      TCGA-BR-8286      TCGA-BR-8289 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8291      TCGA-BR-8295      TCGA-BR-8296      TCGA-BR-8297 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8360      TCGA-BR-8361      TCGA-BR-8363      TCGA-BR-8364 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8365      TCGA-BR-8366      TCGA-BR-8367      TCGA-BR-8368 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8369      TCGA-BR-8370      TCGA-BR-8371      TCGA-BR-8372 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8373      TCGA-BR-8380      TCGA-BR-8381      TCGA-BR-8382 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8384      TCGA-BR-8483      TCGA-BR-8484      TCGA-BR-8485 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8486      TCGA-BR-8487      TCGA-BR-8588      TCGA-BR-8589 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8590      TCGA-BR-8591      TCGA-BR-8592      TCGA-BR-8676 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8677      TCGA-BR-8678      TCGA-BR-8679      TCGA-BR-8680 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8682      TCGA-BR-8683      TCGA-BR-8686      TCGA-BR-8687 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8690      TCGA-BR-A44T      TCGA-BR-A44U      TCGA-BR-A452 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-A453      TCGA-BR-A4CQ      TCGA-BR-A4CR      TCGA-BR-A4CS 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-A4IU      TCGA-BR-A4IV      TCGA-BR-A4IY      TCGA-BR-A4IZ 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-A4J1      TCGA-BR-A4J2      TCGA-BR-A4J4      TCGA-BR-A4J6 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-A4J7      TCGA-BR-A4J8      TCGA-BR-A4PD      TCGA-BR-A4PE 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-A4PF      TCGA-BR-A4QI      TCGA-BR-A4QM      TCGA-CD-5800 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-CD-5801      TCGA-CD-5804      TCGA-CD-8524      TCGA-CD-8525 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-CD-8526      TCGA-CD-8527      TCGA-CD-8528      TCGA-CD-8529 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-CD-8530      TCGA-CD-8531      TCGA-CD-8532      TCGA-CD-8534 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-CD-8535      TCGA-CD-8536      TCGA-CD-A487      TCGA-CG-4300 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-CG-4301      TCGA-CG-4304      TCGA-CG-4305      TCGA-CG-4306 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-CG-4436      TCGA-CG-4437      TCGA-CG-4438      TCGA-CG-4440 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-CG-4441      TCGA-CG-4443      TCGA-CG-4444      TCGA-CG-4449 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-CG-4455      TCGA-CG-4462      TCGA-CG-4465      TCGA-CG-4466 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-CG-4469      TCGA-CG-4474      TCGA-CG-4475      TCGA-CG-4476 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-CG-4477      TCGA-CG-5717      TCGA-CG-5718      TCGA-CG-5719 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-CG-5720      TCGA-CG-5721      TCGA-CG-5722      TCGA-CG-5723 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-CG-5724      TCGA-CG-5726      TCGA-CG-5727      TCGA-CG-5728 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-CG-5730      TCGA-CG-5732      TCGA-CG-5733      TCGA-CG-5734 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-D7-5577      TCGA-D7-5578      TCGA-D7-5579      TCGA-D7-6518 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-D7-6519      TCGA-D7-6520      TCGA-D7-6521      TCGA-D7-6522 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-D7-6524      TCGA-D7-6525      TCGA-D7-6526      TCGA-D7-6527 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-D7-6528      TCGA-D7-6815      TCGA-D7-6817      TCGA-D7-6818 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-D7-6820      TCGA-D7-6822      TCGA-D7-8570      TCGA-D7-8572 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-D7-8573      TCGA-D7-8574      TCGA-D7-8575      TCGA-D7-8576 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-D7-8578      TCGA-D7-8579      TCGA-D7-A4YT      TCGA-D7-A4YU 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-D7-A4YV      TCGA-D7-A4YX      TCGA-D7-A4YY      TCGA-D7-A4Z0 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-EQ-5647      TCGA-EQ-A4SO      TCGA-F1-6177      TCGA-F1-6874 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-F1-6875      TCGA-F1-A448      TCGA-FP-7735      TCGA-FP-7829 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-FP-7998      TCGA-FP-8099      TCGA-FP-8209      TCGA-FP-8211 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-FP-8631      TCGA-FP-A4BE      TCGA-FP-A4BF      TCGA-HF-7132 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-HF-7133      TCGA-HF-7136      TCGA-HJ-7597      TCGA-HU-8243 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-HU-8245      TCGA-HU-8249      TCGA-HU-8602      TCGA-HU-8604 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-HU-8608      TCGA-HU-8610      TCGA-HU-A4G2      TCGA-HU-A4G3 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-HU-A4G6      TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-HU-A4GF      TCGA-HU-A4GH      TCGA-HU-A4GN      TCGA-HU-A4GP 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-HU-A4GQ      TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-HU-A4GY      TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-HU-A4H4      TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-HU-A4HD      TCGA-IN-7806      TCGA-IN-8462      TCGA-IN-8663 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-IP-7968 
"SPHK2 WILD-TYPE" 
D386V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SPHK2 MUTATED       1                         0     1
  SPHK2 WILD-TYPE    75                         4   167
D386V12, multiclass
[1] "Remove cluster labels:" "SPHK2 MUTATED"         
clus
  SPHK2 MUTATED SPHK2 WILD-TYPE 
              2             246 
     TCGA-B7-5816      TCGA-B7-5818      TCGA-BR-4183      TCGA-BR-4184 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-4187      TCGA-BR-4188      TCGA-BR-4191      TCGA-BR-4201 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256      TCGA-BR-4257 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4292 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-4294      TCGA-BR-4357      TCGA-BR-4361      TCGA-BR-4362 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-4363      TCGA-BR-4366      TCGA-BR-4368      TCGA-BR-4369 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-4370      TCGA-BR-4371      TCGA-BR-6452      TCGA-BR-6453 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-6852      TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-7707      TCGA-BR-7715      TCGA-BR-7716      TCGA-BR-7717 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-7722      TCGA-BR-7723      TCGA-BR-7851      TCGA-BR-7901 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-7957      TCGA-BR-7958      TCGA-BR-7959      TCGA-BR-8058 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8059      TCGA-BR-8077      TCGA-BR-8078      TCGA-BR-8080 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8081      TCGA-BR-8284      TCGA-BR-8286      TCGA-BR-8289 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8291      TCGA-BR-8295      TCGA-BR-8296      TCGA-BR-8297 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8360      TCGA-BR-8361      TCGA-BR-8363      TCGA-BR-8364 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8365      TCGA-BR-8366      TCGA-BR-8367      TCGA-BR-8368 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8369      TCGA-BR-8370      TCGA-BR-8371      TCGA-BR-8372 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8373      TCGA-BR-8380      TCGA-BR-8381      TCGA-BR-8382 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8384      TCGA-BR-8483      TCGA-BR-8484      TCGA-BR-8485 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8486      TCGA-BR-8487      TCGA-BR-8588      TCGA-BR-8589 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8590      TCGA-BR-8591      TCGA-BR-8592      TCGA-BR-8676 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8677      TCGA-BR-8678      TCGA-BR-8679      TCGA-BR-8680 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8682      TCGA-BR-8683      TCGA-BR-8686      TCGA-BR-8687 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-8690      TCGA-BR-A44T      TCGA-BR-A44U      TCGA-BR-A452 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-A453      TCGA-BR-A4CQ      TCGA-BR-A4CR      TCGA-BR-A4CS 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-A4IU      TCGA-BR-A4IV      TCGA-BR-A4IY      TCGA-BR-A4IZ 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-A4J1      TCGA-BR-A4J2      TCGA-BR-A4J4      TCGA-BR-A4J6 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-A4J7      TCGA-BR-A4J8      TCGA-BR-A4PD      TCGA-BR-A4PE 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-BR-A4PF      TCGA-BR-A4QI      TCGA-BR-A4QM      TCGA-CD-5798 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-CD-5799      TCGA-CD-5800      TCGA-CD-5801      TCGA-CD-5802 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-CD-5803      TCGA-CD-5804      TCGA-CD-5813      TCGA-CD-8524 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-CD-8525      TCGA-CD-8526      TCGA-CD-8527      TCGA-CD-8528 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-CD-8529      TCGA-CD-8530      TCGA-CD-8531      TCGA-CD-8532 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-CD-8534      TCGA-CD-8535      TCGA-CD-8536      TCGA-CD-A486 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-CD-A487      TCGA-CD-A489      TCGA-CD-A48A      TCGA-CD-A48C 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-CD-A4MG      TCGA-CD-A4MH      TCGA-CD-A4MI      TCGA-CD-A4MJ 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-D7-5577      TCGA-D7-5578      TCGA-D7-5579      TCGA-D7-6518 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-D7-6519      TCGA-D7-6520      TCGA-D7-6521      TCGA-D7-6522 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-D7-6524      TCGA-D7-6525      TCGA-D7-6526      TCGA-D7-6527 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-D7-6528      TCGA-D7-6815      TCGA-D7-6817      TCGA-D7-6818 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-D7-6820      TCGA-D7-6822      TCGA-D7-8570      TCGA-D7-8572 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-D7-8573      TCGA-D7-8574      TCGA-D7-8575      TCGA-D7-8576 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-D7-8578      TCGA-D7-8579      TCGA-D7-A4YT      TCGA-D7-A4YU 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-D7-A4YV      TCGA-D7-A4YX      TCGA-D7-A4YY      TCGA-D7-A4Z0 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-EQ-5647      TCGA-EQ-8122      TCGA-EQ-A4SO      TCGA-F1-6177 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-F1-6874      TCGA-F1-6875      TCGA-F1-A448      TCGA-FP-7735 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-FP-7829      TCGA-FP-7916      TCGA-FP-7998      TCGA-FP-8099 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-FP-8209      TCGA-FP-8210      TCGA-FP-8211      TCGA-FP-8631 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-FP-A4BE      TCGA-FP-A4BF      TCGA-HJ-7597      TCGA-HU-8243 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-HU-8245      TCGA-HU-8249      TCGA-HU-8602      TCGA-HU-8604 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-HU-8608      TCGA-HU-8610      TCGA-HU-A4G2      TCGA-HU-A4G3 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-HU-A4G6      TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-HU-A4GF      TCGA-HU-A4GH      TCGA-HU-A4GN      TCGA-HU-A4GP 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-HU-A4GQ      TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-HU-A4GY      TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-HU-A4H4      TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-HU-A4HD      TCGA-IN-7806      TCGA-IN-7808      TCGA-IN-8462 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 
     TCGA-IN-8663      TCGA-IP-7968 
"SPHK2 WILD-TYPE" "SPHK2 WILD-TYPE" 

Clustering(387) Variable = RUSC2 MUTATION ANALYSIS
D387V1, survival
                 sevent
clus2               0   1
  RUSC2 MUTATED    11   5
  RUSC2 WILD-TYPE 170  75
  RUSC2 MUTATED RUSC2 WILD-TYPE 
             16             245 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
              5              75 
$`RUSC2 MUTATED`
TCGA-B7-5816 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8487 
       26.70         6.61        34.68        12.26        19.50         1.12 
TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-5579 
        0.10         1.02         6.02        28.96        65.10        11.93 
TCGA-HJ-7597 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4H4 
       26.47        11.84         0.10        23.84 

$`RUSC2 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       30.90         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
       16.31         2.20        15.58         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
        0.99       105.07        12.03        79.07         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        12.36        12.66        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       11.08         5.52         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       12.95        19.36        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  RUSC2 MUTATED RUSC2 WILD-TYPE 
            0.1             0.0 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
          65.10          105.07 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
         12.095          12.660 
[1] "0.1 - 65.1 (12.1)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.2"
D387V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RUSC2 MUTATED         1        1        2        1         2         4
  RUSC2 WILD-TYPE       0        8       25       25        29        40
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RUSC2 MUTATED           1          1          1          2        2
  RUSC2 WILD-TYPE         2         48         35         22       22
D387V3, multiclass
            clus
vv           RUSC2 MUTATED RUSC2 WILD-TYPE
  STAGE I                1               0
  STAGE IA               1               8
  STAGE IB               2              25
  STAGE II               1              25
  STAGE IIA              2              29
  STAGE IIB              4              40
  STAGE III              1               2
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             2              22
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RUSC2 MUTATED     2   5   7   5
  RUSC2 WILD-TYPE   9  67 115  70
D387V4, multiclass
    clus
vv   RUSC2 MUTATED RUSC2 WILD-TYPE
  T1             2               9
  T2             5              67
  T3             7             115
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  RUSC2 MUTATED    7  6  5  0
  RUSC2 WILD-TYPE 86 75 45 53
D387V5, multiclass
    clus
vv   RUSC2 MUTATED RUSC2 WILD-TYPE
  N0             7              86
  N1             6              75
  N2             5              45
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D387V6, binary
                 cls
clus                0   1
  RUSC2 MUTATED    15   1
  RUSC2 WILD-TYPE 242  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC2 MUTATED     15    1
  RUSC2 WILD-TYPE  242   17
   clus
vv  RUSC2 MUTATED RUSC2 WILD-TYPE
  0            15             242
  1             1              17
[1] 2 2
[1] FALSE
D387V7, binary
                 cls
clus                0   1
  RUSC2 MUTATED    11   8
  RUSC2 WILD-TYPE  99 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC2 MUTATED     11    8
  RUSC2 WILD-TYPE   99  171
        clus
vv       RUSC2 MUTATED RUSC2 WILD-TYPE
  FEMALE            11              99
  MALE               8             171
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RUSC2 MUTATED                                       2
  RUSC2 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RUSC2 MUTATED                                                        9
  RUSC2 WILD-TYPE                                                    126
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RUSC2 MUTATED                                                                   3
  RUSC2 WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RUSC2 MUTATED                                                  2
  RUSC2 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RUSC2 MUTATED                                                          2
  RUSC2 WILD-TYPE                                                       14
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RUSC2 MUTATED                                                           0
  RUSC2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RUSC2 MUTATED                                          1
  RUSC2 WILD-TYPE                                        2
D387V8, multiclass
                                                                   clus
vv                                                                  RUSC2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  RUSC2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D387V9, binary
                 cls
clus                0   1
  RUSC2 MUTATED     1  18
  RUSC2 WILD-TYPE   4 266
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC2 MUTATED      1   18
  RUSC2 WILD-TYPE    4  266
     clus
vv    RUSC2 MUTATED RUSC2 WILD-TYPE
  NO              1               4
  YES            18             266
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RUSC2 MUTATED    13   1   1   2
  RUSC2 WILD-TYPE 214   9   9  22
D387V10, multiclass
    clus
vv   RUSC2 MUTATED RUSC2 WILD-TYPE
  R0            13             214
  R1             1               9
  R2             1               9
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D387V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RUSC2 MUTATED       4                         1     9
  RUSC2 WILD-TYPE    72                         3   159
D387V12, multiclass
                           clus
vv                          RUSC2 MUTATED RUSC2 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 9             159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(388) Variable = CHST15 MUTATION ANALYSIS
D388V1, survival
                  sevent
clus2                0   1
  CHST15 MUTATED     6   5
  CHST15 WILD-TYPE 175  75
  CHST15 MUTATED CHST15 WILD-TYPE 
              11              250 
  CHST15 MUTATED CHST15 WILD-TYPE 
               5               75 
$`CHST15 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8360 TCGA-BR-8382 TCGA-BR-8487 
       26.70         6.97        30.90         6.18        15.85         1.12 
TCGA-BR-A4PE TCGA-CD-8536 TCGA-CG-4306 TCGA-CG-5726 TCGA-HU-A4GQ 
       20.42         0.10         1.02        28.96         0.10 

$`CHST15 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 
       11.70         6.61         4.64         7.43        18.35         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        2.66        16.31         2.20        15.58         7.40        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.13         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        11.77        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  CHST15 MUTATED CHST15 WILD-TYPE 
             0.1              0.0 
  CHST15 MUTATED CHST15 WILD-TYPE 
           30.90           105.07 
  CHST15 MUTATED CHST15 WILD-TYPE 
            6.97            12.64 
[1] "0.1 - 30.9 (7.0)"   "0.0 - 105.1 (12.6)"
[1] "hr=" "1.5"
D388V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CHST15 MUTATED         0        1        1        2         2         1
  CHST15 WILD-TYPE       1        8       26       24        29        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHST15 MUTATED           0          2          0          2        1
  CHST15 WILD-TYPE         3         47         36         22       23
D388V3, multiclass
            clus
vv           CHST15 MUTATED CHST15 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                1               26
  STAGE II                2               24
  STAGE IIA               2               29
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              0               36
  STAGE IIIC              2               22
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CHST15 MUTATED     1   3   5   4
  CHST15 WILD-TYPE  10  69 117  71
D388V4, multiclass
    clus
vv   CHST15 MUTATED CHST15 WILD-TYPE
  T1              1               10
  T2              3               69
  T3              5              117
  T4              4               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CHST15 MUTATED    7  2  2  1
  CHST15 WILD-TYPE 86 79 48 52
D388V5, multiclass
    clus
vv   CHST15 MUTATED CHST15 WILD-TYPE
  N0              7               86
  N1              2               79
  N2              2               48
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D388V6, binary
                  cls
clus                 0   1
  CHST15 MUTATED    11   1
  CHST15 WILD-TYPE 246  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHST15 MUTATED     11    1
  CHST15 WILD-TYPE  246   17
   clus
vv  CHST15 MUTATED CHST15 WILD-TYPE
  0             11              246
  1              1               17
[1] 2 2
[1] FALSE
D388V7, binary
                  cls
clus                 0   1
  CHST15 MUTATED     6   7
  CHST15 WILD-TYPE 104 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHST15 MUTATED      6    7
  CHST15 WILD-TYPE  104  172
        clus
vv       CHST15 MUTATED CHST15 WILD-TYPE
  FEMALE              6              104
  MALE                7              172
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CHST15 MUTATED                                       1
  CHST15 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CHST15 MUTATED                                                        8
  CHST15 WILD-TYPE                                                    127
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CHST15 MUTATED                                                                   2
  CHST15 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CHST15 MUTATED                                                  1
  CHST15 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CHST15 MUTATED                                                          1
  CHST15 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CHST15 MUTATED                                                           0
  CHST15 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CHST15 MUTATED                                          0
  CHST15 WILD-TYPE                                        3
D388V8, multiclass
                                                                   clus
vv                                                                  CHST15 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  CHST15 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D388V9, binary
                  cls
clus                 0   1
  CHST15 MUTATED     1  12
  CHST15 WILD-TYPE   4 272
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHST15 MUTATED      1   12
  CHST15 WILD-TYPE    4  272
     clus
vv    CHST15 MUTATED CHST15 WILD-TYPE
  NO               1                4
  YES             12              272
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CHST15 MUTATED     9   0   1   3
  CHST15 WILD-TYPE 218  10   9  21
D388V10, multiclass
    clus
vv   CHST15 MUTATED CHST15 WILD-TYPE
  R0              9              218
  R1              0               10
  R2              1                9
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D388V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CHST15 MUTATED       2                         0     8
  CHST15 WILD-TYPE    74                         4   160
D388V12, multiclass
                           clus
vv                          CHST15 MUTATED CHST15 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  8              160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(389) Variable = TAF1L MUTATION ANALYSIS
D389V1, survival
                 sevent
clus2               0   1
  TAF1L MUTATED    15   5
  TAF1L WILD-TYPE 166  75
  TAF1L MUTATED TAF1L WILD-TYPE 
             20             241 
  TAF1L MUTATED TAF1L WILD-TYPE 
              5              75 
$`TAF1L MUTATED`
TCGA-B7-5818 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6705 TCGA-BR-6802 
       11.70        30.90         6.61        34.68        25.61        30.90 
TCGA-BR-7707 TCGA-BR-8284 TCGA-BR-8297 TCGA-BR-8485 TCGA-BR-8591 TCGA-BR-8680 
       23.93         8.05         7.40         9.21        13.45        15.81 
TCGA-BR-A4QL TCGA-CG-4305 TCGA-CG-4477 TCGA-D7-6521 TCGA-D7-A4YX TCGA-HU-A4G8 
       11.57        15.95        30.97        18.54        15.16        11.84 
TCGA-HU-A4GH TCGA-HU-A4GQ 
       11.77         0.10 

$`TAF1L WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 
       19.33        39.12        26.10         9.17        32.78        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       19.89         8.98        21.11        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 
       12.95         2.66        16.31         2.20        15.58         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 
        0.26        15.85         3.72         5.39        25.18        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        15.81         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       11.93        19.13        20.55        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       16.44         5.92        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        24.20         3.25        22.75        25.81 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  TAF1L MUTATED TAF1L WILD-TYPE 
            0.1             0.0 
  TAF1L MUTATED TAF1L WILD-TYPE 
          34.68          105.07 
  TAF1L MUTATED TAF1L WILD-TYPE 
         14.305          12.590 
[1] "0.1 - 34.7 (14.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.6"
D389V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TAF1L MUTATED         1        1        3        1         1         2
  TAF1L WILD-TYPE       0        8       24       25        30        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TAF1L MUTATED           1          2          2          5        1
  TAF1L WILD-TYPE         2         47         34         19       23
D389V3, multiclass
            clus
vv           TAF1L MUTATED TAF1L WILD-TYPE
  STAGE I                1               0
  STAGE IA               1               8
  STAGE IB               3              24
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              2              42
  STAGE III              1               2
  STAGE IIIA             2              47
  STAGE IIIB             2              34
  STAGE IIIC             5              19
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TAF1L MUTATED     2   8   6   6
  TAF1L WILD-TYPE   9  64 116  69
D389V4, multiclass
    clus
vv   TAF1L MUTATED TAF1L WILD-TYPE
  T1             2               9
  T2             8              64
  T3             6             116
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  TAF1L MUTATED    5  6  4  6
  TAF1L WILD-TYPE 88 75 46 47
D389V5, multiclass
    clus
vv   TAF1L MUTATED TAF1L WILD-TYPE
  N0             5              88
  N1             6              75
  N2             4              46
  N3             6              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D389V6, binary
                 cls
clus                0   1
  TAF1L MUTATED    21   1
  TAF1L WILD-TYPE 236  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1L MUTATED     21    1
  TAF1L WILD-TYPE  236   17
   clus
vv  TAF1L MUTATED TAF1L WILD-TYPE
  0            21             236
  1             1              17
[1] 2 2
[1] FALSE
D389V7, binary
                 cls
clus                0   1
  TAF1L MUTATED    11  12
  TAF1L WILD-TYPE  99 167
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1L MUTATED     11   12
  TAF1L WILD-TYPE   99  167
        clus
vv       TAF1L MUTATED TAF1L WILD-TYPE
  FEMALE            11              99
  MALE              12             167
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TAF1L MUTATED                                       4
  TAF1L WILD-TYPE                                    46
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TAF1L MUTATED                                                       13
  TAF1L WILD-TYPE                                                    122
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TAF1L MUTATED                                                                   2
  TAF1L WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TAF1L MUTATED                                                  4
  TAF1L WILD-TYPE                                               34
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TAF1L MUTATED                                                          0
  TAF1L WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TAF1L MUTATED                                                           0
  TAF1L WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TAF1L MUTATED                                          0
  TAF1L WILD-TYPE                                        3
D389V8, multiclass
                                                                   clus
vv                                                                  TAF1L MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       13
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  TAF1L WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        122
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D389V9, binary
                 cls
clus                0   1
  TAF1L MUTATED     0  23
  TAF1L WILD-TYPE   5 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1L MUTATED      0   23
  TAF1L WILD-TYPE    5  261
     clus
vv    TAF1L MUTATED TAF1L WILD-TYPE
  NO              0               5
  YES            23             261
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TAF1L MUTATED    18   0   0   4
  TAF1L WILD-TYPE 209  10  10  20
D389V10, multiclass
    clus
vv   TAF1L MUTATED TAF1L WILD-TYPE
  R0            18             209
  R1             0              10
  R2             0              10
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D389V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TAF1L MUTATED       4                         1    16
  TAF1L WILD-TYPE    72                         3   152
D389V12, multiclass
                           clus
vv                          TAF1L MUTATED TAF1L WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                16             152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(390) Variable = USP8 MUTATION ANALYSIS
D390V1, survival
                sevent
clus2              0   1
  USP8 MUTATED     5   0
  USP8 WILD-TYPE 176  80
  USP8 MUTATED USP8 WILD-TYPE 
             5            256 
  USP8 MUTATED USP8 WILD-TYPE 
             0             80 
$`USP8 MUTATED`
TCGA-BR-6452 TCGA-BR-8382 TCGA-BR-8487 TCGA-CG-4436 TCGA-HU-A4H8 
       34.68        15.85         1.12         7.99         8.88 

$`USP8 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       19.17        14.79         0.26         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
       19.36        23.84        12.30         9.67        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  USP8 MUTATED USP8 WILD-TYPE 
          1.12           0.00 
  USP8 MUTATED USP8 WILD-TYPE 
         34.68         105.07 
  USP8 MUTATED USP8 WILD-TYPE 
          8.88          12.64 
[1] "1.1 - 34.7 (8.9)"   "0.0 - 105.1 (12.6)"
[1] "hr="     "9200000"
D390V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  USP8 MUTATED         0        0        2        0         2         0
  USP8 WILD-TYPE       1        9       25       26        29        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  USP8 MUTATED           0          1          0          1        0
  USP8 WILD-TYPE         3         48         36         23       24
D390V3, multiclass
            clus
vv           USP8 MUTATED USP8 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              0             26
  STAGE IIA             2             29
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            1             23
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  USP8 MUTATED     2   1   2   2
  USP8 WILD-TYPE   9  71 120  73
D390V4, multiclass
    clus
vv   USP8 MUTATED USP8 WILD-TYPE
  T1            2              9
  T2            1             71
  T3            2            120
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  USP8 MUTATED    4  1  0  1
  USP8 WILD-TYPE 89 80 50 52
D390V5, multiclass
    clus
vv   USP8 MUTATED USP8 WILD-TYPE
  N0            4             89
  N1            1             80
  N2            0             50
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D390V6, binary
                cls
clus               0   1
  USP8 MUTATED     7   0
  USP8 WILD-TYPE 250  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP8 MUTATED      7    0
  USP8 WILD-TYPE  250   18
   clus
vv  USP8 MUTATED USP8 WILD-TYPE
  0            7            250
  1            0             18
[1] 2 2
[1] FALSE
D390V7, binary
                cls
clus               0   1
  USP8 MUTATED     5   2
  USP8 WILD-TYPE 105 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP8 MUTATED      5    2
  USP8 WILD-TYPE  105  177
        clus
vv       USP8 MUTATED USP8 WILD-TYPE
  FEMALE            5            105
  MALE              2            177
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  USP8 MUTATED                                       0
  USP8 WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  USP8 MUTATED                                                        5
  USP8 WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  USP8 MUTATED                                                                   1
  USP8 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  USP8 MUTATED                                                  1
  USP8 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  USP8 MUTATED                                                          0
  USP8 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  USP8 MUTATED                                                           0
  USP8 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  USP8 MUTATED                                          0
  USP8 WILD-TYPE                                        3
D390V8, multiclass
                                                                   clus
vv                                                                  USP8 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  USP8 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D390V9, binary
                cls
clus               0   1
  USP8 MUTATED     0   7
  USP8 WILD-TYPE   5 277
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP8 MUTATED      0    7
  USP8 WILD-TYPE    5  277
     clus
vv    USP8 MUTATED USP8 WILD-TYPE
  NO             0              5
  YES            7            277
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  USP8 MUTATED     5   0   0   2
  USP8 WILD-TYPE 222  10  10  22
D390V10, multiclass
    clus
vv   USP8 MUTATED USP8 WILD-TYPE
  R0            5            222
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D390V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  USP8 MUTATED       1                         0     5
  USP8 WILD-TYPE    75                         4   163
D390V12, multiclass
                           clus
vv                          USP8 MUTATED USP8 WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                5            163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(391) Variable = MYB MUTATION ANALYSIS
D391V1, survival
               sevent
clus2             0   1
  MYB MUTATED     4   1
  MYB WILD-TYPE 177  79
  MYB MUTATED MYB WILD-TYPE 
            5           256 
  MYB MUTATED MYB WILD-TYPE 
            1            79 
$`MYB MUTATED`
TCGA-BR-4201 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8081 TCGA-HU-A4GU 
       30.90        32.78        23.93        20.55         6.25 

$`MYB WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69        12.26         9.60         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  MYB MUTATED MYB WILD-TYPE 
         6.25          0.00 
  MYB MUTATED MYB WILD-TYPE 
        32.78        105.07 
  MYB MUTATED MYB WILD-TYPE 
       23.930        12.575 
[1] "6.2 - 32.8 (23.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.8"
D391V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MYB MUTATED         0        0        2        0         1         2
  MYB WILD-TYPE       1        9       25       26        30        42
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MYB MUTATED           0          0          0          0        0
  MYB WILD-TYPE         3         49         36         24       24
D391V3, multiclass
            clus
vv           MYB MUTATED MYB WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             9
  STAGE IB             2            25
  STAGE II             0            26
  STAGE IIA            1            30
  STAGE IIB            2            42
  STAGE III            0             3
  STAGE IIIA           0            49
  STAGE IIIB           0            36
  STAGE IIIC           0            24
  STAGE IV             0            24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MYB MUTATED     0   3   2   1
  MYB WILD-TYPE  11  69 120  74
D391V4, multiclass
    clus
vv   MYB MUTATED MYB WILD-TYPE
  T1           0            11
  T2           3            69
  T3           2           120
  T4           1            74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  MYB MUTATED    4  1  0  0
  MYB WILD-TYPE 89 80 50 53
D391V5, multiclass
    clus
vv   MYB MUTATED MYB WILD-TYPE
  N0           4            89
  N1           1            80
  N2           0            50
  N3           0            53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D391V6, binary
               cls
clus              0   1
  MYB MUTATED     6   0
  MYB WILD-TYPE 251  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  MYB MUTATED      6    0
  MYB WILD-TYPE  251   18
   clus
vv  MYB MUTATED MYB WILD-TYPE
  0           6           251
  1           0            18
[1] 2 2
[1] FALSE
D391V7, binary
               cls
clus              0   1
  MYB MUTATED     4   2
  MYB WILD-TYPE 106 177
[1] "tbl2"
               cls
clus            [,1] [,2]
  MYB MUTATED      4    2
  MYB WILD-TYPE  106  177
        clus
vv       MYB MUTATED MYB WILD-TYPE
  FEMALE           4           106
  MALE             2           177
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MYB MUTATED                                       1
  MYB WILD-TYPE                                    49
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MYB MUTATED                                                        4
  MYB WILD-TYPE                                                    131
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MYB MUTATED                                                                   1
  MYB WILD-TYPE                                                                39
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MYB MUTATED                                                  0
  MYB WILD-TYPE                                               38
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MYB MUTATED                                                          0
  MYB WILD-TYPE                                                       16
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MYB MUTATED                                                           0
  MYB WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MYB MUTATED                                          0
  MYB WILD-TYPE                                        3
D391V8, multiclass
                                                                   clus
vv                                                                  MYB MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  MYB WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D391V9, binary
               cls
clus              0   1
  MYB MUTATED     0   6
  MYB WILD-TYPE   5 278
[1] "tbl2"
               cls
clus            [,1] [,2]
  MYB MUTATED      0    6
  MYB WILD-TYPE    5  278
     clus
vv    MYB MUTATED MYB WILD-TYPE
  NO            0             5
  YES           6           278
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  MYB MUTATED     5   0   0   1
  MYB WILD-TYPE 222  10  10  23
D391V10, multiclass
    clus
vv   MYB MUTATED MYB WILD-TYPE
  R0           5           222
  R1           0            10
  R2           0            10
  RX           1            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D391V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MYB MUTATED       1                         0     4
  MYB WILD-TYPE    75                         4   164
D391V12, multiclass
                           clus
vv                          MYB MUTATED MYB WILD-TYPE
  ASIAN                               1            75
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                               4           164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(392) Variable = CREM MUTATION ANALYSIS
D392V1, survival
                sevent
clus2              0   1
  CREM MUTATED     4   0
  CREM WILD-TYPE 177  80
  CREM MUTATED CREM WILD-TYPE 
             4            257 
  CREM MUTATED CREM WILD-TYPE 
             0             80 
$`CREM MUTATED`
TCGA-B7-5816 TCGA-BR-8680 TCGA-HU-A4H4 TCGA-HU-A4H8 
       26.70        15.81        23.84         8.88 

$`CREM WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
        2.10        12.95        19.36        12.30         9.67        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  CREM MUTATED CREM WILD-TYPE 
          8.88           0.00 
  CREM MUTATED CREM WILD-TYPE 
         26.70         105.07 
  CREM MUTATED CREM WILD-TYPE 
        19.825         12.590 
[1] "8.9 - 26.7 (19.8)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "9200000"
D392V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CREM MUTATED         0        0        1        0         0         2
  CREM WILD-TYPE       1        9       26       26        31        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CREM MUTATED           0          0          0          0        1
  CREM WILD-TYPE         3         49         36         24       23
D392V3, multiclass
            clus
vv           CREM MUTATED CREM WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             0             31
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CREM MUTATED     1   1   0   2
  CREM WILD-TYPE  10  71 122  73
D392V4, multiclass
    clus
vv   CREM MUTATED CREM WILD-TYPE
  T1            1             10
  T2            1             71
  T3            0            122
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  CREM MUTATED    1  1  2  0
  CREM WILD-TYPE 92 80 48 53
D392V5, multiclass
    clus
vv   CREM MUTATED CREM WILD-TYPE
  N0            1             92
  N1            1             80
  N2            2             48
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D392V6, binary
                cls
clus               0   1
  CREM MUTATED     3   1
  CREM WILD-TYPE 254  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  CREM MUTATED      3    1
  CREM WILD-TYPE  254   17
   clus
vv  CREM MUTATED CREM WILD-TYPE
  0            3            254
  1            1             17
[1] 2 2
[1] FALSE
D392V7, binary
                cls
clus               0   1
  CREM MUTATED     2   2
  CREM WILD-TYPE 108 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  CREM MUTATED      2    2
  CREM WILD-TYPE  108  177
        clus
vv       CREM MUTATED CREM WILD-TYPE
  FEMALE            2            108
  MALE              2            177
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CREM MUTATED                                       1
  CREM WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CREM MUTATED                                                        0
  CREM WILD-TYPE                                                    135
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CREM MUTATED                                                                   0
  CREM WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CREM MUTATED                                                  3
  CREM WILD-TYPE                                               35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CREM MUTATED                                                          0
  CREM WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CREM MUTATED                                                           0
  CREM WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CREM MUTATED                                          0
  CREM WILD-TYPE                                        3
D392V8, multiclass
                                                                   clus
vv                                                                  CREM MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       0
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  CREM WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       135
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D392V9, binary
                cls
clus               0   1
  CREM MUTATED     0   4
  CREM WILD-TYPE   5 280
[1] "tbl2"
                cls
clus             [,1] [,2]
  CREM MUTATED      0    4
  CREM WILD-TYPE    5  280
     clus
vv    CREM MUTATED CREM WILD-TYPE
  NO             0              5
  YES            4            280
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CREM MUTATED     4   0   0   0
  CREM WILD-TYPE 223  10  10  24
D392V10, multiclass
    clus
vv   CREM MUTATED CREM WILD-TYPE
  R0            4            223
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D392V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CREM MUTATED       3                         0     1
  CREM WILD-TYPE    73                         4   167
D392V12, multiclass
                           clus
vv                          CREM MUTATED CREM WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                1            167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(393) Variable = CD93 MUTATION ANALYSIS
D393V1, survival
                sevent
clus2              0   1
  CD93 MUTATED     8   2
  CD93 WILD-TYPE 173  78
  CD93 MUTATED CD93 WILD-TYPE 
            10            251 
  CD93 MUTATED CD93 WILD-TYPE 
             2             78 
$`CD93 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8360 TCGA-BR-8382 TCGA-BR-8678 
        6.97        34.68        24.76         6.18        15.85        11.54 
TCGA-D7-A4YV TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H3 
        5.92         6.51         6.25        19.36 

$`CD93 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 
       30.90        31.20        32.94        12.82         9.21        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        2.66        16.31         2.20        15.58         7.40        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         0.10        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       12.95        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  CD93 MUTATED CD93 WILD-TYPE 
          5.92           0.00 
  CD93 MUTATED CD93 WILD-TYPE 
         34.68         105.07 
  CD93 MUTATED CD93 WILD-TYPE 
         9.255         12.660 
[1] "5.9 - 34.7 (9.3)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.5"
D393V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CD93 MUTATED         0        1        1        0         3         2
  CD93 WILD-TYPE       1        8       26       26        28        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CD93 MUTATED           0          1          0          2        0
  CD93 WILD-TYPE         3         48         36         22       24
D393V3, multiclass
            clus
vv           CD93 MUTATED CD93 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             3             28
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            2             22
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CD93 MUTATED     1   1   6   2
  CD93 WILD-TYPE  10  71 116  73
D393V4, multiclass
    clus
vv   CD93 MUTATED CD93 WILD-TYPE
  T1            1             10
  T2            1             71
  T3            6            116
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  CD93 MUTATED    5  4  0  2
  CD93 WILD-TYPE 88 77 50 51
D393V5, multiclass
    clus
vv   CD93 MUTATED CD93 WILD-TYPE
  N0            5             88
  N1            4             77
  N2            0             50
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D393V6, binary
                cls
clus               0   1
  CD93 MUTATED    10   0
  CD93 WILD-TYPE 247  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD93 MUTATED     10    0
  CD93 WILD-TYPE  247   18
   clus
vv  CD93 MUTATED CD93 WILD-TYPE
  0           10            247
  1            0             18
[1] 2 2
[1] FALSE
D393V7, binary
                cls
clus               0   1
  CD93 MUTATED     6   5
  CD93 WILD-TYPE 104 174
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD93 MUTATED      6    5
  CD93 WILD-TYPE  104  174
        clus
vv       CD93 MUTATED CD93 WILD-TYPE
  FEMALE            6            104
  MALE              5            174
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CD93 MUTATED                                       2
  CD93 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CD93 MUTATED                                                        5
  CD93 WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CD93 MUTATED                                                                   1
  CD93 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CD93 MUTATED                                                  2
  CD93 WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CD93 MUTATED                                                          0
  CD93 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CD93 MUTATED                                                           1
  CD93 WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CD93 MUTATED                                          0
  CD93 WILD-TYPE                                        3
D393V8, multiclass
                                                                   clus
vv                                                                  CD93 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  CD93 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D393V9, binary
                cls
clus               0   1
  CD93 MUTATED     0  11
  CD93 WILD-TYPE   5 273
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD93 MUTATED      0   11
  CD93 WILD-TYPE    5  273
     clus
vv    CD93 MUTATED CD93 WILD-TYPE
  NO             0              5
  YES           11            273
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CD93 MUTATED     9   0   0   2
  CD93 WILD-TYPE 218  10  10  22
D393V10, multiclass
    clus
vv   CD93 MUTATED CD93 WILD-TYPE
  R0            9            218
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D393V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD93 MUTATED       3                         0     8
  CD93 WILD-TYPE    73                         4   160
D393V12, multiclass
                           clus
vv                          CD93 MUTATED CD93 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                8            160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(394) Variable = B3GNT5 MUTATION ANALYSIS
D394V1, survival
                  sevent
clus2                0   1
  B3GNT5 MUTATED     9   0
  B3GNT5 WILD-TYPE 172  80
  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
               9              252 
  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
               0               80 
$`B3GNT5 MUTATED`
TCGA-BR-7851 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-5721 
       12.43         4.31        15.85         1.12        15.81         6.02 
TCGA-CG-5723 TCGA-HU-A4GU TCGA-HU-A4GX 
      105.07         6.25        10.19 

$`B3GNT5 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
       36.00         1.02         0.99         0.99        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         0.10         6.51         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
            1.12             0.00 
  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
          105.07            79.07 
  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
           10.19            12.71 
[1] "1.1 - 105.1 (10.2)" "0.0 - 79.1 (12.7)" 
[1] "hr="     "2.9e+07"
D394V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  B3GNT5 MUTATED         0        0        1        1         1         2
  B3GNT5 WILD-TYPE       1        9       26       25        30        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  B3GNT5 MUTATED           0          0          0          2        3
  B3GNT5 WILD-TYPE         3         49         36         22       21
D394V3, multiclass
            clus
vv           B3GNT5 MUTATED B3GNT5 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                1               25
  STAGE IIA               1               30
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              2               22
  STAGE IV                3               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  B3GNT5 MUTATED     0   2   2   6
  B3GNT5 WILD-TYPE  11  70 120  69
D394V4, multiclass
    clus
vv   B3GNT5 MUTATED B3GNT5 WILD-TYPE
  T1              0               11
  T2              2               70
  T3              2              120
  T4              6               69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  B3GNT5 MUTATED    3  3  3  1
  B3GNT5 WILD-TYPE 90 78 47 52
D394V5, multiclass
    clus
vv   B3GNT5 MUTATED B3GNT5 WILD-TYPE
  N0              3               90
  N1              3               78
  N2              3               47
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D394V6, binary
                  cls
clus                 0   1
  B3GNT5 MUTATED     9   1
  B3GNT5 WILD-TYPE 248  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  B3GNT5 MUTATED      9    1
  B3GNT5 WILD-TYPE  248   17
   clus
vv  B3GNT5 MUTATED B3GNT5 WILD-TYPE
  0              9              248
  1              1               17
[1] 2 2
[1] FALSE
D394V7, binary
                  cls
clus                 0   1
  B3GNT5 MUTATED     5   5
  B3GNT5 WILD-TYPE 105 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  B3GNT5 MUTATED      5    5
  B3GNT5 WILD-TYPE  105  174
        clus
vv       B3GNT5 MUTATED B3GNT5 WILD-TYPE
  FEMALE              5              105
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  B3GNT5 MUTATED                                       2
  B3GNT5 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  B3GNT5 MUTATED                                                        5
  B3GNT5 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  B3GNT5 MUTATED                                                                   2
  B3GNT5 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  B3GNT5 MUTATED                                                  1
  B3GNT5 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  B3GNT5 MUTATED                                                          0
  B3GNT5 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  B3GNT5 MUTATED                                                           0
  B3GNT5 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  B3GNT5 MUTATED                                          0
  B3GNT5 WILD-TYPE                                        3
D394V8, multiclass
                                                                   clus
vv                                                                  B3GNT5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  B3GNT5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D394V9, binary
                  cls
clus                 0   1
  B3GNT5 MUTATED     0  10
  B3GNT5 WILD-TYPE   5 274
[1] "tbl2"
                  cls
clus               [,1] [,2]
  B3GNT5 MUTATED      0   10
  B3GNT5 WILD-TYPE    5  274
     clus
vv    B3GNT5 MUTATED B3GNT5 WILD-TYPE
  NO               0                5
  YES             10              274
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  B3GNT5 MUTATED     9   0   0   1
  B3GNT5 WILD-TYPE 218  10  10  23
D394V10, multiclass
    clus
vv   B3GNT5 MUTATED B3GNT5 WILD-TYPE
  R0              9              218
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D394V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  B3GNT5 MUTATED       3                         0     5
  B3GNT5 WILD-TYPE    73                         4   163
D394V12, multiclass
                           clus
vv                          B3GNT5 MUTATED B3GNT5 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  5              163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(395) Variable = ART1 MUTATION ANALYSIS
D395V1, survival
                sevent
clus2              0   1
  ART1 MUTATED     5   1
  ART1 WILD-TYPE 176  79
  ART1 MUTATED ART1 WILD-TYPE 
             6            255 
  ART1 MUTATED ART1 WILD-TYPE 
             1             79 
$`ART1 MUTATED`
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8078 TCGA-CD-5800 TCGA-F1-6874 TCGA-HU-A4H8 
        6.61        34.68        12.26        13.15        14.47         8.88 

$`ART1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
       18.35        30.90         6.18         9.57        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 
       11.57         5.13         2.83         3.25        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.99        16.24        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  ART1 MUTATED ART1 WILD-TYPE 
          6.61           0.00 
  ART1 MUTATED ART1 WILD-TYPE 
         34.68         105.07 
  ART1 MUTATED ART1 WILD-TYPE 
        12.705         12.620 
[1] "6.6 - 34.7 (12.7)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2"  
D395V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ART1 MUTATED         0        0        3        1         1         1
  ART1 WILD-TYPE       1        9       24       25        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ART1 MUTATED           1          0          0          0        0
  ART1 WILD-TYPE         2         49         36         24       24
D395V3, multiclass
            clus
vv           ART1 MUTATED ART1 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              3             24
  STAGE II              1             25
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             1              2
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ART1 MUTATED     1   3   2   1
  ART1 WILD-TYPE  10  69 120  74
D395V4, multiclass
    clus
vv   ART1 MUTATED ART1 WILD-TYPE
  T1            1             10
  T2            3             69
  T3            2            120
  T4            1             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  ART1 MUTATED    5  2  0  0
  ART1 WILD-TYPE 88 79 50 53
D395V5, multiclass
    clus
vv   ART1 MUTATED ART1 WILD-TYPE
  N0            5             88
  N1            2             79
  N2            0             50
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D395V6, binary
                cls
clus               0   1
  ART1 MUTATED     7   0
  ART1 WILD-TYPE 250  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART1 MUTATED      7    0
  ART1 WILD-TYPE  250   18
   clus
vv  ART1 MUTATED ART1 WILD-TYPE
  0            7            250
  1            0             18
[1] 2 2
[1] FALSE
D395V7, binary
                cls
clus               0   1
  ART1 MUTATED     4   3
  ART1 WILD-TYPE 106 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART1 MUTATED      4    3
  ART1 WILD-TYPE  106  176
        clus
vv       ART1 MUTATED ART1 WILD-TYPE
  FEMALE            4            106
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ART1 MUTATED                                       0
  ART1 WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ART1 MUTATED                                                        3
  ART1 WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ART1 MUTATED                                                                   2
  ART1 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ART1 MUTATED                                                  1
  ART1 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ART1 MUTATED                                                          0
  ART1 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ART1 MUTATED                                                           1
  ART1 WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ART1 MUTATED                                          0
  ART1 WILD-TYPE                                        3
D395V8, multiclass
                                                                   clus
vv                                                                  ART1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  ART1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D395V9, binary
                cls
clus               0   1
  ART1 MUTATED     0   7
  ART1 WILD-TYPE   5 277
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART1 MUTATED      0    7
  ART1 WILD-TYPE    5  277
     clus
vv    ART1 MUTATED ART1 WILD-TYPE
  NO             0              5
  YES            7            277
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ART1 MUTATED     6   0   0   1
  ART1 WILD-TYPE 221  10  10  23
D395V10, multiclass
    clus
vv   ART1 MUTATED ART1 WILD-TYPE
  R0            6            221
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D395V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ART1 MUTATED       2                         0     4
  ART1 WILD-TYPE    74                         4   164
D395V12, multiclass
                           clus
vv                          ART1 MUTATED ART1 WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                4            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(396) Variable = IKBKE MUTATION ANALYSIS
D396V1, survival
                 sevent
clus2               0   1
  IKBKE MUTATED     7   3
  IKBKE WILD-TYPE 174  77
  IKBKE MUTATED IKBKE WILD-TYPE 
             10             251 
  IKBKE MUTATED IKBKE WILD-TYPE 
              3              77 
$`IKBKE MUTATED`
TCGA-BR-6452 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4437 TCGA-CG-4465 
       34.68        15.81        11.57         6.58         8.05         9.01 
TCGA-CG-5717 TCGA-HU-A4GX TCGA-HU-A4H8 TCGA-IN-7806 
        6.97        10.19         8.88        21.21 

$`IKBKE WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         7.99        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        22.98        30.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51         6.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42         3.45        18.81         3.39         2.53 

  IKBKE MUTATED IKBKE WILD-TYPE 
           6.58            0.00 
  IKBKE MUTATED IKBKE WILD-TYPE 
          34.68          105.07 
  IKBKE MUTATED IKBKE WILD-TYPE 
           9.60           12.76 
[1] "6.6 - 34.7 (9.6)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1"  
D396V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IKBKE MUTATED         0        0        1        3         2         1
  IKBKE WILD-TYPE       1        9       26       23        29        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IKBKE MUTATED           0          1          1          1        2
  IKBKE WILD-TYPE         3         48         35         23       22
D396V3, multiclass
            clus
vv           IKBKE MUTATED IKBKE WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               3              23
  STAGE IIA              2              29
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IKBKE MUTATED     1   3   4   4
  IKBKE WILD-TYPE  10  69 118  71
D396V4, multiclass
    clus
vv   IKBKE MUTATED IKBKE WILD-TYPE
  T1             1              10
  T2             3              69
  T3             4             118
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  IKBKE MUTATED    3  5  2  2
  IKBKE WILD-TYPE 90 76 48 51
D396V5, multiclass
    clus
vv   IKBKE MUTATED IKBKE WILD-TYPE
  N0             3              90
  N1             5              76
  N2             2              48
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D396V6, binary
                 cls
clus                0   1
  IKBKE MUTATED    10   2
  IKBKE WILD-TYPE 247  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKE MUTATED     10    2
  IKBKE WILD-TYPE  247   16
   clus
vv  IKBKE MUTATED IKBKE WILD-TYPE
  0            10             247
  1             2              16
[1] 2 2
[1] FALSE
D396V7, binary
                 cls
clus                0   1
  IKBKE MUTATED     5   7
  IKBKE WILD-TYPE 105 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKE MUTATED      5    7
  IKBKE WILD-TYPE  105  172
        clus
vv       IKBKE MUTATED IKBKE WILD-TYPE
  FEMALE             5             105
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  IKBKE MUTATED                                       4
  IKBKE WILD-TYPE                                    46
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IKBKE MUTATED                                                        4
  IKBKE WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IKBKE MUTATED                                                                   1
  IKBKE WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  IKBKE MUTATED                                                  2
  IKBKE WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  IKBKE MUTATED                                                          1
  IKBKE WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  IKBKE MUTATED                                                           0
  IKBKE WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  IKBKE MUTATED                                          0
  IKBKE WILD-TYPE                                        3
D396V8, multiclass
                                                                   clus
vv                                                                  IKBKE MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  IKBKE WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D396V9, binary
                 cls
clus                0   1
  IKBKE MUTATED     1  11
  IKBKE WILD-TYPE   4 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKE MUTATED      1   11
  IKBKE WILD-TYPE    4  273
     clus
vv    IKBKE MUTATED IKBKE WILD-TYPE
  NO              1               4
  YES            11             273
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IKBKE MUTATED     9   0   1   1
  IKBKE WILD-TYPE 218  10   9  23
D396V10, multiclass
    clus
vv   IKBKE MUTATED IKBKE WILD-TYPE
  R0             9             218
  R1             0              10
  R2             1               9
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D396V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IKBKE MUTATED       4                         0     4
  IKBKE WILD-TYPE    72                         4   164
D396V12, multiclass
                           clus
vv                          IKBKE MUTATED IKBKE WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(397) Variable = TIMM44 MUTATION ANALYSIS
D397V1, survival
                  sevent
clus2                0   1
  TIMM44 MUTATED     5   0
  TIMM44 WILD-TYPE 176  80
  TIMM44 MUTATED TIMM44 WILD-TYPE 
               5              256 
  TIMM44 MUTATED TIMM44 WILD-TYPE 
               0               80 
$`TIMM44 MUTATED`
TCGA-BR-8487 TCGA-BR-8680 TCGA-F1-6874 TCGA-HU-8602 TCGA-HU-A4H3 
        1.12        15.81        14.47        11.41        19.36 

$`TIMM44 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 
       14.76         0.62         7.99        16.24        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  TIMM44 MUTATED TIMM44 WILD-TYPE 
            1.12             0.00 
  TIMM44 MUTATED TIMM44 WILD-TYPE 
           19.36           105.07 
  TIMM44 MUTATED TIMM44 WILD-TYPE 
          14.470           12.605 
[1] "1.1 - 19.4 (14.5)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "9200000"
D397V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TIMM44 MUTATED         0        0        1        0         1         1
  TIMM44 WILD-TYPE       1        9       26       26        30        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TIMM44 MUTATED           0          0          0          1        1
  TIMM44 WILD-TYPE         3         49         36         23       23
D397V3, multiclass
            clus
vv           TIMM44 MUTATED TIMM44 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TIMM44 MUTATED     0   1   1   3
  TIMM44 WILD-TYPE  11  71 121  72
D397V4, multiclass
    clus
vv   TIMM44 MUTATED TIMM44 WILD-TYPE
  T1              0               11
  T2              1               71
  T3              1              121
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  TIMM44 MUTATED    3  0  1  1
  TIMM44 WILD-TYPE 90 81 49 52
D397V5, multiclass
    clus
vv   TIMM44 MUTATED TIMM44 WILD-TYPE
  N0              3               90
  N1              0               81
  N2              1               49
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D397V6, binary
                  cls
clus                 0   1
  TIMM44 MUTATED     4   1
  TIMM44 WILD-TYPE 253  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TIMM44 MUTATED      4    1
  TIMM44 WILD-TYPE  253   17
   clus
vv  TIMM44 MUTATED TIMM44 WILD-TYPE
  0              4              253
  1              1               17
[1] 2 2
[1] FALSE
D397V7, binary
                  cls
clus                 0   1
  TIMM44 MUTATED     3   2
  TIMM44 WILD-TYPE 107 177
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TIMM44 MUTATED      3    2
  TIMM44 WILD-TYPE  107  177
        clus
vv       TIMM44 MUTATED TIMM44 WILD-TYPE
  FEMALE              3              107
  MALE                2              177
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TIMM44 MUTATED                                       2
  TIMM44 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TIMM44 MUTATED                                                        1
  TIMM44 WILD-TYPE                                                    134
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TIMM44 MUTATED                                                                   1
  TIMM44 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TIMM44 MUTATED                                                  1
  TIMM44 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TIMM44 MUTATED                                                          0
  TIMM44 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TIMM44 MUTATED                                                           0
  TIMM44 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TIMM44 MUTATED                                          0
  TIMM44 WILD-TYPE                                        3
D397V8, multiclass
                                                                   clus
vv                                                                  TIMM44 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         1
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  TIMM44 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D397V9, binary
                  cls
clus                 0   1
  TIMM44 MUTATED     0   5
  TIMM44 WILD-TYPE   5 279
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TIMM44 MUTATED      0    5
  TIMM44 WILD-TYPE    5  279
     clus
vv    TIMM44 MUTATED TIMM44 WILD-TYPE
  NO               0                5
  YES              5              279
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TIMM44 MUTATED     5   0   0   0
  TIMM44 WILD-TYPE 222  10  10  24
D397V10, multiclass
    clus
vv   TIMM44 MUTATED TIMM44 WILD-TYPE
  R0              5              222
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D397V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TIMM44 MUTATED       3                         0     2
  TIMM44 WILD-TYPE    73                         4   166
D397V12, multiclass
                           clus
vv                          TIMM44 MUTATED TIMM44 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  2              166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(398) Variable = ELOVL2 MUTATION ANALYSIS
D398V1, survival
                  sevent
clus2                0   1
  ELOVL2 MUTATED     4   2
  ELOVL2 WILD-TYPE 177  78
  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
               6              255 
  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
               2               78 
$`ELOVL2 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8363 TCGA-CD-8535 TCGA-D7-A4YY TCGA-HU-A4G2 
        6.97        34.68         0.26         0.13        13.78        24.30 

$`ELOVL2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        19.50        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       16.44         5.92        15.16        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 
       14.17        11.41        12.10        10.62         0.76         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
            0.13             0.00 
  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
           34.68           105.07 
  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
          10.375           12.620 
[1] "0.1 - 34.7 (10.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D398V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ELOVL2 MUTATED         0        0        1        0         1         1
  ELOVL2 WILD-TYPE       1        9       26       26        30        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ELOVL2 MUTATED           0          3          1          0        0
  ELOVL2 WILD-TYPE         3         46         35         24       24
D398V3, multiclass
            clus
vv           ELOVL2 MUTATED ELOVL2 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              3               46
  STAGE IIIB              1               35
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ELOVL2 MUTATED     0   1   6   0
  ELOVL2 WILD-TYPE  11  71 116  75
D398V4, multiclass
    clus
vv   ELOVL2 MUTATED ELOVL2 WILD-TYPE
  T1              0               11
  T2              1               71
  T3              6              116
  T4              0               75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ELOVL2 MUTATED    2  4  0  1
  ELOVL2 WILD-TYPE 91 77 50 52
D398V5, multiclass
    clus
vv   ELOVL2 MUTATED ELOVL2 WILD-TYPE
  N0              2               91
  N1              4               77
  N2              0               50
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D398V6, binary
                  cls
clus                 0   1
  ELOVL2 MUTATED     6   0
  ELOVL2 WILD-TYPE 251  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ELOVL2 MUTATED      6    0
  ELOVL2 WILD-TYPE  251   18
   clus
vv  ELOVL2 MUTATED ELOVL2 WILD-TYPE
  0              6              251
  1              0               18
[1] 2 2
[1] FALSE
D398V7, binary
                  cls
clus                 0   1
  ELOVL2 MUTATED     2   5
  ELOVL2 WILD-TYPE 108 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ELOVL2 MUTATED      2    5
  ELOVL2 WILD-TYPE  108  174
        clus
vv       ELOVL2 MUTATED ELOVL2 WILD-TYPE
  FEMALE              2              108
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ELOVL2 MUTATED                                       1
  ELOVL2 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ELOVL2 MUTATED                                                        6
  ELOVL2 WILD-TYPE                                                    129
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ELOVL2 MUTATED                                                                   0
  ELOVL2 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ELOVL2 MUTATED                                                  0
  ELOVL2 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ELOVL2 MUTATED                                                          0
  ELOVL2 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ELOVL2 MUTATED                                                           0
  ELOVL2 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ELOVL2 MUTATED                                          0
  ELOVL2 WILD-TYPE                                        3
D398V8, multiclass
                                                                   clus
vv                                                                  ELOVL2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ELOVL2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D398V9, binary
                  cls
clus                 0   1
  ELOVL2 MUTATED     1   6
  ELOVL2 WILD-TYPE   4 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ELOVL2 MUTATED      1    6
  ELOVL2 WILD-TYPE    4  278
     clus
vv    ELOVL2 MUTATED ELOVL2 WILD-TYPE
  NO               1                4
  YES              6              278
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ELOVL2 MUTATED     5   1   0   1
  ELOVL2 WILD-TYPE 222   9  10  23
D398V10, multiclass
    clus
vv   ELOVL2 MUTATED ELOVL2 WILD-TYPE
  R0              5              222
  R1              1                9
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D398V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ELOVL2 MUTATED       2                         0     4
  ELOVL2 WILD-TYPE    74                         4   164
D398V12, multiclass
                           clus
vv                          ELOVL2 MUTATED ELOVL2 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(399) Variable = ALDH2 MUTATION ANALYSIS
D399V1, survival
                 sevent
clus2               0   1
  ALDH2 MUTATED     6   2
  ALDH2 WILD-TYPE 175  78
  ALDH2 MUTATED ALDH2 WILD-TYPE 
              8             253 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
              2              78 
$`ALDH2 MUTATED`
TCGA-BR-7703 TCGA-BR-8078 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CG-5721 TCGA-CG-5726 
       24.76        12.26        13.45        11.57         6.02        28.96 
TCGA-HU-A4GQ TCGA-HU-A4GU 
        0.10         6.25 

$`ALDH2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       11.77        29.98         8.98         6.51        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  ALDH2 MUTATED ALDH2 WILD-TYPE 
            0.1             0.0 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
          28.96          105.07 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
         11.915          12.660 
[1] "0.1 - 29.0 (11.9)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.1"
D399V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ALDH2 MUTATED         0        2        0        0         0         2
  ALDH2 WILD-TYPE       1        7       27       26        31        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ALDH2 MUTATED           0          1          1          2        1
  ALDH2 WILD-TYPE         3         48         35         22       23
D399V3, multiclass
            clus
vv           ALDH2 MUTATED ALDH2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               2               7
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              0              31
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             2              22
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ALDH2 MUTATED     2   0   2   5
  ALDH2 WILD-TYPE   9  72 120  70
D399V4, multiclass
    clus
vv   ALDH2 MUTATED ALDH2 WILD-TYPE
  T1             2               9
  T2             0              72
  T3             2             120
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ALDH2 MUTATED    4  2  1  2
  ALDH2 WILD-TYPE 89 79 49 51
D399V5, multiclass
    clus
vv   ALDH2 MUTATED ALDH2 WILD-TYPE
  N0             4              89
  N1             2              79
  N2             1              49
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D399V6, binary
                 cls
clus                0   1
  ALDH2 MUTATED     9   0
  ALDH2 WILD-TYPE 248  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDH2 MUTATED      9    0
  ALDH2 WILD-TYPE  248   18
   clus
vv  ALDH2 MUTATED ALDH2 WILD-TYPE
  0             9             248
  1             0              18
[1] 2 2
[1] FALSE
D399V7, binary
                 cls
clus                0   1
  ALDH2 MUTATED     3   6
  ALDH2 WILD-TYPE 107 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDH2 MUTATED      3    6
  ALDH2 WILD-TYPE  107  173
        clus
vv       ALDH2 MUTATED ALDH2 WILD-TYPE
  FEMALE             3             107
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ALDH2 MUTATED                                       1
  ALDH2 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ALDH2 MUTATED                                                        4
  ALDH2 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ALDH2 MUTATED                                                                   2
  ALDH2 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ALDH2 MUTATED                                                  1
  ALDH2 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ALDH2 MUTATED                                                          0
  ALDH2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ALDH2 MUTATED                                                           1
  ALDH2 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ALDH2 MUTATED                                          0
  ALDH2 WILD-TYPE                                        3
D399V8, multiclass
                                                                   clus
vv                                                                  ALDH2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ALDH2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D399V9, binary
                 cls
clus                0   1
  ALDH2 MUTATED     0   9
  ALDH2 WILD-TYPE   5 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDH2 MUTATED      0    9
  ALDH2 WILD-TYPE    5  275
     clus
vv    ALDH2 MUTATED ALDH2 WILD-TYPE
  NO              0               5
  YES             9             275
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ALDH2 MUTATED     8   0   0   1
  ALDH2 WILD-TYPE 219  10  10  23
D399V10, multiclass
    clus
vv   ALDH2 MUTATED ALDH2 WILD-TYPE
  R0             8             219
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D399V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ALDH2 MUTATED       2                         0     5
  ALDH2 WILD-TYPE    74                         4   163
D399V12, multiclass
                           clus
vv                          ALDH2 MUTATED ALDH2 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(400) Variable = H2AFY2 MUTATION ANALYSIS
D400V1, survival
                  sevent
clus2                0   1
  H2AFY2 MUTATED     4   2
  H2AFY2 WILD-TYPE 177  78
  H2AFY2 MUTATED H2AFY2 WILD-TYPE 
               6              255 
  H2AFY2 MUTATED H2AFY2 WILD-TYPE 
               2               78 
$`H2AFY2 MUTATED`
TCGA-BR-8591 TCGA-BR-A4QL TCGA-CG-4306 TCGA-D7-6822 TCGA-D7-A4YV TCGA-HU-A4GX 
       13.45        11.57         1.02        12.33         5.92        10.19 

$`H2AFY2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       15.81         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        10.55        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       16.44        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  H2AFY2 MUTATED H2AFY2 WILD-TYPE 
            1.02             0.00 
  H2AFY2 MUTATED H2AFY2 WILD-TYPE 
           13.45           105.07 
  H2AFY2 MUTATED H2AFY2 WILD-TYPE 
           10.88            12.76 
[1] "1.0 - 13.4 (10.9)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.9"
D400V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  H2AFY2 MUTATED         0        0        1        0         0         1
  H2AFY2 WILD-TYPE       1        9       26       26        31        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  H2AFY2 MUTATED           0          0          1          2        2
  H2AFY2 WILD-TYPE         3         49         35         22       22
D400V3, multiclass
            clus
vv           H2AFY2 MUTATED H2AFY2 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               0               31
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              1               35
  STAGE IIIC              2               22
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  H2AFY2 MUTATED     0   1   3   3
  H2AFY2 WILD-TYPE  11  71 119  72
D400V4, multiclass
    clus
vv   H2AFY2 MUTATED H2AFY2 WILD-TYPE
  T1              0               11
  T2              1               71
  T3              3              119
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  H2AFY2 MUTATED    1  1  3  2
  H2AFY2 WILD-TYPE 92 80 47 51
D400V5, multiclass
    clus
vv   H2AFY2 MUTATED H2AFY2 WILD-TYPE
  N0              1               92
  N1              1               80
  N2              3               47
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D400V6, binary
                  cls
clus                 0   1
  H2AFY2 MUTATED     6   1
  H2AFY2 WILD-TYPE 251  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  H2AFY2 MUTATED      6    1
  H2AFY2 WILD-TYPE  251   17
   clus
vv  H2AFY2 MUTATED H2AFY2 WILD-TYPE
  0              6              251
  1              1               17
[1] 2 2
[1] FALSE
D400V7, binary
                  cls
clus                 0   1
  H2AFY2 MUTATED     4   3
  H2AFY2 WILD-TYPE 106 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  H2AFY2 MUTATED      4    3
  H2AFY2 WILD-TYPE  106  176
        clus
vv       H2AFY2 MUTATED H2AFY2 WILD-TYPE
  FEMALE              4              106
  MALE                3              176
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  H2AFY2 MUTATED                                       1
  H2AFY2 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  H2AFY2 MUTATED                                                        4
  H2AFY2 WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  H2AFY2 MUTATED                                                                   0
  H2AFY2 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  H2AFY2 MUTATED                                                  2
  H2AFY2 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  H2AFY2 MUTATED                                                          0
  H2AFY2 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  H2AFY2 MUTATED                                                           0
  H2AFY2 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  H2AFY2 MUTATED                                          0
  H2AFY2 WILD-TYPE                                        3
D400V8, multiclass
                                                                   clus
vv                                                                  H2AFY2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  H2AFY2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D400V9, binary
                  cls
clus                 0   1
  H2AFY2 MUTATED     0   7
  H2AFY2 WILD-TYPE   5 277
[1] "tbl2"
                  cls
clus               [,1] [,2]
  H2AFY2 MUTATED      0    7
  H2AFY2 WILD-TYPE    5  277
     clus
vv    H2AFY2 MUTATED H2AFY2 WILD-TYPE
  NO               0                5
  YES              7              277
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  H2AFY2 MUTATED     5   0   1   1
  H2AFY2 WILD-TYPE 222  10   9  23
D400V10, multiclass
    clus
vv   H2AFY2 MUTATED H2AFY2 WILD-TYPE
  R0              5              222
  R1              0               10
  R2              1                9
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D400V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  H2AFY2 MUTATED       1                         0     5
  H2AFY2 WILD-TYPE    75                         4   163
D400V12, multiclass
                           clus
vv                          H2AFY2 MUTATED H2AFY2 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  5              163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(401) Variable = SOHLH2 MUTATION ANALYSIS
D401V1, survival
                  sevent
clus2                0   1
  SOHLH2 MUTATED     9   5
  SOHLH2 WILD-TYPE 172  75
  SOHLH2 MUTATED SOHLH2 WILD-TYPE 
              14              247 
  SOHLH2 MUTATED SOHLH2 WILD-TYPE 
               5               75 
$`SOHLH2 MUTATED`
TCGA-BR-8297 TCGA-BR-8367 TCGA-BR-8485 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-8525 
        7.40        26.33         9.21        20.65        13.64         0.07 
TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CG-4465 TCGA-HU-A4G9 TCGA-HU-A4GN 
        0.10        11.31         6.58         9.01        24.20        29.98 
TCGA-HU-A4GQ TCGA-HU-A4H2 
        0.10        12.95 

$`SOHLH2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
       19.36        13.51        20.42         1.15        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.39         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
        0.16         0.10         0.10         0.13         3.42         9.34 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
       12.03         0.00        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        11.84         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       25.81        11.77         8.98         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  SOHLH2 MUTATED SOHLH2 WILD-TYPE 
            0.07             0.00 
  SOHLH2 MUTATED SOHLH2 WILD-TYPE 
           29.98           105.07 
  SOHLH2 MUTATED SOHLH2 WILD-TYPE 
           10.26            12.66 
[1] "0.1 - 30.0 (10.3)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.3"
D401V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SOHLH2 MUTATED         0        1        0        1         4         1
  SOHLH2 WILD-TYPE       1        8       27       25        27        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SOHLH2 MUTATED           0          1          2          3        1
  SOHLH2 WILD-TYPE         3         48         34         21       23
D401V3, multiclass
            clus
vv           SOHLH2 MUTATED SOHLH2 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                0               27
  STAGE II                1               25
  STAGE IIA               4               27
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              2               34
  STAGE IIIC              3               21
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SOHLH2 MUTATED     1   1   7   5
  SOHLH2 WILD-TYPE  10  71 115  70
D401V4, multiclass
    clus
vv   SOHLH2 MUTATED SOHLH2 WILD-TYPE
  T1              1               10
  T2              1               71
  T3              7              115
  T4              5               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  SOHLH2 MUTATED    6  2  1  5
  SOHLH2 WILD-TYPE 87 79 49 48
D401V5, multiclass
    clus
vv   SOHLH2 MUTATED SOHLH2 WILD-TYPE
  N0              6               87
  N1              2               79
  N2              1               49
  N3              5               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D401V6, binary
                  cls
clus                 0   1
  SOHLH2 MUTATED    13   1
  SOHLH2 WILD-TYPE 244  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SOHLH2 MUTATED     13    1
  SOHLH2 WILD-TYPE  244   17
   clus
vv  SOHLH2 MUTATED SOHLH2 WILD-TYPE
  0             13              244
  1              1               17
[1] 2 2
[1] FALSE
D401V7, binary
                  cls
clus                 0   1
  SOHLH2 MUTATED     7   7
  SOHLH2 WILD-TYPE 103 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SOHLH2 MUTATED      7    7
  SOHLH2 WILD-TYPE  103  172
        clus
vv       SOHLH2 MUTATED SOHLH2 WILD-TYPE
  FEMALE              7              103
  MALE                7              172
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SOHLH2 MUTATED                                       4
  SOHLH2 WILD-TYPE                                    46
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SOHLH2 MUTATED                                                        5
  SOHLH2 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SOHLH2 MUTATED                                                                   0
  SOHLH2 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SOHLH2 MUTATED                                                  4
  SOHLH2 WILD-TYPE                                               34
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SOHLH2 MUTATED                                                          1
  SOHLH2 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SOHLH2 MUTATED                                                           0
  SOHLH2 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SOHLH2 MUTATED                                          0
  SOHLH2 WILD-TYPE                                        3
D401V8, multiclass
                                                                   clus
vv                                                                  SOHLH2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  SOHLH2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D401V9, binary
                  cls
clus                 0   1
  SOHLH2 MUTATED     0  14
  SOHLH2 WILD-TYPE   5 270
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SOHLH2 MUTATED      0   14
  SOHLH2 WILD-TYPE    5  270
     clus
vv    SOHLH2 MUTATED SOHLH2 WILD-TYPE
  NO               0                5
  YES             14              270
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SOHLH2 MUTATED    11   0   1   0
  SOHLH2 WILD-TYPE 216  10   9  24
D401V10, multiclass
    clus
vv   SOHLH2 MUTATED SOHLH2 WILD-TYPE
  R0             11              216
  R1              0               10
  R2              1                9
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D401V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SOHLH2 MUTATED       8                         0     5
  SOHLH2 WILD-TYPE    68                         4   163
D401V12, multiclass
                           clus
vv                          SOHLH2 MUTATED SOHLH2 WILD-TYPE
  ASIAN                                  8               68
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  5              163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(402) Variable = CROT MUTATION ANALYSIS
D402V1, survival
                sevent
clus2              0   1
  CROT MUTATED     9   1
  CROT WILD-TYPE 172  79
  CROT MUTATED CROT WILD-TYPE 
            10            251 
  CROT MUTATED CROT WILD-TYPE 
             1             79 
$`CROT MUTATED`
TCGA-BR-4184 TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8589 TCGA-BR-8680 TCGA-CD-8529 
        6.97        20.55         4.31        15.81        15.81         0.13 
TCGA-CG-5721 TCGA-HU-8602 TCGA-HU-A4GU TCGA-HU-A4H8 
        6.02        11.41         6.25         8.88 

$`CROT WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       17.49        14.43         0.69        12.26         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        12.79         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        5.52        26.47         5.92        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
       12.95        19.36        23.84        12.30         9.67        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  CROT MUTATED CROT WILD-TYPE 
          0.13           0.00 
  CROT MUTATED CROT WILD-TYPE 
         20.55         105.07 
  CROT MUTATED CROT WILD-TYPE 
         7.925         12.760 
[1] "0.1 - 20.6 (7.9)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "2"  
D402V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CROT MUTATED         0        0        2        0         0         3
  CROT WILD-TYPE       1        9       25       26        31        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CROT MUTATED           0          1          1          0        3
  CROT WILD-TYPE         3         48         35         24       21
D402V3, multiclass
            clus
vv           CROT MUTATED CROT WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              0             26
  STAGE IIA             0             31
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            0             24
  STAGE IV              3             21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CROT MUTATED     1   1   2   6
  CROT WILD-TYPE  10  71 120  69
D402V4, multiclass
    clus
vv   CROT MUTATED CROT WILD-TYPE
  T1            1             10
  T2            1             71
  T3            2            120
  T4            6             69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  CROT MUTATED    4  6  1  0
  CROT WILD-TYPE 89 75 49 53
D402V5, multiclass
    clus
vv   CROT MUTATED CROT WILD-TYPE
  N0            4             89
  N1            6             75
  N2            1             49
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D402V6, binary
                cls
clus               0   1
  CROT MUTATED     8   2
  CROT WILD-TYPE 249  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  CROT MUTATED      8    2
  CROT WILD-TYPE  249   16
   clus
vv  CROT MUTATED CROT WILD-TYPE
  0            8            249
  1            2             16
[1] 2 2
[1] FALSE
D402V7, binary
                cls
clus               0   1
  CROT MUTATED     4   7
  CROT WILD-TYPE 106 172
[1] "tbl2"
                cls
clus             [,1] [,2]
  CROT MUTATED      4    7
  CROT WILD-TYPE  106  172
        clus
vv       CROT MUTATED CROT WILD-TYPE
  FEMALE            4            106
  MALE              7            172
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CROT MUTATED                                       2
  CROT WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CROT MUTATED                                                        5
  CROT WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CROT MUTATED                                                                   1
  CROT WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CROT MUTATED                                                  2
  CROT WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CROT MUTATED                                                          1
  CROT WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CROT MUTATED                                                           0
  CROT WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CROT MUTATED                                          0
  CROT WILD-TYPE                                        3
D402V8, multiclass
                                                                   clus
vv                                                                  CROT MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  CROT WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D402V9, binary
                cls
clus               0   1
  CROT MUTATED     0  11
  CROT WILD-TYPE   5 273
[1] "tbl2"
                cls
clus             [,1] [,2]
  CROT MUTATED      0   11
  CROT WILD-TYPE    5  273
     clus
vv    CROT MUTATED CROT WILD-TYPE
  NO             0              5
  YES           11            273
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CROT MUTATED     9   0   0   2
  CROT WILD-TYPE 218  10  10  22
D402V10, multiclass
    clus
vv   CROT MUTATED CROT WILD-TYPE
  R0            9            218
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D402V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CROT MUTATED       5                         0     5
  CROT WILD-TYPE    71                         4   163
D402V12, multiclass
                           clus
vv                          CROT MUTATED CROT WILD-TYPE
  ASIAN                                5             71
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                5            163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(403) Variable = GON4L MUTATION ANALYSIS
D403V1, survival
                 sevent
clus2               0   1
  GON4L MUTATED     8   1
  GON4L WILD-TYPE 173  79
  GON4L MUTATED GON4L WILD-TYPE 
              9             252 
  GON4L MUTATED GON4L WILD-TYPE 
              1              79 
$`GON4L MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8372 TCGA-CD-A4MI TCGA-CD-A4MJ 
       26.70        34.68        12.26        19.17         0.10        12.62 
TCGA-CG-4466 TCGA-CG-5733 TCGA-HU-A4H3 
       18.97        21.07        19.36 

$`GON4L WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        6.58        12.20        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10         4.01        69.04         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  GON4L MUTATED GON4L WILD-TYPE 
            0.1             0.0 
  GON4L MUTATED GON4L WILD-TYPE 
          34.68          105.07 
  GON4L MUTATED GON4L WILD-TYPE 
         19.170          12.495 
[1] "0.1 - 34.7 (19.2)"  "0.0 - 105.1 (12.5)"
[1] "hr=" "4"  
D403V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GON4L MUTATED         1        0        2        0         1         2
  GON4L WILD-TYPE       0        9       25       26        30        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GON4L MUTATED           0          1          1          2        0
  GON4L WILD-TYPE         3         48         35         22       24
D403V3, multiclass
            clus
vv           GON4L MUTATED GON4L WILD-TYPE
  STAGE I                1               0
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             2              22
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GON4L MUTATED     1   3   2   4
  GON4L WILD-TYPE  10  69 120  71
D403V4, multiclass
    clus
vv   GON4L MUTATED GON4L WILD-TYPE
  T1             1              10
  T2             3              69
  T3             2             120
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  GON4L MUTATED    5  2  1  2
  GON4L WILD-TYPE 88 79 49 51
D403V5, multiclass
    clus
vv   GON4L MUTATED GON4L WILD-TYPE
  N0             5              88
  N1             2              79
  N2             1              49
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D403V6, binary
                 cls
clus                0   1
  GON4L MUTATED     9   0
  GON4L WILD-TYPE 248  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GON4L MUTATED      9    0
  GON4L WILD-TYPE  248   18
   clus
vv  GON4L MUTATED GON4L WILD-TYPE
  0             9             248
  1             0              18
[1] 2 2
[1] FALSE
D403V7, binary
                 cls
clus                0   1
  GON4L MUTATED     6   4
  GON4L WILD-TYPE 104 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GON4L MUTATED      6    4
  GON4L WILD-TYPE  104  175
        clus
vv       GON4L MUTATED GON4L WILD-TYPE
  FEMALE             6             104
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GON4L MUTATED                                       2
  GON4L WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GON4L MUTATED                                                        6
  GON4L WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GON4L MUTATED                                                                   2
  GON4L WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GON4L MUTATED                                                  0
  GON4L WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GON4L MUTATED                                                          0
  GON4L WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GON4L MUTATED                                                           0
  GON4L WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GON4L MUTATED                                          0
  GON4L WILD-TYPE                                        3
D403V8, multiclass
                                                                   clus
vv                                                                  GON4L MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  GON4L WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D403V9, binary
                 cls
clus                0   1
  GON4L MUTATED     0  10
  GON4L WILD-TYPE   5 274
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GON4L MUTATED      0   10
  GON4L WILD-TYPE    5  274
     clus
vv    GON4L MUTATED GON4L WILD-TYPE
  NO              0               5
  YES            10             274
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GON4L MUTATED     8   0   0   0
  GON4L WILD-TYPE 219  10  10  24
D403V10, multiclass
    clus
vv   GON4L MUTATED GON4L WILD-TYPE
  R0             8             219
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D403V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GON4L MUTATED       3                         1     4
  GON4L WILD-TYPE    73                         3   164
D403V12, multiclass
                           clus
vv                          GON4L MUTATED GON4L WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(404) Variable = CNKSR2 MUTATION ANALYSIS
D404V1, survival
                  sevent
clus2                0   1
  CNKSR2 MUTATED     6   3
  CNKSR2 WILD-TYPE 175  77
  CNKSR2 MUTATED CNKSR2 WILD-TYPE 
               9              252 
  CNKSR2 MUTATED CNKSR2 WILD-TYPE 
               3               77 
$`CNKSR2 MUTATED`
TCGA-BR-6455 TCGA-BR-7703 TCGA-BR-8372 TCGA-BR-8590 TCGA-BR-A4PF TCGA-CG-4444 
       13.87        24.76        19.17         9.34         1.15        47.05 
TCGA-CG-5718 TCGA-CG-5721 TCGA-CG-5730 
       36.00         6.02         4.01 

$`CNKSR2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        12.79        15.81        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51        20.65        20.42        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
       18.97         7.07        22.98        30.97         6.97         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  CNKSR2 MUTATED CNKSR2 WILD-TYPE 
            1.15             0.00 
  CNKSR2 MUTATED CNKSR2 WILD-TYPE 
           47.05           105.07 
  CNKSR2 MUTATED CNKSR2 WILD-TYPE 
          13.870           12.605 
[1] "1.1 - 47.0 (13.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D404V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CNKSR2 MUTATED         0        1        0        1         0         1
  CNKSR2 WILD-TYPE       1        8       27       25        31        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNKSR2 MUTATED           0          1          1          2        2
  CNKSR2 WILD-TYPE         3         48         35         22       22
D404V3, multiclass
            clus
vv           CNKSR2 MUTATED CNKSR2 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                0               27
  STAGE II                1               25
  STAGE IIA               0               31
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              2               22
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CNKSR2 MUTATED     1   3   1   4
  CNKSR2 WILD-TYPE  10  69 121  71
D404V4, multiclass
    clus
vv   CNKSR2 MUTATED CNKSR2 WILD-TYPE
  T1              1               10
  T2              3               69
  T3              1              121
  T4              4               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CNKSR2 MUTATED    1  5  3  1
  CNKSR2 WILD-TYPE 92 76 47 52
D404V5, multiclass
    clus
vv   CNKSR2 MUTATED CNKSR2 WILD-TYPE
  N0              1               92
  N1              5               76
  N2              3               47
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D404V6, binary
                  cls
clus                 0   1
  CNKSR2 MUTATED    11   1
  CNKSR2 WILD-TYPE 246  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNKSR2 MUTATED     11    1
  CNKSR2 WILD-TYPE  246   17
   clus
vv  CNKSR2 MUTATED CNKSR2 WILD-TYPE
  0             11              246
  1              1               17
[1] 2 2
[1] FALSE
D404V7, binary
                  cls
clus                 0   1
  CNKSR2 MUTATED     4   8
  CNKSR2 WILD-TYPE 106 171
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNKSR2 MUTATED      4    8
  CNKSR2 WILD-TYPE  106  171
        clus
vv       CNKSR2 MUTATED CNKSR2 WILD-TYPE
  FEMALE              4              106
  MALE                8              171
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CNKSR2 MUTATED                                       1
  CNKSR2 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CNKSR2 MUTATED                                                        7
  CNKSR2 WILD-TYPE                                                    128
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CNKSR2 MUTATED                                                                   3
  CNKSR2 WILD-TYPE                                                                37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CNKSR2 MUTATED                                                  0
  CNKSR2 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CNKSR2 MUTATED                                                          0
  CNKSR2 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CNKSR2 MUTATED                                                           1
  CNKSR2 WILD-TYPE                                                         5
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CNKSR2 MUTATED                                          0
  CNKSR2 WILD-TYPE                                        3
D404V8, multiclass
                                                                   clus
vv                                                                  CNKSR2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  CNKSR2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D404V9, binary
                  cls
clus                 0   1
  CNKSR2 MUTATED     0  12
  CNKSR2 WILD-TYPE   5 272
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNKSR2 MUTATED      0   12
  CNKSR2 WILD-TYPE    5  272
     clus
vv    CNKSR2 MUTATED CNKSR2 WILD-TYPE
  NO               0                5
  YES             12              272
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CNKSR2 MUTATED     8   0   1   3
  CNKSR2 WILD-TYPE 219  10   9  21
D404V10, multiclass
    clus
vv   CNKSR2 MUTATED CNKSR2 WILD-TYPE
  R0              8              219
  R1              0               10
  R2              1                9
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D404V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CNKSR2 MUTATED       0                         0     8
  CNKSR2 WILD-TYPE    76                         4   160
D404V12, multiclass
                           clus
vv                          CNKSR2 MUTATED CNKSR2 WILD-TYPE
  ASIAN                                  0               76
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  8              160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(405) Variable = UHRF1BP1 MUTATION ANALYSIS
D405V1, survival
                    sevent
clus2                  0   1
  UHRF1BP1 MUTATED    10   4
  UHRF1BP1 WILD-TYPE 171  76
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
                14                247 
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
                 4                 76 
$`UHRF1BP1 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8363 TCGA-BR-8680 TCGA-CG-5717 
       30.90        34.68        32.78         0.26        15.81         6.97 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 TCGA-F1-A448 TCGA-HU-A4G3 
        0.99       105.07        65.10        21.07        21.27         5.59 
TCGA-HU-A4H3 TCGA-HU-A4H8 
       19.36         8.88 

$`UHRF1BP1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       18.35         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       19.50        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 
        9.01        18.97         7.07        22.98        30.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        1.02         0.99         6.02        12.03        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        7.99        16.24        14.47        72.23         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        9.67        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
              0.26               0.00 
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
            105.07              79.07 
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
            20.215             12.560 
[1] "0.3 - 105.1 (20.2)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "2"  
D405V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UHRF1BP1 MUTATED         0        0        3        2         2         1
  UHRF1BP1 WILD-TYPE       1        9       24       24        29        43
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UHRF1BP1 MUTATED           0          1          1          1        2
  UHRF1BP1 WILD-TYPE         3         48         35         23       22
D405V3, multiclass
            clus
vv           UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  3                 24
  STAGE II                  2                 24
  STAGE IIA                 2                 29
  STAGE IIB                 1                 43
  STAGE III                 0                  3
  STAGE IIIA                1                 48
  STAGE IIIB                1                 35
  STAGE IIIC                1                 23
  STAGE IV                  2                 22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  UHRF1BP1 MUTATED     2   7   4   2
  UHRF1BP1 WILD-TYPE   9  65 118  73
D405V4, multiclass
    clus
vv   UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  T1                2                  9
  T2                7                 65
  T3                4                118
  T4                2                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  UHRF1BP1 MUTATED    4  3  4  2
  UHRF1BP1 WILD-TYPE 89 78 46 51
D405V5, multiclass
    clus
vv   UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  N0                4                 89
  N1                3                 78
  N2                4                 46
  N3                2                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D405V6, binary
                    cls
clus                   0   1
  UHRF1BP1 MUTATED    13   2
  UHRF1BP1 WILD-TYPE 244  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  UHRF1BP1 MUTATED     13    2
  UHRF1BP1 WILD-TYPE  244   16
   clus
vv  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  0               13                244
  1                2                 16
[1] 2 2
[1] FALSE
D405V7, binary
                    cls
clus                   0   1
  UHRF1BP1 MUTATED     9   6
  UHRF1BP1 WILD-TYPE 101 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  UHRF1BP1 MUTATED      9    6
  UHRF1BP1 WILD-TYPE  101  173
        clus
vv       UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  FEMALE                9                101
  MALE                  6                173
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  UHRF1BP1 MUTATED                                       1
  UHRF1BP1 WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  UHRF1BP1 MUTATED                                                        7
  UHRF1BP1 WILD-TYPE                                                    128
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  UHRF1BP1 MUTATED                                                                   3
  UHRF1BP1 WILD-TYPE                                                                37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  UHRF1BP1 MUTATED                                                  3
  UHRF1BP1 WILD-TYPE                                               35
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  UHRF1BP1 MUTATED                                                          1
  UHRF1BP1 WILD-TYPE                                                       15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  UHRF1BP1 MUTATED                                                           0
  UHRF1BP1 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  UHRF1BP1 MUTATED                                          0
  UHRF1BP1 WILD-TYPE                                        3
D405V8, multiclass
                                                                   clus
vv                                                                  UHRF1BP1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  UHRF1BP1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D405V9, binary
                    cls
clus                   0   1
  UHRF1BP1 MUTATED     0  15
  UHRF1BP1 WILD-TYPE   5 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  UHRF1BP1 MUTATED      0   15
  UHRF1BP1 WILD-TYPE    5  269
     clus
vv    UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  NO                 0                  5
  YES               15                269
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  UHRF1BP1 MUTATED    12   0   1   2
  UHRF1BP1 WILD-TYPE 215  10   9  22
D405V10, multiclass
    clus
vv   UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  R0               12                215
  R1                0                 10
  R2                1                  9
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D405V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UHRF1BP1 MUTATED       4                         0     6
  UHRF1BP1 WILD-TYPE    72                         4   162
D405V12, multiclass
                           clus
vv                          UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  ASIAN                                    4                 72
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    6                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(406) Variable = OR7C1 MUTATION ANALYSIS
D406V1, survival
                 sevent
clus2               0   1
  OR7C1 MUTATED     5   1
  OR7C1 WILD-TYPE 176  79
  OR7C1 MUTATED OR7C1 WILD-TYPE 
              6             255 
  OR7C1 MUTATED OR7C1 WILD-TYPE 
              1              79 
$`OR7C1 MUTATED`
TCGA-BR-4280 TCGA-BR-8078 TCGA-BR-8372 TCGA-CG-5728 TCGA-FP-A4BE TCGA-HU-A4G8 
        6.61        12.26        19.17        65.10        11.08        11.84 

$`OR7C1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        0.99       105.07        12.03        28.96        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  OR7C1 MUTATED OR7C1 WILD-TYPE 
           6.61            0.00 
  OR7C1 MUTATED OR7C1 WILD-TYPE 
          65.10          105.07 
  OR7C1 MUTATED OR7C1 WILD-TYPE 
          12.05           12.66 
[1] "6.6 - 65.1 (12.1)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "2.4"
D406V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OR7C1 MUTATED         0        0        1        0         1         2
  OR7C1 WILD-TYPE       1        9       26       26        30        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR7C1 MUTATED           1          0          0          1        0
  OR7C1 WILD-TYPE         2         49         36         23       24
D406V3, multiclass
            clus
vv           OR7C1 MUTATED OR7C1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              2              42
  STAGE III              1               2
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR7C1 MUTATED     0   2   2   2
  OR7C1 WILD-TYPE  11  70 120  73
D406V4, multiclass
    clus
vv   OR7C1 MUTATED OR7C1 WILD-TYPE
  T1             0              11
  T2             2              70
  T3             2             120
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  OR7C1 MUTATED    3  2  0  1
  OR7C1 WILD-TYPE 90 79 50 52
D406V5, multiclass
    clus
vv   OR7C1 MUTATED OR7C1 WILD-TYPE
  N0             3              90
  N1             2              79
  N2             0              50
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D406V6, binary
                 cls
clus                0   1
  OR7C1 MUTATED     6   0
  OR7C1 WILD-TYPE 251  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C1 MUTATED      6    0
  OR7C1 WILD-TYPE  251   18
   clus
vv  OR7C1 MUTATED OR7C1 WILD-TYPE
  0             6             251
  1             0              18
[1] 2 2
[1] FALSE
D406V7, binary
                 cls
clus                0   1
  OR7C1 MUTATED     4   2
  OR7C1 WILD-TYPE 106 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C1 MUTATED      4    2
  OR7C1 WILD-TYPE  106  177
        clus
vv       OR7C1 MUTATED OR7C1 WILD-TYPE
  FEMALE             4             106
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  OR7C1 MUTATED                                       1
  OR7C1 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OR7C1 MUTATED                                                        4
  OR7C1 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OR7C1 MUTATED                                                                   1
  OR7C1 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  OR7C1 MUTATED                                                  0
  OR7C1 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  OR7C1 MUTATED                                                          0
  OR7C1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  OR7C1 MUTATED                                                           0
  OR7C1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  OR7C1 MUTATED                                          0
  OR7C1 WILD-TYPE                                        3
D406V8, multiclass
                                                                   clus
vv                                                                  OR7C1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  OR7C1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D406V9, binary
                 cls
clus                0   1
  OR7C1 MUTATED     0   6
  OR7C1 WILD-TYPE   5 278
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C1 MUTATED      0    6
  OR7C1 WILD-TYPE    5  278
     clus
vv    OR7C1 MUTATED OR7C1 WILD-TYPE
  NO              0               5
  YES             6             278
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR7C1 MUTATED     4   0   0   1
  OR7C1 WILD-TYPE 223  10  10  23
D406V10, multiclass
    clus
vv   OR7C1 MUTATED OR7C1 WILD-TYPE
  R0             4             223
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D406V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR7C1 MUTATED       1                         1     3
  OR7C1 WILD-TYPE    75                         3   165
D406V12, multiclass
                           clus
vv                          OR7C1 MUTATED OR7C1 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(407) Variable = ABLIM2 MUTATION ANALYSIS
D407V1, survival
                  sevent
clus2                0   1
  ABLIM2 MUTATED     8   2
  ABLIM2 WILD-TYPE 173  78
  ABLIM2 MUTATED ABLIM2 WILD-TYPE 
              10              251 
  ABLIM2 MUTATED ABLIM2 WILD-TYPE 
               2               78 
$`ABLIM2 MUTATED`
TCGA-BR-4184 TCGA-BR-7851 TCGA-BR-8372 TCGA-CG-4306 TCGA-CG-5723 TCGA-CG-5728 
        6.97        12.43        19.17         1.02       105.07        65.10 
TCGA-FP-A4BE TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H4 
       11.08        10.19         0.26        23.84 

$`ABLIM2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        79.07         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H0 
       29.98         8.98         0.10         6.51         6.25         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       12.95        19.36        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  ABLIM2 MUTATED ABLIM2 WILD-TYPE 
            0.26             0.00 
  ABLIM2 MUTATED ABLIM2 WILD-TYPE 
          105.07            79.07 
  ABLIM2 MUTATED ABLIM2 WILD-TYPE 
          11.755           12.660 
[1] "0.3 - 105.1 (11.8)" "0.0 - 79.1 (12.7)" 
[1] "hr=" "2.5"
D407V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABLIM2 MUTATED         1        0        1        1         1         2
  ABLIM2 WILD-TYPE       0        9       26       25        30        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ABLIM2 MUTATED           0          2          0          2        1
  ABLIM2 WILD-TYPE         3         47         36         22       23
D407V3, multiclass
            clus
vv           ABLIM2 MUTATED ABLIM2 WILD-TYPE
  STAGE I                 1                0
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                1               25
  STAGE IIA               1               30
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              0               36
  STAGE IIIC              2               22
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ABLIM2 MUTATED     1   3   3   4
  ABLIM2 WILD-TYPE  10  69 119  71
D407V4, multiclass
    clus
vv   ABLIM2 MUTATED ABLIM2 WILD-TYPE
  T1              1               10
  T2              3               69
  T3              3              119
  T4              4               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ABLIM2 MUTATED    3  4  3  1
  ABLIM2 WILD-TYPE 90 77 47 52
D407V5, multiclass
    clus
vv   ABLIM2 MUTATED ABLIM2 WILD-TYPE
  N0              3               90
  N1              4               77
  N2              3               47
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D407V6, binary
                  cls
clus                 0   1
  ABLIM2 MUTATED     8   1
  ABLIM2 WILD-TYPE 249  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABLIM2 MUTATED      8    1
  ABLIM2 WILD-TYPE  249   17
   clus
vv  ABLIM2 MUTATED ABLIM2 WILD-TYPE
  0              8              249
  1              1               17
[1] 2 2
[1] FALSE
D407V7, binary
                  cls
clus                 0   1
  ABLIM2 MUTATED     4   7
  ABLIM2 WILD-TYPE 106 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABLIM2 MUTATED      4    7
  ABLIM2 WILD-TYPE  106  172
        clus
vv       ABLIM2 MUTATED ABLIM2 WILD-TYPE
  FEMALE              4              106
  MALE                7              172
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ABLIM2 MUTATED                                       2
  ABLIM2 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ABLIM2 MUTATED                                                        6
  ABLIM2 WILD-TYPE                                                    129
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ABLIM2 MUTATED                                                                   2
  ABLIM2 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ABLIM2 MUTATED                                                  1
  ABLIM2 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ABLIM2 MUTATED                                                          0
  ABLIM2 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ABLIM2 MUTATED                                                           0
  ABLIM2 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ABLIM2 MUTATED                                          0
  ABLIM2 WILD-TYPE                                        3
D407V8, multiclass
                                                                   clus
vv                                                                  ABLIM2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ABLIM2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D407V9, binary
                  cls
clus                 0   1
  ABLIM2 MUTATED     0  11
  ABLIM2 WILD-TYPE   5 273
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABLIM2 MUTATED      0   11
  ABLIM2 WILD-TYPE    5  273
     clus
vv    ABLIM2 MUTATED ABLIM2 WILD-TYPE
  NO               0                5
  YES             11              273
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ABLIM2 MUTATED     9   0   1   1
  ABLIM2 WILD-TYPE 218  10   9  23
D407V10, multiclass
    clus
vv   ABLIM2 MUTATED ABLIM2 WILD-TYPE
  R0              9              218
  R1              0               10
  R2              1                9
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D407V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ABLIM2 MUTATED       3                         2     3
  ABLIM2 WILD-TYPE    73                         2   165
D407V12, multiclass
                           clus
vv                          ABLIM2 MUTATED ABLIM2 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              2                2
  WHITE                                  3              165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(408) Variable = TPTE2 MUTATION ANALYSIS
D408V1, survival
                 sevent
clus2               0   1
  TPTE2 MUTATED     4   5
  TPTE2 WILD-TYPE 177  75
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              9             252 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              5              75 
$`TPTE2 MUTATED`
TCGA-BR-4184 TCGA-BR-6565 TCGA-BR-8680 TCGA-BR-8690 TCGA-CG-5721 TCGA-D7-A4Z0 
        6.97         9.17        15.81        10.68         6.02        14.76 
TCGA-EQ-8122 TCGA-HJ-7597 TCGA-HU-8243 
        7.99        26.47         5.92 

$`TPTE2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        9.86        15.68         8.22        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 
        5.92        15.16        13.78         0.62        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.52        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  TPTE2 MUTATED TPTE2 WILD-TYPE 
           5.92            0.00 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
          26.47          105.07 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
           9.17           12.71 
[1] "5.9 - 26.5 (9.2)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "2.3"
D408V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TPTE2 MUTATED         0        0        1        0         0         3
  TPTE2 WILD-TYPE       1        9       26       26        31        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TPTE2 MUTATED           0          1          1          1        2
  TPTE2 WILD-TYPE         3         48         35         23       22
D408V3, multiclass
            clus
vv           TPTE2 MUTATED TPTE2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              0              31
  STAGE IIB              3              41
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TPTE2 MUTATED     0   3   3   4
  TPTE2 WILD-TYPE  11  69 119  71
D408V4, multiclass
    clus
vv   TPTE2 MUTATED TPTE2 WILD-TYPE
  T1             0              11
  T2             3              69
  T3             3             119
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  TPTE2 MUTATED    2  3  2  2
  TPTE2 WILD-TYPE 91 78 48 51
D408V5, multiclass
    clus
vv   TPTE2 MUTATED TPTE2 WILD-TYPE
  N0             2              91
  N1             3              78
  N2             2              48
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D408V6, binary
                 cls
clus                0   1
  TPTE2 MUTATED     6   1
  TPTE2 WILD-TYPE 251  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      6    1
  TPTE2 WILD-TYPE  251   17
   clus
vv  TPTE2 MUTATED TPTE2 WILD-TYPE
  0             6             251
  1             1              17
[1] 2 2
[1] FALSE
D408V7, binary
                 cls
clus                0   1
  TPTE2 MUTATED     5   5
  TPTE2 WILD-TYPE 105 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      5    5
  TPTE2 WILD-TYPE  105  174
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  FEMALE             5             105
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TPTE2 MUTATED                                       0
  TPTE2 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TPTE2 MUTATED                                                        4
  TPTE2 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TPTE2 MUTATED                                                                   2
  TPTE2 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TPTE2 MUTATED                                                  2
  TPTE2 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TPTE2 MUTATED                                                          1
  TPTE2 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TPTE2 MUTATED                                                           0
  TPTE2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TPTE2 MUTATED                                          1
  TPTE2 WILD-TYPE                                        2
D408V8, multiclass
                                                                   clus
vv                                                                  TPTE2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  TPTE2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D408V9, binary
                 cls
clus                0   1
  TPTE2 MUTATED     0  10
  TPTE2 WILD-TYPE   5 274
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      0   10
  TPTE2 WILD-TYPE    5  274
     clus
vv    TPTE2 MUTATED TPTE2 WILD-TYPE
  NO              0               5
  YES            10             274
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TPTE2 MUTATED     7   0   0   2
  TPTE2 WILD-TYPE 220  10  10  22
D408V10, multiclass
    clus
vv   TPTE2 MUTATED TPTE2 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D408V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TPTE2 MUTATED       2                         0     7
  TPTE2 WILD-TYPE    74                         4   161
D408V12, multiclass
                           clus
vv                          TPTE2 MUTATED TPTE2 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 7             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(409) Variable = OLFML3 MUTATION ANALYSIS
D409V1, survival
                  sevent
clus2                0   1
  OLFML3 MUTATED     2   2
  OLFML3 WILD-TYPE 179  78
  OLFML3 MUTATED OLFML3 WILD-TYPE 
               4              257 
  OLFML3 MUTATED OLFML3 WILD-TYPE 
               2               78 
$`OLFML3 MUTATED`
TCGA-BR-4184 TCGA-BR-8360 TCGA-HJ-7597 TCGA-HU-A4H8 
        6.97         6.18        26.47         8.88 

$`OLFML3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
       12.95        19.36        23.84        12.30         9.67        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  OLFML3 MUTATED OLFML3 WILD-TYPE 
            6.18             0.00 
  OLFML3 MUTATED OLFML3 WILD-TYPE 
           26.47           105.07 
  OLFML3 MUTATED OLFML3 WILD-TYPE 
           7.925           12.660 
[1] "6.2 - 26.5 (7.9)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.9"
D409V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OLFML3 MUTATED         0        0        2        0         1         0
  OLFML3 WILD-TYPE       1        9       25       26        30        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OLFML3 MUTATED           0          1          0          0        0
  OLFML3 WILD-TYPE         3         48         36         24       24
D409V3, multiclass
            clus
vv           OLFML3 MUTATED OLFML3 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                2               25
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OLFML3 MUTATED     1   1   2   0
  OLFML3 WILD-TYPE  10  71 120  75
D409V4, multiclass
    clus
vv   OLFML3 MUTATED OLFML3 WILD-TYPE
  T1              1               10
  T2              1               71
  T3              2              120
  T4              0               75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  OLFML3 MUTATED    2  2  0  0
  OLFML3 WILD-TYPE 91 79 50 53
D409V5, multiclass
    clus
vv   OLFML3 MUTATED OLFML3 WILD-TYPE
  N0              2               91
  N1              2               79
  N2              0               50
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D409V6, binary
                  cls
clus                 0   1
  OLFML3 MUTATED     2   0
  OLFML3 WILD-TYPE 255  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OLFML3 MUTATED      2    0
  OLFML3 WILD-TYPE  255   18
   clus
vv  OLFML3 MUTATED OLFML3 WILD-TYPE
  0              2              255
  1              0               18
[1] 2 2
[1] FALSE
D409V7, binary
                  cls
clus                 0   1
  OLFML3 MUTATED     1   3
  OLFML3 WILD-TYPE 109 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OLFML3 MUTATED      1    3
  OLFML3 WILD-TYPE  109  176
        clus
vv       OLFML3 MUTATED OLFML3 WILD-TYPE
  FEMALE              1              109
  MALE                3              176
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  OLFML3 MUTATED                                       0
  OLFML3 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OLFML3 MUTATED                                                        1
  OLFML3 WILD-TYPE                                                    134
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OLFML3 MUTATED                                                                   1
  OLFML3 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  OLFML3 MUTATED                                                  1
  OLFML3 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  OLFML3 MUTATED                                                          0
  OLFML3 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  OLFML3 MUTATED                                                           0
  OLFML3 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  OLFML3 MUTATED                                          1
  OLFML3 WILD-TYPE                                        2
D409V8, multiclass
                                                                   clus
vv                                                                  OLFML3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         1
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       1
                                                                   clus
vv                                                                  OLFML3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D409V9, binary
                  cls
clus                 0   1
  OLFML3 MUTATED     0   4
  OLFML3 WILD-TYPE   5 280
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OLFML3 MUTATED      0    4
  OLFML3 WILD-TYPE    5  280
     clus
vv    OLFML3 MUTATED OLFML3 WILD-TYPE
  NO               0                5
  YES              4              280
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OLFML3 MUTATED     3   0   0   1
  OLFML3 WILD-TYPE 224  10  10  23
D409V10, multiclass
    clus
vv   OLFML3 MUTATED OLFML3 WILD-TYPE
  R0              3              224
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D409V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OLFML3 MUTATED       1                         0     3
  OLFML3 WILD-TYPE    75                         4   165
D409V12, multiclass
                           clus
vv                          OLFML3 MUTATED OLFML3 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  3              165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(410) Variable = RINT1 MUTATION ANALYSIS
D410V1, survival
                 sevent
clus2               0   1
  RINT1 MUTATED     2   2
  RINT1 WILD-TYPE 179  78
  RINT1 MUTATED RINT1 WILD-TYPE 
              4             257 
  RINT1 MUTATED RINT1 WILD-TYPE 
              2              78 
$`RINT1 MUTATED`
TCGA-BR-8078 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-5726 
       12.26        15.81         6.58        28.96 

$`RINT1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  RINT1 MUTATED RINT1 WILD-TYPE 
           6.58            0.00 
  RINT1 MUTATED RINT1 WILD-TYPE 
          28.96          105.07 
  RINT1 MUTATED RINT1 WILD-TYPE 
         14.035          12.620 
[1] "6.6 - 29.0 (14.0)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D410V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RINT1 MUTATED         1        1        0        0         1         1
  RINT1 WILD-TYPE       0        8       27       26        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RINT1 MUTATED           0          0          0          0        1
  RINT1 WILD-TYPE         3         49         36         24       23
D410V3, multiclass
            clus
vv           RINT1 MUTATED RINT1 WILD-TYPE
  STAGE I                1               0
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RINT1 MUTATED     2   0   1   2
  RINT1 WILD-TYPE   9  72 121  73
D410V4, multiclass
    clus
vv   RINT1 MUTATED RINT1 WILD-TYPE
  T1             2               9
  T2             0              72
  T3             1             121
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  RINT1 MUTATED    3  1  1  0
  RINT1 WILD-TYPE 90 80 49 53
D410V5, multiclass
    clus
vv   RINT1 MUTATED RINT1 WILD-TYPE
  N0             3              90
  N1             1              80
  N2             1              49
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D410V6, binary
                 cls
clus                0   1
  RINT1 MUTATED     3   1
  RINT1 WILD-TYPE 254  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RINT1 MUTATED      3    1
  RINT1 WILD-TYPE  254   17
   clus
vv  RINT1 MUTATED RINT1 WILD-TYPE
  0             3             254
  1             1              17
[1] 2 2
[1] FALSE
D410V7, binary
                 cls
clus                0   1
  RINT1 MUTATED     1   4
  RINT1 WILD-TYPE 109 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RINT1 MUTATED      1    4
  RINT1 WILD-TYPE  109  175
        clus
vv       RINT1 MUTATED RINT1 WILD-TYPE
  FEMALE             1             109
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RINT1 MUTATED                                       1
  RINT1 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RINT1 MUTATED                                                        2
  RINT1 WILD-TYPE                                                    133
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RINT1 MUTATED                                                                   1
  RINT1 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RINT1 MUTATED                                                  1
  RINT1 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RINT1 MUTATED                                                          0
  RINT1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RINT1 MUTATED                                                           0
  RINT1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RINT1 MUTATED                                          0
  RINT1 WILD-TYPE                                        3
D410V8, multiclass
                                                                   clus
vv                                                                  RINT1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  RINT1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D410V9, binary
                 cls
clus                0   1
  RINT1 MUTATED     0   5
  RINT1 WILD-TYPE   5 279
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RINT1 MUTATED      0    5
  RINT1 WILD-TYPE    5  279
     clus
vv    RINT1 MUTATED RINT1 WILD-TYPE
  NO              0               5
  YES             5             279
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RINT1 MUTATED     4   0   0   0
  RINT1 WILD-TYPE 223  10  10  24
D410V10, multiclass
    clus
vv   RINT1 MUTATED RINT1 WILD-TYPE
  R0             4             223
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D410V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RINT1 MUTATED       2                         1     1
  RINT1 WILD-TYPE    74                         3   167
D410V12, multiclass
                           clus
vv                          RINT1 MUTATED RINT1 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 1             167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(411) Variable = CA2 MUTATION ANALYSIS
D411V1, survival
               sevent
clus2             0   1
  CA2 MUTATED     4   0
  CA2 WILD-TYPE 177  80
  CA2 MUTATED CA2 WILD-TYPE 
            4           257 
  CA2 MUTATED CA2 WILD-TYPE 
            0            80 
$`CA2 MUTATED`
TCGA-BR-8368 TCGA-BR-8372 TCGA-HU-8602 TCGA-HU-A4GX 
        4.31        19.17        11.41        10.19 

$`CA2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       26.47         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  CA2 MUTATED CA2 WILD-TYPE 
         4.31          0.00 
  CA2 MUTATED CA2 WILD-TYPE 
        19.17        105.07 
  CA2 MUTATED CA2 WILD-TYPE 
        10.80         12.66 
[1] "4.3 - 19.2 (10.8)"  "0.0 - 105.1 (12.7)"
[1] "hr="     "9100000"
D411V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CA2 MUTATED         1        0        1        0         0         1
  CA2 WILD-TYPE       0        9       26       26        31        43
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CA2 MUTATED           0          0          0          2        0
  CA2 WILD-TYPE         3         49         36         22       24
D411V3, multiclass
            clus
vv           CA2 MUTATED CA2 WILD-TYPE
  STAGE I              1             0
  STAGE IA             0             9
  STAGE IB             1            26
  STAGE II             0            26
  STAGE IIA            0            31
  STAGE IIB            1            43
  STAGE III            0             3
  STAGE IIIA           0            49
  STAGE IIIB           0            36
  STAGE IIIC           2            22
  STAGE IV             0            24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CA2 MUTATED     1   1   0   3
  CA2 WILD-TYPE  10  71 122  72
D411V4, multiclass
    clus
vv   CA2 MUTATED CA2 WILD-TYPE
  T1           1            10
  T2           1            71
  T3           0           122
  T4           3            72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  CA2 MUTATED    2  1  1  1
  CA2 WILD-TYPE 91 80 49 52
D411V5, multiclass
    clus
vv   CA2 MUTATED CA2 WILD-TYPE
  N0           2            91
  N1           1            80
  N2           1            49
  N3           1            52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D411V6, binary
               cls
clus              0   1
  CA2 MUTATED     4   0
  CA2 WILD-TYPE 253  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  CA2 MUTATED      4    0
  CA2 WILD-TYPE  253   18
   clus
vv  CA2 MUTATED CA2 WILD-TYPE
  0           4           253
  1           0            18
[1] 2 2
[1] FALSE
D411V7, binary
               cls
clus              0   1
  CA2 MUTATED     3   2
  CA2 WILD-TYPE 107 177
[1] "tbl2"
               cls
clus            [,1] [,2]
  CA2 MUTATED      3    2
  CA2 WILD-TYPE  107  177
        clus
vv       CA2 MUTATED CA2 WILD-TYPE
  FEMALE           3           107
  MALE             2           177
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CA2 MUTATED                                       2
  CA2 WILD-TYPE                                    48
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CA2 MUTATED                                                        3
  CA2 WILD-TYPE                                                    132
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CA2 MUTATED                                                                   0
  CA2 WILD-TYPE                                                                40
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CA2 MUTATED                                                  0
  CA2 WILD-TYPE                                               38
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CA2 MUTATED                                                          0
  CA2 WILD-TYPE                                                       16
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CA2 MUTATED                                                           0
  CA2 WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CA2 MUTATED                                          0
  CA2 WILD-TYPE                                        3
D411V8, multiclass
                                                                   clus
vv                                                                  CA2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  CA2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D411V9, binary
               cls
clus              0   1
  CA2 MUTATED     0   5
  CA2 WILD-TYPE   5 279
[1] "tbl2"
               cls
clus            [,1] [,2]
  CA2 MUTATED      0    5
  CA2 WILD-TYPE    5  279
     clus
vv    CA2 MUTATED CA2 WILD-TYPE
  NO            0             5
  YES           5           279
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  CA2 MUTATED     5   0   0   0
  CA2 WILD-TYPE 222  10  10  24
D411V10, multiclass
    clus
vv   CA2 MUTATED CA2 WILD-TYPE
  R0           5           222
  R1           0            10
  R2           0            10
  RX           0            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D411V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CA2 MUTATED       2                         1     2
  CA2 WILD-TYPE    74                         3   166
D411V12, multiclass
                           clus
vv                          CA2 MUTATED CA2 WILD-TYPE
  ASIAN                               2            74
  BLACK OR AFRICAN AMERICAN           1             3
  WHITE                               2           166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(412) Variable = IRS1 MUTATION ANALYSIS
D412V1, survival
                sevent
clus2              0   1
  IRS1 MUTATED    12   4
  IRS1 WILD-TYPE 169  76
  IRS1 MUTATED IRS1 WILD-TYPE 
            16            245 
  IRS1 MUTATED IRS1 WILD-TYPE 
             4             76 
$`IRS1 MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4J8 
       34.68        12.26         0.26         1.12        15.81        13.51 
TCGA-BR-A4QL TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5732 TCGA-D7-A4YY 
       11.57         6.02       105.07        28.96        69.04        13.78 
TCGA-HJ-7597 TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4H3 
       26.47        29.98         6.51        19.36 

$`IRS1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        19.50        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4PD 
        0.72        14.17         0.53         0.66        19.36        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99         0.99        12.03        79.07        65.10         4.01 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        5.92        15.16        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       11.08         5.52         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       12.95        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  IRS1 MUTATED IRS1 WILD-TYPE 
          0.26           0.00 
  IRS1 MUTATED IRS1 WILD-TYPE 
        105.07          79.07 
  IRS1 MUTATED IRS1 WILD-TYPE 
        14.795         12.560 
[1] "0.3 - 105.1 (14.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "2.2"
D412V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IRS1 MUTATED         0        1        2        1         4         1
  IRS1 WILD-TYPE       1        8       25       25        27        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IRS1 MUTATED           0          2          3          1        3
  IRS1 WILD-TYPE         3         47         33         23       21
D412V3, multiclass
            clus
vv           IRS1 MUTATED IRS1 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              2             25
  STAGE II              1             25
  STAGE IIA             4             27
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            3             33
  STAGE IIIC            1             23
  STAGE IV              3             21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IRS1 MUTATED     1   5   7   5
  IRS1 WILD-TYPE  10  67 115  70
D412V4, multiclass
    clus
vv   IRS1 MUTATED IRS1 WILD-TYPE
  T1            1             10
  T2            5             67
  T3            7            115
  T4            5             70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  IRS1 MUTATED    8  6  1  5
  IRS1 WILD-TYPE 85 75 49 48
D412V5, multiclass
    clus
vv   IRS1 MUTATED IRS1 WILD-TYPE
  N0            8             85
  N1            6             75
  N2            1             49
  N3            5             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D412V6, binary
                cls
clus               0   1
  IRS1 MUTATED    18   1
  IRS1 WILD-TYPE 239  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS1 MUTATED     18    1
  IRS1 WILD-TYPE  239   17
   clus
vv  IRS1 MUTATED IRS1 WILD-TYPE
  0           18            239
  1            1             17
[1] 2 2
[1] FALSE
D412V7, binary
                cls
clus               0   1
  IRS1 MUTATED    11   9
  IRS1 WILD-TYPE  99 170
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS1 MUTATED     11    9
  IRS1 WILD-TYPE   99  170
        clus
vv       IRS1 MUTATED IRS1 WILD-TYPE
  FEMALE           11             99
  MALE              9            170
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  IRS1 MUTATED                                       1
  IRS1 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IRS1 MUTATED                                                       12
  IRS1 WILD-TYPE                                                    123
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IRS1 MUTATED                                                                   3
  IRS1 WILD-TYPE                                                                37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  IRS1 MUTATED                                                  3
  IRS1 WILD-TYPE                                               35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  IRS1 MUTATED                                                          0
  IRS1 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  IRS1 MUTATED                                                           0
  IRS1 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  IRS1 MUTATED                                          1
  IRS1 WILD-TYPE                                        2
D412V8, multiclass
                                                                   clus
vv                                                                  IRS1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      12
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  IRS1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       123
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D412V9, binary
                cls
clus               0   1
  IRS1 MUTATED     0  20
  IRS1 WILD-TYPE   5 264
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS1 MUTATED      0   20
  IRS1 WILD-TYPE    5  264
     clus
vv    IRS1 MUTATED IRS1 WILD-TYPE
  NO             0              5
  YES           20            264
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IRS1 MUTATED    17   0   0   3
  IRS1 WILD-TYPE 210  10  10  21
D412V10, multiclass
    clus
vv   IRS1 MUTATED IRS1 WILD-TYPE
  R0           17            210
  R1            0             10
  R2            0             10
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D412V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IRS1 MUTATED       5                         0    11
  IRS1 WILD-TYPE    71                         4   157
D412V12, multiclass
                           clus
vv                          IRS1 MUTATED IRS1 WILD-TYPE
  ASIAN                                5             71
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               11            157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(413) Variable = FKBP9 MUTATION ANALYSIS
D413V1, survival
                 sevent
clus2               0   1
  FKBP9 MUTATED     4   2
  FKBP9 WILD-TYPE 177  78
  FKBP9 MUTATED FKBP9 WILD-TYPE 
              6             255 
  FKBP9 MUTATED FKBP9 WILD-TYPE 
              2              78 
$`FKBP9 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6706 TCGA-BR-7707 TCGA-BR-7851 TCGA-HU-A4H3 
       30.90        34.68        18.05        23.93        12.43        19.36 

$`FKBP9 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       18.35         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       32.78        25.61        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 
       31.20        32.94        12.82         9.21        24.76        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       28.01        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        20.55         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.25        10.19         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  FKBP9 MUTATED FKBP9 WILD-TYPE 
          12.43            0.00 
  FKBP9 MUTATED FKBP9 WILD-TYPE 
          34.68          105.07 
  FKBP9 MUTATED FKBP9 WILD-TYPE 
         21.645          12.560 
[1] "12.4 - 34.7 (21.6)" "0.0 - 105.1 (12.6)"
[1] "hr=" "1.7"
D413V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FKBP9 MUTATED         0        0        1        0         1         1
  FKBP9 WILD-TYPE       1        9       26       26        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FKBP9 MUTATED           0          1          0          1        0
  FKBP9 WILD-TYPE         3         48         36         23       24
D413V3, multiclass
            clus
vv           FKBP9 MUTATED FKBP9 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FKBP9 MUTATED     0   2   2   2
  FKBP9 WILD-TYPE  11  70 120  73
D413V4, multiclass
    clus
vv   FKBP9 MUTATED FKBP9 WILD-TYPE
  T1             0              11
  T2             2              70
  T3             2             120
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  FKBP9 MUTATED    3  1  0  1
  FKBP9 WILD-TYPE 90 80 50 52
D413V5, multiclass
    clus
vv   FKBP9 MUTATED FKBP9 WILD-TYPE
  N0             3              90
  N1             1              80
  N2             0              50
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D413V6, binary
                 cls
clus                0   1
  FKBP9 MUTATED     6   0
  FKBP9 WILD-TYPE 251  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP9 MUTATED      6    0
  FKBP9 WILD-TYPE  251   18
   clus
vv  FKBP9 MUTATED FKBP9 WILD-TYPE
  0             6             251
  1             0              18
[1] 2 2
[1] FALSE
D413V7, binary
                 cls
clus                0   1
  FKBP9 MUTATED     4   2
  FKBP9 WILD-TYPE 106 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP9 MUTATED      4    2
  FKBP9 WILD-TYPE  106  177
        clus
vv       FKBP9 MUTATED FKBP9 WILD-TYPE
  FEMALE             4             106
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FKBP9 MUTATED                                       1
  FKBP9 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FKBP9 MUTATED                                                        4
  FKBP9 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FKBP9 MUTATED                                                                   1
  FKBP9 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FKBP9 MUTATED                                                  0
  FKBP9 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FKBP9 MUTATED                                                          0
  FKBP9 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FKBP9 MUTATED                                                           0
  FKBP9 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FKBP9 MUTATED                                          0
  FKBP9 WILD-TYPE                                        3
D413V8, multiclass
                                                                   clus
vv                                                                  FKBP9 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  FKBP9 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D413V9, binary
                 cls
clus                0   1
  FKBP9 MUTATED     0   6
  FKBP9 WILD-TYPE   5 278
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP9 MUTATED      0    6
  FKBP9 WILD-TYPE    5  278
     clus
vv    FKBP9 MUTATED FKBP9 WILD-TYPE
  NO              0               5
  YES             6             278
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FKBP9 MUTATED     5   0   0   1
  FKBP9 WILD-TYPE 222  10  10  23
D413V10, multiclass
    clus
vv   FKBP9 MUTATED FKBP9 WILD-TYPE
  R0             5             222
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D413V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FKBP9 MUTATED       1                         0     5
  FKBP9 WILD-TYPE    75                         4   163
D413V12, multiclass
                           clus
vv                          FKBP9 MUTATED FKBP9 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(414) Variable = LMTK3 MUTATION ANALYSIS
D414V1, survival
                 sevent
clus2               0   1
  LMTK3 MUTATED     6   2
  LMTK3 WILD-TYPE 175  78
  LMTK3 MUTATED LMTK3 WILD-TYPE 
              8             253 
  LMTK3 MUTATED LMTK3 WILD-TYPE 
              2              78 
$`LMTK3 MUTATED`
TCGA-BR-6802 TCGA-BR-7851 TCGA-BR-8368 TCGA-BR-A452 TCGA-CG-4465 TCGA-CG-5721 
       30.90        12.43         4.31         7.53         9.01         6.02 
TCGA-FP-A4BE TCGA-HU-8602 
       11.08        11.41 

$`LMTK3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        5.52        26.47         5.92        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  LMTK3 MUTATED LMTK3 WILD-TYPE 
           4.31            0.00 
  LMTK3 MUTATED LMTK3 WILD-TYPE 
          30.90          105.07 
  LMTK3 MUTATED LMTK3 WILD-TYPE 
         10.045          12.790 
[1] "4.3 - 30.9 (10.0)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1"  
D414V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LMTK3 MUTATED         0        0        1        0         1         2
  LMTK3 WILD-TYPE       1        9       26       26        30        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LMTK3 MUTATED           0          2          0          0        2
  LMTK3 WILD-TYPE         3         47         36         24       22
D414V3, multiclass
            clus
vv           LMTK3 MUTATED LMTK3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LMTK3 MUTATED     0   1   2   5
  LMTK3 WILD-TYPE  11  71 120  70
D414V4, multiclass
    clus
vv   LMTK3 MUTATED LMTK3 WILD-TYPE
  T1             0              11
  T2             1              71
  T3             2             120
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  LMTK3 MUTATED    4  2  1  1
  LMTK3 WILD-TYPE 89 79 49 52
D414V5, multiclass
    clus
vv   LMTK3 MUTATED LMTK3 WILD-TYPE
  N0             4              89
  N1             2              79
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D414V6, binary
                 cls
clus                0   1
  LMTK3 MUTATED     7   1
  LMTK3 WILD-TYPE 250  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMTK3 MUTATED      7    1
  LMTK3 WILD-TYPE  250   17
   clus
vv  LMTK3 MUTATED LMTK3 WILD-TYPE
  0             7             250
  1             1              17
[1] 2 2
[1] FALSE
D414V7, binary
                 cls
clus                0   1
  LMTK3 MUTATED     3   5
  LMTK3 WILD-TYPE 107 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMTK3 MUTATED      3    5
  LMTK3 WILD-TYPE  107  174
        clus
vv       LMTK3 MUTATED LMTK3 WILD-TYPE
  FEMALE             3             107
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  LMTK3 MUTATED                                       2
  LMTK3 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LMTK3 MUTATED                                                        3
  LMTK3 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LMTK3 MUTATED                                                                   2
  LMTK3 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  LMTK3 MUTATED                                                  1
  LMTK3 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  LMTK3 MUTATED                                                          0
  LMTK3 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  LMTK3 MUTATED                                                           0
  LMTK3 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  LMTK3 MUTATED                                          0
  LMTK3 WILD-TYPE                                        3
D414V8, multiclass
                                                                   clus
vv                                                                  LMTK3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  LMTK3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D414V9, binary
                 cls
clus                0   1
  LMTK3 MUTATED     0   8
  LMTK3 WILD-TYPE   5 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMTK3 MUTATED      0    8
  LMTK3 WILD-TYPE    5  276
     clus
vv    LMTK3 MUTATED LMTK3 WILD-TYPE
  NO              0               5
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LMTK3 MUTATED     7   0   1   0
  LMTK3 WILD-TYPE 220  10   9  24
D414V10, multiclass
    clus
vv   LMTK3 MUTATED LMTK3 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             1               9
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D414V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LMTK3 MUTATED       2                         1     3
  LMTK3 WILD-TYPE    74                         3   165
D414V12, multiclass
                           clus
vv                          LMTK3 MUTATED LMTK3 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(415) Variable = DNAH5 MUTATION ANALYSIS
D415V1, survival
                 sevent
clus2               0   1
  DNAH5 MUTATED    31  17
  DNAH5 WILD-TYPE 150  63
  DNAH5 MUTATED DNAH5 WILD-TYPE 
             48             213 
  DNAH5 MUTATED DNAH5 WILD-TYPE 
             17              63 
$`DNAH5 MUTATED`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4280 
       26.70        11.70         6.97         7.43        30.90         6.61 
TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-7717 
       34.68        19.33        32.78        32.94        23.93        18.15 
TCGA-BR-7851 TCGA-BR-8059 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8297 TCGA-BR-8360 
       12.43        14.43         8.05        12.95         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8589 
        0.26        14.79        15.85         9.21         1.12        15.81 
TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4IY TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
       13.45        15.81        12.89         2.83        13.15        13.18 
TCGA-CD-A48C TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-5720 
       11.61        12.62        15.95         1.02        14.01         0.99 
TCGA-CG-5721 TCGA-CG-5733 TCGA-D7-6525 TCGA-D7-A4Z0 TCGA-EQ-A4SO TCGA-F1-6874 
        6.02        21.07        13.35        14.76        16.24        14.47 
TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4GC TCGA-HU-A4H2 TCGA-HU-A4H8 
       11.08        26.47        11.41         3.25        12.95         8.88 

$`DNAH5 WILD-TYPE`
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 
        6.61         4.64        18.35         6.18         9.57        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 
       31.20        12.82         9.21        24.76        15.42        28.01 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8289 
       17.49         0.69        12.26         9.60        20.55         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
       16.31         2.20        15.58        19.50        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 
       19.17         0.26         3.72         5.39        25.18        20.22 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       12.79         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       13.51         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
       11.57         5.13         3.25         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43         6.58        12.20         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       20.02         3.02        27.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
       36.00         1.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10         4.01        69.04         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-EQ-5647 
       14.27        16.44         5.92        15.16        13.78         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        7.99        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        5.52         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 
        6.51         6.25        10.19         0.26         2.10        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  DNAH5 MUTATED DNAH5 WILD-TYPE 
           0.26            0.00 
  DNAH5 MUTATED DNAH5 WILD-TYPE 
          34.68          105.07 
  DNAH5 MUTATED DNAH5 WILD-TYPE 
          13.05           12.36 
[1] "0.3 - 34.7 (13.1)"  "0.0 - 105.1 (12.4)"
[1] "hr=" "1.2"
D415V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DNAH5 MUTATED         0        0        9        5         7         7
  DNAH5 WILD-TYPE       1        9       18       21        24        37
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAH5 MUTATED           2          7          4          6        5
  DNAH5 WILD-TYPE         1         42         32         18       19
D415V3, multiclass
            clus
vv           DNAH5 MUTATED DNAH5 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               9              18
  STAGE II               5              21
  STAGE IIA              7              24
  STAGE IIB              7              37
  STAGE III              2               1
  STAGE IIIA             7              42
  STAGE IIIB             4              32
  STAGE IIIC             6              18
  STAGE IV               5              19
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DNAH5 MUTATED     1  16  19  19
  DNAH5 WILD-TYPE  10  56 103  56
D415V4, multiclass
    clus
vv   DNAH5 MUTATED DNAH5 WILD-TYPE
  T1             1              10
  T2            16              56
  T3            19             103
  T4            19              56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  DNAH5 MUTATED   22 16  8  7
  DNAH5 WILD-TYPE 71 65 42 46
D415V5, multiclass
    clus
vv   DNAH5 MUTATED DNAH5 WILD-TYPE
  N0            22              71
  N1            16              65
  N2             8              42
  N3             7              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D415V6, binary
                 cls
clus                0   1
  DNAH5 MUTATED    49   2
  DNAH5 WILD-TYPE 208  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH5 MUTATED     49    2
  DNAH5 WILD-TYPE  208   16
   clus
vv  DNAH5 MUTATED DNAH5 WILD-TYPE
  0            49             208
  1             2              16
[1] 2 2
[1] FALSE
D415V7, binary
                 cls
clus                0   1
  DNAH5 MUTATED    24  32
  DNAH5 WILD-TYPE  86 147
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH5 MUTATED     24   32
  DNAH5 WILD-TYPE   86  147
        clus
vv       DNAH5 MUTATED DNAH5 WILD-TYPE
  FEMALE            24              86
  MALE              32             147
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DNAH5 MUTATED                                       6
  DNAH5 WILD-TYPE                                    44
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DNAH5 MUTATED                                                       32
  DNAH5 WILD-TYPE                                                    103
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DNAH5 MUTATED                                                                  10
  DNAH5 WILD-TYPE                                                                30
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DNAH5 MUTATED                                                  3
  DNAH5 WILD-TYPE                                               35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DNAH5 MUTATED                                                          3
  DNAH5 WILD-TYPE                                                       13
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DNAH5 MUTATED                                                           1
  DNAH5 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DNAH5 MUTATED                                          1
  DNAH5 WILD-TYPE                                        2
D415V8, multiclass
                                                                   clus
vv                                                                  DNAH5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       32
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            10
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  DNAH5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          44
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        103
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              30
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D415V9, binary
                 cls
clus                0   1
  DNAH5 MUTATED     1  55
  DNAH5 WILD-TYPE   4 229
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH5 MUTATED      1   55
  DNAH5 WILD-TYPE    4  229
     clus
vv    DNAH5 MUTATED DNAH5 WILD-TYPE
  NO              1               4
  YES            55             229
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DNAH5 MUTATED    44   1   1   7
  DNAH5 WILD-TYPE 183   9   9  17
D415V10, multiclass
    clus
vv   DNAH5 MUTATED DNAH5 WILD-TYPE
  R0            44             183
  R1             1               9
  R2             1               9
  RX             7              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D415V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DNAH5 MUTATED      12                         1    35
  DNAH5 WILD-TYPE    64                         3   133
D415V12, multiclass
                           clus
vv                          DNAH5 MUTATED DNAH5 WILD-TYPE
  ASIAN                                12              64
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                35             133
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(416) Variable = GPATCH2 MUTATION ANALYSIS
D416V1, survival
                   sevent
clus2                 0   1
  GPATCH2 MUTATED     3   1
  GPATCH2 WILD-TYPE 178  79
  GPATCH2 MUTATED GPATCH2 WILD-TYPE 
                4               257 
  GPATCH2 MUTATED GPATCH2 WILD-TYPE 
                1                79 
$`GPATCH2 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-CG-5721 TCGA-HU-A4GQ 
       34.68        32.94         6.02         0.10 

$`GPATCH2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  GPATCH2 MUTATED GPATCH2 WILD-TYPE 
              0.1               0.0 
  GPATCH2 MUTATED GPATCH2 WILD-TYPE 
            34.68            105.07 
  GPATCH2 MUTATED GPATCH2 WILD-TYPE 
            19.48             12.62 
[1] "0.1 - 34.7 (19.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.8"
D416V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPATCH2 MUTATED         1        0        1        0         2         0
  GPATCH2 WILD-TYPE       0        9       26       26        29        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPATCH2 MUTATED           0          0          0          1        1
  GPATCH2 WILD-TYPE         3         49         36         23       23
D416V3, multiclass
            clus
vv           GPATCH2 MUTATED GPATCH2 WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 0                26
  STAGE IIA                2                29
  STAGE IIB                0                44
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               0                36
  STAGE IIIC               1                23
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GPATCH2 MUTATED     2   1   2   2
  GPATCH2 WILD-TYPE   9  71 120  73
D416V4, multiclass
    clus
vv   GPATCH2 MUTATED GPATCH2 WILD-TYPE
  T1               2                 9
  T2               1                71
  T3               2               120
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  GPATCH2 MUTATED    3  2  1  0
  GPATCH2 WILD-TYPE 90 79 49 53
D416V5, multiclass
    clus
vv   GPATCH2 MUTATED GPATCH2 WILD-TYPE
  N0               3                90
  N1               2                79
  N2               1                49
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D416V6, binary
                   cls
clus                  0   1
  GPATCH2 MUTATED     6   0
  GPATCH2 WILD-TYPE 251  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH2 MUTATED      6    0
  GPATCH2 WILD-TYPE  251   18
   clus
vv  GPATCH2 MUTATED GPATCH2 WILD-TYPE
  0               6               251
  1               0                18
[1] 2 2
[1] FALSE
D416V7, binary
                   cls
clus                  0   1
  GPATCH2 MUTATED     3   4
  GPATCH2 WILD-TYPE 107 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH2 MUTATED      3    4
  GPATCH2 WILD-TYPE  107  175
        clus
vv       GPATCH2 MUTATED GPATCH2 WILD-TYPE
  FEMALE               3               107
  MALE                 4               175
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GPATCH2 MUTATED                                       0
  GPATCH2 WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPATCH2 MUTATED                                                        4
  GPATCH2 WILD-TYPE                                                    131
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPATCH2 MUTATED                                                                   2
  GPATCH2 WILD-TYPE                                                                38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GPATCH2 MUTATED                                                  1
  GPATCH2 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GPATCH2 MUTATED                                                          0
  GPATCH2 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GPATCH2 MUTATED                                                           0
  GPATCH2 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GPATCH2 MUTATED                                          0
  GPATCH2 WILD-TYPE                                        3
D416V8, multiclass
                                                                   clus
vv                                                                  GPATCH2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  GPATCH2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D416V9, binary
                   cls
clus                  0   1
  GPATCH2 MUTATED     0   7
  GPATCH2 WILD-TYPE   5 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH2 MUTATED      0    7
  GPATCH2 WILD-TYPE    5  277
     clus
vv    GPATCH2 MUTATED GPATCH2 WILD-TYPE
  NO                0                 5
  YES               7               277
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  GPATCH2 MUTATED     6   0   0   1
  GPATCH2 WILD-TYPE 221  10  10  23
D416V10, multiclass
    clus
vv   GPATCH2 MUTATED GPATCH2 WILD-TYPE
  R0               6               221
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D416V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPATCH2 MUTATED       1                         1     3
  GPATCH2 WILD-TYPE    75                         3   165
D416V12, multiclass
                           clus
vv                          GPATCH2 MUTATED GPATCH2 WILD-TYPE
  ASIAN                                   1                75
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   3               165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(417) Variable = KCNH2 MUTATION ANALYSIS
D417V1, survival
                 sevent
clus2               0   1
  KCNH2 MUTATED    10   2
  KCNH2 WILD-TYPE 171  78
  KCNH2 MUTATED KCNH2 WILD-TYPE 
             12             249 
  KCNH2 MUTATED KCNH2 WILD-TYPE 
              2              78 
$`KCNH2 MUTATED`
TCGA-B7-5816 TCGA-BR-4191 TCGA-BR-7851 TCGA-BR-8077 TCGA-BR-8487 TCGA-CD-8536 
       26.70        18.35        12.43         0.69         1.12         0.10 
TCGA-CG-4305 TCGA-CG-4469 TCGA-CG-5723 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GX 
       15.95         7.07       105.07        11.41        11.84        10.19 

$`KCNH2 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
       11.70         6.61         6.97         4.64         7.43        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 
        0.13         0.16         0.10         0.10         0.13         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
        0.10        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  KCNH2 MUTATED KCNH2 WILD-TYPE 
            0.1             0.0 
  KCNH2 MUTATED KCNH2 WILD-TYPE 
         105.07           79.07 
  KCNH2 MUTATED KCNH2 WILD-TYPE 
         11.625          12.760 
[1] "0.1 - 105.1 (11.6)" "0.0 - 79.1 (12.8)" 
[1] "hr=" "2.2"
D417V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCNH2 MUTATED         0        0        0        3         1         4
  KCNH2 WILD-TYPE       1        9       27       23        30        40
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCNH2 MUTATED           0          0          1          1        1
  KCNH2 WILD-TYPE         3         49         35         23       23
D417V3, multiclass
            clus
vv           KCNH2 MUTATED KCNH2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               3              23
  STAGE IIA              1              30
  STAGE IIB              4              40
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCNH2 MUTATED     0   2   4   5
  KCNH2 WILD-TYPE  11  70 118  70
D417V4, multiclass
    clus
vv   KCNH2 MUTATED KCNH2 WILD-TYPE
  T1             0              11
  T2             2              70
  T3             4             118
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  KCNH2 MUTATED    5  5  1  1
  KCNH2 WILD-TYPE 88 76 49 52
D417V5, multiclass
    clus
vv   KCNH2 MUTATED KCNH2 WILD-TYPE
  N0             5              88
  N1             5              76
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D417V6, binary
                 cls
clus                0   1
  KCNH2 MUTATED    13   0
  KCNH2 WILD-TYPE 244  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH2 MUTATED     13    0
  KCNH2 WILD-TYPE  244   18
   clus
vv  KCNH2 MUTATED KCNH2 WILD-TYPE
  0            13             244
  1             0              18
[1] 2 2
[1] FALSE
D417V7, binary
                 cls
clus                0   1
  KCNH2 MUTATED     7   6
  KCNH2 WILD-TYPE 103 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH2 MUTATED      7    6
  KCNH2 WILD-TYPE  103  173
        clus
vv       KCNH2 MUTATED KCNH2 WILD-TYPE
  FEMALE             7             103
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KCNH2 MUTATED                                       4
  KCNH2 WILD-TYPE                                    46
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KCNH2 MUTATED                                                        6
  KCNH2 WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KCNH2 MUTATED                                                                   3
  KCNH2 WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KCNH2 MUTATED                                                  0
  KCNH2 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KCNH2 MUTATED                                                          0
  KCNH2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KCNH2 MUTATED                                                           0
  KCNH2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KCNH2 MUTATED                                          0
  KCNH2 WILD-TYPE                                        3
D417V8, multiclass
                                                                   clus
vv                                                                  KCNH2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  KCNH2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D417V9, binary
                 cls
clus                0   1
  KCNH2 MUTATED     0  13
  KCNH2 WILD-TYPE   5 271
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH2 MUTATED      0   13
  KCNH2 WILD-TYPE    5  271
     clus
vv    KCNH2 MUTATED KCNH2 WILD-TYPE
  NO              0               5
  YES            13             271
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KCNH2 MUTATED     9   1   0   2
  KCNH2 WILD-TYPE 218   9  10  22
D417V10, multiclass
    clus
vv   KCNH2 MUTATED KCNH2 WILD-TYPE
  R0             9             218
  R1             1               9
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D417V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KCNH2 MUTATED       4                         0     6
  KCNH2 WILD-TYPE    72                         4   162
D417V12, multiclass
                           clus
vv                          KCNH2 MUTATED KCNH2 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(418) Variable = SGOL2 MUTATION ANALYSIS
D418V1, survival
                 sevent
clus2               0   1
  SGOL2 MUTATED     5   4
  SGOL2 WILD-TYPE 176  76
  SGOL2 MUTATED SGOL2 WILD-TYPE 
              9             252 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
              4              76 
$`SGOL2 MUTATED`
TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8680 TCGA-CD-5801 TCGA-CG-4306 TCGA-CG-5728 
       34.68         0.26        15.81        13.18         1.02        65.10 
TCGA-CG-5733 TCGA-HU-A4GX TCGA-HU-A4H3 
       21.07        10.19        19.36 

$`SGOL2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        19.50        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
       11.57         5.13         2.83         3.25        13.15         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       12.03        28.96        79.07         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51         6.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  SGOL2 MUTATED SGOL2 WILD-TYPE 
           0.26            0.00 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
          65.10          105.07 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
         15.810          12.575 
[1] "0.3 - 65.1 (15.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D418V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SGOL2 MUTATED         0        0        2        1         1         0
  SGOL2 WILD-TYPE       1        9       25       25        30        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SGOL2 MUTATED           0          2          0          2        2
  SGOL2 WILD-TYPE         3         47         36         22       22
D418V3, multiclass
            clus
vv           SGOL2 MUTATED SGOL2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             0              36
  STAGE IIIC             2              22
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SGOL2 MUTATED     0   3   4   3
  SGOL2 WILD-TYPE  11  69 118  72
D418V4, multiclass
    clus
vv   SGOL2 MUTATED SGOL2 WILD-TYPE
  T1             0              11
  T2             3              69
  T3             4             118
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  SGOL2 MUTATED    4  2  4  1
  SGOL2 WILD-TYPE 89 79 46 52
D418V5, multiclass
    clus
vv   SGOL2 MUTATED SGOL2 WILD-TYPE
  N0             4              89
  N1             2              79
  N2             4              46
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D418V6, binary
                 cls
clus                0   1
  SGOL2 MUTATED     9   2
  SGOL2 WILD-TYPE 248  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED      9    2
  SGOL2 WILD-TYPE  248   16
   clus
vv  SGOL2 MUTATED SGOL2 WILD-TYPE
  0             9             248
  1             2              16
[1] 2 2
[1] FALSE
D418V7, binary
                 cls
clus                0   1
  SGOL2 MUTATED     7   4
  SGOL2 WILD-TYPE 103 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED      7    4
  SGOL2 WILD-TYPE  103  175
        clus
vv       SGOL2 MUTATED SGOL2 WILD-TYPE
  FEMALE             7             103
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SGOL2 MUTATED                                       3
  SGOL2 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SGOL2 MUTATED                                                        5
  SGOL2 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SGOL2 MUTATED                                                                   2
  SGOL2 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SGOL2 MUTATED                                                  1
  SGOL2 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SGOL2 MUTATED                                                          0
  SGOL2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SGOL2 MUTATED                                                           0
  SGOL2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SGOL2 MUTATED                                          0
  SGOL2 WILD-TYPE                                        3
D418V8, multiclass
                                                                   clus
vv                                                                  SGOL2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  SGOL2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D418V9, binary
                 cls
clus                0   1
  SGOL2 MUTATED     0  11
  SGOL2 WILD-TYPE   5 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED      0   11
  SGOL2 WILD-TYPE    5  273
     clus
vv    SGOL2 MUTATED SGOL2 WILD-TYPE
  NO              0               5
  YES            11             273
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SGOL2 MUTATED     9   0   1   1
  SGOL2 WILD-TYPE 218  10   9  23
D418V10, multiclass
    clus
vv   SGOL2 MUTATED SGOL2 WILD-TYPE
  R0             9             218
  R1             0              10
  R2             1               9
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D418V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SGOL2 MUTATED       5                         0     3
  SGOL2 WILD-TYPE    71                         4   165
D418V12, multiclass
                           clus
vv                          SGOL2 MUTATED SGOL2 WILD-TYPE
  ASIAN                                 5              71
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(419) Variable = ADAMTSL4 MUTATION ANALYSIS
D419V1, survival
                    sevent
clus2                  0   1
  ADAMTSL4 MUTATED     9   5
  ADAMTSL4 WILD-TYPE 172  75
  ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE 
                14                247 
  ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE 
                 5                 75 
$`ADAMTSL4 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-8078 TCGA-BR-A4QL 
       26.70         6.97        34.68        30.90        12.26        11.57 
TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-5726 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4GT 
        1.02         9.01        28.96        11.84         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4H8 
        6.25         8.88 

$`ADAMTSL4 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       25.61        18.05        19.89         8.98        21.11        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        20.55         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       47.05        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GX 
       22.75        25.81        11.77        29.98         8.98        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        9.67        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE 
               0.1                0.0 
  ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE 
             34.68             105.07 
  ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE 
             10.29              12.79 
[1] "0.1 - 34.7 (10.3)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.1"
D419V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ADAMTSL4 MUTATED         0        1        1        0         2         4
  ADAMTSL4 WILD-TYPE       1        8       26       26        29        40
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAMTSL4 MUTATED           0          2          1          1        2
  ADAMTSL4 WILD-TYPE         3         47         35         23       22
D419V3, multiclass
            clus
vv           ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  1                  8
  STAGE IB                  1                 26
  STAGE II                  0                 26
  STAGE IIA                 2                 29
  STAGE IIB                 4                 40
  STAGE III                 0                  3
  STAGE IIIA                2                 47
  STAGE IIIB                1                 35
  STAGE IIIC                1                 23
  STAGE IV                  2                 22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ADAMTSL4 MUTATED     2   0   8   4
  ADAMTSL4 WILD-TYPE   9  72 114  71
D419V4, multiclass
    clus
vv   ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE
  T1                2                  9
  T2                0                 72
  T3                8                114
  T4                4                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  ADAMTSL4 MUTATED    5  4  3  2
  ADAMTSL4 WILD-TYPE 88 77 47 51
D419V5, multiclass
    clus
vv   ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE
  N0                5                 88
  N1                4                 77
  N2                3                 47
  N3                2                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D419V6, binary
                    cls
clus                   0   1
  ADAMTSL4 MUTATED    12   2
  ADAMTSL4 WILD-TYPE 245  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTSL4 MUTATED     12    2
  ADAMTSL4 WILD-TYPE  245   16
   clus
vv  ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE
  0               12                245
  1                2                 16
[1] 2 2
[1] FALSE
D419V7, binary
                    cls
clus                   0   1
  ADAMTSL4 MUTATED     8   7
  ADAMTSL4 WILD-TYPE 102 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTSL4 MUTATED      8    7
  ADAMTSL4 WILD-TYPE  102  172
        clus
vv       ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE
  FEMALE                8                102
  MALE                  7                172
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ADAMTSL4 MUTATED                                       4
  ADAMTSL4 WILD-TYPE                                    46
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ADAMTSL4 MUTATED                                                        7
  ADAMTSL4 WILD-TYPE                                                    128
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ADAMTSL4 MUTATED                                                                   1
  ADAMTSL4 WILD-TYPE                                                                39
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ADAMTSL4 MUTATED                                                  3
  ADAMTSL4 WILD-TYPE                                               35
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ADAMTSL4 MUTATED                                                          0
  ADAMTSL4 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ADAMTSL4 MUTATED                                                           0
  ADAMTSL4 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ADAMTSL4 MUTATED                                          0
  ADAMTSL4 WILD-TYPE                                        3
D419V8, multiclass
                                                                   clus
vv                                                                  ADAMTSL4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  ADAMTSL4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D419V9, binary
                    cls
clus                   0   1
  ADAMTSL4 MUTATED     0  15
  ADAMTSL4 WILD-TYPE   5 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTSL4 MUTATED      0   15
  ADAMTSL4 WILD-TYPE    5  269
     clus
vv    ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE
  NO                 0                  5
  YES               15                269
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  ADAMTSL4 MUTATED    10   0   2   2
  ADAMTSL4 WILD-TYPE 217  10   8  22
D419V10, multiclass
    clus
vv   ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE
  R0               10                217
  R1                0                 10
  R2                2                  8
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D419V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ADAMTSL4 MUTATED       5                         0     7
  ADAMTSL4 WILD-TYPE    71                         4   161
D419V12, multiclass
                           clus
vv                          ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE
  ASIAN                                    5                 71
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    7                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(420) Variable = CPB2 MUTATION ANALYSIS
D420V1, survival
                sevent
clus2              0   1
  CPB2 MUTATED     7   1
  CPB2 WILD-TYPE 174  79
  CPB2 MUTATED CPB2 WILD-TYPE 
             8            253 
  CPB2 MUTATED CPB2 WILD-TYPE 
             1             79 
$`CPB2 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-5813 TCGA-CD-8536 
        6.97        34.68        13.45        15.81         0.39         0.10 
TCGA-CG-5728 TCGA-HU-A4G8 
       65.10        11.84 

$`CPB2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.07         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 
        0.13         0.16         0.10         0.10         0.13         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  CPB2 MUTATED CPB2 WILD-TYPE 
           0.1            0.0 
  CPB2 MUTATED CPB2 WILD-TYPE 
         65.10         105.07 
  CPB2 MUTATED CPB2 WILD-TYPE 
        12.645         12.620 
[1] "0.1 - 65.1 (12.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "3.1"
D420V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CPB2 MUTATED         0        0        1        2         1         1
  CPB2 WILD-TYPE       1        9       26       24        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CPB2 MUTATED           0          1          0          1        1
  CPB2 WILD-TYPE         3         48         36         23       23
D420V3, multiclass
            clus
vv           CPB2 MUTATED CPB2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              2             24
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            1             23
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CPB2 MUTATED     0   1   5   2
  CPB2 WILD-TYPE  11  71 117  73
D420V4, multiclass
    clus
vv   CPB2 MUTATED CPB2 WILD-TYPE
  T1            0             11
  T2            1             71
  T3            5            117
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  CPB2 MUTATED    4  2  1  1
  CPB2 WILD-TYPE 89 79 49 52
D420V5, multiclass
    clus
vv   CPB2 MUTATED CPB2 WILD-TYPE
  N0            4             89
  N1            2             79
  N2            1             49
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D420V6, binary
                cls
clus               0   1
  CPB2 MUTATED     7   1
  CPB2 WILD-TYPE 250  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPB2 MUTATED      7    1
  CPB2 WILD-TYPE  250   17
   clus
vv  CPB2 MUTATED CPB2 WILD-TYPE
  0            7            250
  1            1             17
[1] 2 2
[1] FALSE
D420V7, binary
                cls
clus               0   1
  CPB2 MUTATED     4   5
  CPB2 WILD-TYPE 106 174
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPB2 MUTATED      4    5
  CPB2 WILD-TYPE  106  174
        clus
vv       CPB2 MUTATED CPB2 WILD-TYPE
  FEMALE            4            106
  MALE              5            174
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CPB2 MUTATED                                       1
  CPB2 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CPB2 MUTATED                                                        5
  CPB2 WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CPB2 MUTATED                                                                   1
  CPB2 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CPB2 MUTATED                                                  1
  CPB2 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CPB2 MUTATED                                                          1
  CPB2 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CPB2 MUTATED                                                           0
  CPB2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CPB2 MUTATED                                          0
  CPB2 WILD-TYPE                                        3
D420V8, multiclass
                                                                   clus
vv                                                                  CPB2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  CPB2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D420V9, binary
                cls
clus               0   1
  CPB2 MUTATED     0   9
  CPB2 WILD-TYPE   5 275
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPB2 MUTATED      0    9
  CPB2 WILD-TYPE    5  275
     clus
vv    CPB2 MUTATED CPB2 WILD-TYPE
  NO             0              5
  YES            9            275
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CPB2 MUTATED     5   0   0   2
  CPB2 WILD-TYPE 222  10  10  22
D420V10, multiclass
    clus
vv   CPB2 MUTATED CPB2 WILD-TYPE
  R0            5            222
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D420V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CPB2 MUTATED       4                         0     4
  CPB2 WILD-TYPE    72                         4   164
D420V12, multiclass
                           clus
vv                          CPB2 MUTATED CPB2 WILD-TYPE
  ASIAN                                4             72
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                4            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(421) Variable = THEMIS MUTATION ANALYSIS
D421V1, survival
                  sevent
clus2                0   1
  THEMIS MUTATED     4   3
  THEMIS WILD-TYPE 177  77
  THEMIS MUTATED THEMIS WILD-TYPE 
               7              254 
  THEMIS MUTATED THEMIS WILD-TYPE 
               3               77 
$`THEMIS MUTATED`
TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8680 TCGA-BR-A4QL 
        6.97         7.43        30.90        34.68        15.81        11.57 
TCGA-CG-5723 
      105.07 

$`THEMIS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4267 
       26.70        11.70         6.61         4.64        18.35         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         6.02         0.99        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  THEMIS MUTATED THEMIS WILD-TYPE 
            6.97             0.00 
  THEMIS MUTATED THEMIS WILD-TYPE 
          105.07            79.07 
  THEMIS MUTATED THEMIS WILD-TYPE 
          15.810           12.605 
[1] "7.0 - 105.1 (15.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.4"
D421V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  THEMIS MUTATED         1        0        0        1         1         0
  THEMIS WILD-TYPE       0        9       27       25        30        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  THEMIS MUTATED           0          1          1          0        1
  THEMIS WILD-TYPE         3         48         35         24       23
D421V3, multiclass
            clus
vv           THEMIS MUTATED THEMIS WILD-TYPE
  STAGE I                 1                0
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                1               25
  STAGE IIA               1               30
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              0               24
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  THEMIS MUTATED     1   2   3   1
  THEMIS WILD-TYPE  10  70 119  74
D421V4, multiclass
    clus
vv   THEMIS MUTATED THEMIS WILD-TYPE
  T1              1               10
  T2              2               70
  T3              3              119
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  THEMIS MUTATED    1  4  1  1
  THEMIS WILD-TYPE 92 77 49 52
D421V5, multiclass
    clus
vv   THEMIS MUTATED THEMIS WILD-TYPE
  N0              1               92
  N1              4               77
  N2              1               49
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D421V6, binary
                  cls
clus                 0   1
  THEMIS MUTATED     5   1
  THEMIS WILD-TYPE 252  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED      5    1
  THEMIS WILD-TYPE  252   17
   clus
vv  THEMIS MUTATED THEMIS WILD-TYPE
  0              5              252
  1              1               17
[1] 2 2
[1] FALSE
D421V7, binary
                  cls
clus                 0   1
  THEMIS MUTATED     4   4
  THEMIS WILD-TYPE 106 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED      4    4
  THEMIS WILD-TYPE  106  175
        clus
vv       THEMIS MUTATED THEMIS WILD-TYPE
  FEMALE              4              106
  MALE                4              175
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  THEMIS MUTATED                                       0
  THEMIS WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  THEMIS MUTATED                                                        7
  THEMIS WILD-TYPE                                                    128
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  THEMIS MUTATED                                                                   0
  THEMIS WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  THEMIS MUTATED                                                  1
  THEMIS WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  THEMIS MUTATED                                                          0
  THEMIS WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  THEMIS MUTATED                                                           0
  THEMIS WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  THEMIS MUTATED                                          0
  THEMIS WILD-TYPE                                        3
D421V8, multiclass
                                                                   clus
vv                                                                  THEMIS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  THEMIS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D421V9, binary
                  cls
clus                 0   1
  THEMIS MUTATED     0   8
  THEMIS WILD-TYPE   5 276
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED      0    8
  THEMIS WILD-TYPE    5  276
     clus
vv    THEMIS MUTATED THEMIS WILD-TYPE
  NO               0                5
  YES              8              276
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  THEMIS MUTATED     5   0   0   3
  THEMIS WILD-TYPE 222  10  10  21
D421V10, multiclass
    clus
vv   THEMIS MUTATED THEMIS WILD-TYPE
  R0              5              222
  R1              0               10
  R2              0               10
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D421V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  THEMIS MUTATED       1                         1     5
  THEMIS WILD-TYPE    75                         3   163
D421V12, multiclass
                           clus
vv                          THEMIS MUTATED THEMIS WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  5              163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(422) Variable = KRTAP10-9 MUTATION ANALYSIS
D422V1, survival
                     sevent
clus2                   0   1
  KRTAP10-9 MUTATED     7   1
  KRTAP10-9 WILD-TYPE 174  79
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
                  8                 253 
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
                  1                  79 
$`KRTAP10-9 MUTATED`
TCGA-BR-4184 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A4MI TCGA-CG-4305 
        6.97         1.12        13.45        15.81         0.10        15.95 
TCGA-CG-5723 TCGA-CG-5730 
      105.07         4.01 

$`KRTAP10-9 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         6.02         0.99        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
                0.1                 0.0 
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
             105.07               79.07 
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
              10.21               12.62 
[1] "0.1 - 105.1 (10.2)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "3.1"
D422V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KRTAP10-9 MUTATED         1        0        0        2         1         0
  KRTAP10-9 WILD-TYPE       0        9       27       24        30        44
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KRTAP10-9 MUTATED           0          1          1          1        2
  KRTAP10-9 WILD-TYPE         3         48         35         23       22
D422V3, multiclass
            clus
vv           KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  STAGE I                    1                   0
  STAGE IA                   0                   9
  STAGE IB                   0                  27
  STAGE II                   2                  24
  STAGE IIA                  1                  30
  STAGE IIB                  0                  44
  STAGE III                  0                   3
  STAGE IIIA                 1                  48
  STAGE IIIB                 1                  35
  STAGE IIIC                 1                  23
  STAGE IV                   2                  22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  KRTAP10-9 MUTATED     1   3   3   2
  KRTAP10-9 WILD-TYPE  10  69 119  73
D422V4, multiclass
    clus
vv   KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  T1                 1                  10
  T2                 3                  69
  T3                 3                 119
  T4                 2                  73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  N0 N1 N2 N3
  KRTAP10-9 MUTATED    1  6  1  1
  KRTAP10-9 WILD-TYPE 92 75 49 52
D422V5, multiclass
    clus
vv   KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  N0                 1                  92
  N1                 6                  75
  N2                 1                  49
  N3                 1                  52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D422V6, binary
                     cls
clus                    0   1
  KRTAP10-9 MUTATED     5   2
  KRTAP10-9 WILD-TYPE 252  16
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP10-9 MUTATED      5    2
  KRTAP10-9 WILD-TYPE  252   16
   clus
vv  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  0                 5                 252
  1                 2                  16
[1] 2 2
[1] FALSE
D422V7, binary
                     cls
clus                    0   1
  KRTAP10-9 MUTATED     2   7
  KRTAP10-9 WILD-TYPE 108 172
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP10-9 MUTATED      2    7
  KRTAP10-9 WILD-TYPE  108  172
        clus
vv       KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  FEMALE                 2                 108
  MALE                   7                 172
[1] 2 2
[1] FALSE
                     vv
clus                  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KRTAP10-9 MUTATED                                       0
  KRTAP10-9 WILD-TYPE                                    50
                     vv
clus                  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KRTAP10-9 MUTATED                                                        7
  KRTAP10-9 WILD-TYPE                                                    128
                     vv
clus                  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KRTAP10-9 MUTATED                                                                   1
  KRTAP10-9 WILD-TYPE                                                                39
                     vv
clus                  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KRTAP10-9 MUTATED                                                  1
  KRTAP10-9 WILD-TYPE                                               37
                     vv
clus                  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KRTAP10-9 MUTATED                                                          0
  KRTAP10-9 WILD-TYPE                                                       16
                     vv
clus                  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KRTAP10-9 MUTATED                                                           0
  KRTAP10-9 WILD-TYPE                                                         6
                     vv
clus                  STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KRTAP10-9 MUTATED                                          0
  KRTAP10-9 WILD-TYPE                                        3
D422V8, multiclass
                                                                   clus
vv                                                                  KRTAP10-9 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          0
                                                                   clus
vv                                                                  KRTAP10-9 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                              50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                   37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                           16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                           6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                            3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D422V9, binary
                     cls
clus                    0   1
  KRTAP10-9 MUTATED     0   9
  KRTAP10-9 WILD-TYPE   5 275
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP10-9 MUTATED      0    9
  KRTAP10-9 WILD-TYPE    5  275
     clus
vv    KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  NO                  0                   5
  YES                 9                 275
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  KRTAP10-9 MUTATED     6   0   1   1
  KRTAP10-9 WILD-TYPE 221  10   9  23
D422V10, multiclass
    clus
vv   KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  R0                 6                 221
  R1                 0                  10
  R2                 1                   9
  RX                 1                  23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D422V11, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRTAP10-9 MUTATED       2                         1     3
  KRTAP10-9 WILD-TYPE    74                         3   165
D422V12, multiclass
                           clus
vv                          KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  ASIAN                                     2                  74
  BLACK OR AFRICAN AMERICAN                 1                   3
  WHITE                                     3                 165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(423) Variable = SGK3 MUTATION ANALYSIS
D423V1, survival
                sevent
clus2              0   1
  SGK3 MUTATED     3   1
  SGK3 WILD-TYPE 178  79
  SGK3 MUTATED SGK3 WILD-TYPE 
             4            257 
  SGK3 MUTATED SGK3 WILD-TYPE 
             1             79 
$`SGK3 MUTATED`
TCGA-BR-4184 TCGA-BR-7851 TCGA-BR-8372 TCGA-HU-A4GU 
        6.97        12.43        19.17         6.25 

$`SGK3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  SGK3 MUTATED SGK3 WILD-TYPE 
          6.25           0.00 
  SGK3 MUTATED SGK3 WILD-TYPE 
         19.17         105.07 
  SGK3 MUTATED SGK3 WILD-TYPE 
          9.70          12.66 
[1] "6.2 - 19.2 (9.7)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.1"
D423V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SGK3 MUTATED         0        0        0        0         0         2
  SGK3 WILD-TYPE       1        9       27       26        31        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SGK3 MUTATED           0          1          0          1        0
  SGK3 WILD-TYPE         3         48         36         23       24
D423V3, multiclass
            clus
vv           SGK3 MUTATED SGK3 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              0             26
  STAGE IIA             0             31
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            1             23
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SGK3 MUTATED     0   0   2   2
  SGK3 WILD-TYPE  11  72 120  73
D423V4, multiclass
    clus
vv   SGK3 MUTATED SGK3 WILD-TYPE
  T1            0             11
  T2            0             72
  T3            2            120
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  SGK3 MUTATED    1  2  0  1
  SGK3 WILD-TYPE 92 79 50 52
D423V5, multiclass
    clus
vv   SGK3 MUTATED SGK3 WILD-TYPE
  N0            1             92
  N1            2             79
  N2            0             50
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D423V6, binary
                cls
clus               0   1
  SGK3 MUTATED     4   0
  SGK3 WILD-TYPE 253  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK3 MUTATED      4    0
  SGK3 WILD-TYPE  253   18
   clus
vv  SGK3 MUTATED SGK3 WILD-TYPE
  0            4            253
  1            0             18
[1] 2 2
[1] FALSE
D423V7, binary
                cls
clus               0   1
  SGK3 MUTATED     1   4
  SGK3 WILD-TYPE 109 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK3 MUTATED      1    4
  SGK3 WILD-TYPE  109  175
        clus
vv       SGK3 MUTATED SGK3 WILD-TYPE
  FEMALE            1            109
  MALE              4            175
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SGK3 MUTATED                                       1
  SGK3 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SGK3 MUTATED                                                        3
  SGK3 WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SGK3 MUTATED                                                                   1
  SGK3 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SGK3 MUTATED                                                  0
  SGK3 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SGK3 MUTATED                                                          0
  SGK3 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SGK3 MUTATED                                                           0
  SGK3 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SGK3 MUTATED                                          0
  SGK3 WILD-TYPE                                        3
D423V8, multiclass
                                                                   clus
vv                                                                  SGK3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  SGK3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D423V9, binary
                cls
clus               0   1
  SGK3 MUTATED     0   5
  SGK3 WILD-TYPE   5 279
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK3 MUTATED      0    5
  SGK3 WILD-TYPE    5  279
     clus
vv    SGK3 MUTATED SGK3 WILD-TYPE
  NO             0              5
  YES            5            279
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SGK3 MUTATED     3   0   0   2
  SGK3 WILD-TYPE 224  10  10  22
D423V10, multiclass
    clus
vv   SGK3 MUTATED SGK3 WILD-TYPE
  R0            3            224
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D423V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SGK3 MUTATED       1                         0     4
  SGK3 WILD-TYPE    75                         4   164
D423V12, multiclass
                           clus
vv                          SGK3 MUTATED SGK3 WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                4            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(424) Variable = YIF1A MUTATION ANALYSIS
D424V1, survival
                 sevent
clus2               0   1
  YIF1A MUTATED     1   0
  YIF1A WILD-TYPE 180  80
  YIF1A MUTATED YIF1A WILD-TYPE 
              1             260 
  YIF1A MUTATED YIF1A WILD-TYPE 
              0              80 
$`YIF1A MUTATED`
TCGA-BR-8591 
       13.45 

$`YIF1A WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       15.81         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  YIF1A MUTATED YIF1A WILD-TYPE 
          13.45            0.00 
  YIF1A MUTATED YIF1A WILD-TYPE 
          13.45          105.07 
  YIF1A MUTATED YIF1A WILD-TYPE 
         13.450          12.605 
[1] "13.4 - 13.4 (13.4)" "0.0 - 105.1 (12.6)"
[1] "Remove cluster labels:" "YIF1A MUTATED"         
D424V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  YIF1A MUTATED         0        0        1        0         0         0
  YIF1A WILD-TYPE       1        9       26       26        31        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  YIF1A MUTATED           0          1          0          1        0
  YIF1A WILD-TYPE         3         48         36         23       24
D424V3, multiclass
            clus
vv           YIF1A MUTATED YIF1A WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              0              31
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  YIF1A MUTATED     0   1   0   2
  YIF1A WILD-TYPE  11  71 122  73
D424V4, multiclass
    clus
vv   YIF1A MUTATED YIF1A WILD-TYPE
  T1             0              11
  T2             1              71
  T3             0             122
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  YIF1A MUTATED    2  0  0  1
  YIF1A WILD-TYPE 91 81 50 52
D424V5, multiclass
    clus
vv   YIF1A MUTATED YIF1A WILD-TYPE
  N0             2              91
  N1             0              81
  N2             0              50
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D424V6, binary
                 cls
clus                0   1
  YIF1A MUTATED     3   0
  YIF1A WILD-TYPE 254  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIF1A MUTATED      3    0
  YIF1A WILD-TYPE  254   18
   clus
vv  YIF1A MUTATED YIF1A WILD-TYPE
  0             3             254
  1             0              18
[1] 2 2
[1] FALSE
D424V7, binary
                 cls
clus                0   1
  YIF1A MUTATED     1   2
  YIF1A WILD-TYPE 109 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIF1A MUTATED      1    2
  YIF1A WILD-TYPE  109  177
        clus
vv       YIF1A MUTATED YIF1A WILD-TYPE
  FEMALE             1             109
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  YIF1A MUTATED                                       0
  YIF1A WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  YIF1A MUTATED                                                        2
  YIF1A WILD-TYPE                                                    133
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  YIF1A MUTATED                                                                   1
  YIF1A WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  YIF1A MUTATED                                                  0
  YIF1A WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  YIF1A MUTATED                                                          0
  YIF1A WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  YIF1A MUTATED                                                           0
  YIF1A WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  YIF1A MUTATED                                          0
  YIF1A WILD-TYPE                                        3
D424V8, multiclass
                                                                   clus
vv                                                                  YIF1A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  YIF1A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D424V9, binary
                 cls
clus                0   1
  YIF1A MUTATED     0   3
  YIF1A WILD-TYPE   5 281
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIF1A MUTATED      0    3
  YIF1A WILD-TYPE    5  281
     clus
vv    YIF1A MUTATED YIF1A WILD-TYPE
  NO              0               5
  YES             3             281
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  YIF1A MUTATED     2   0   0   1
  YIF1A WILD-TYPE 225  10  10  23
D424V10, multiclass
    clus
vv   YIF1A MUTATED YIF1A WILD-TYPE
  R0             2             225
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D424V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  YIF1A MUTATED       0                         0     2
  YIF1A WILD-TYPE    76                         4   166
D424V12, multiclass
[1] "Remove cluster labels:" "YIF1A MUTATED"         
clus
  YIF1A MUTATED YIF1A WILD-TYPE 
              2             246 
     TCGA-B7-5816      TCGA-B7-5818      TCGA-BR-4183      TCGA-BR-4184 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-4187      TCGA-BR-4188      TCGA-BR-4191      TCGA-BR-4201 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256      TCGA-BR-4257 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4292 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-4294      TCGA-BR-4357      TCGA-BR-4362      TCGA-BR-4363 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-4366      TCGA-BR-4368      TCGA-BR-4369      TCGA-BR-4370 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-4371      TCGA-BR-6452      TCGA-BR-6453      TCGA-BR-6454 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457      TCGA-BR-6458 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565      TCGA-BR-6566 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707      TCGA-BR-6710 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803      TCGA-BR-6852 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703      TCGA-BR-7707 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-7715      TCGA-BR-7716      TCGA-BR-7717      TCGA-BR-7722 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-7723      TCGA-BR-7851      TCGA-BR-7901      TCGA-BR-7957 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-7958      TCGA-BR-7959      TCGA-BR-8058      TCGA-BR-8059 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-8077      TCGA-BR-8078      TCGA-BR-8080      TCGA-BR-8081 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-8284      TCGA-BR-8286      TCGA-BR-8289      TCGA-BR-8291 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-8295      TCGA-BR-8296      TCGA-BR-8297      TCGA-BR-8360 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-8361      TCGA-BR-8363      TCGA-BR-8364      TCGA-BR-8365 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-8366      TCGA-BR-8367      TCGA-BR-8368      TCGA-BR-8369 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-8370      TCGA-BR-8371      TCGA-BR-8372      TCGA-BR-8373 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-8380      TCGA-BR-8381      TCGA-BR-8382      TCGA-BR-8384 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-8483      TCGA-BR-8484      TCGA-BR-8485      TCGA-BR-8486 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-8487      TCGA-BR-8588      TCGA-BR-8589      TCGA-BR-8590 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-8592      TCGA-BR-8676      TCGA-BR-8677      TCGA-BR-8678 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-8679      TCGA-BR-8680      TCGA-BR-8682      TCGA-BR-8683 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-8686      TCGA-BR-8687      TCGA-BR-8690      TCGA-BR-A44T 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-A44U      TCGA-BR-A452      TCGA-BR-A453      TCGA-BR-A4CQ 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-A4CR      TCGA-BR-A4CS      TCGA-BR-A4IU      TCGA-BR-A4IV 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-A4IY      TCGA-BR-A4IZ      TCGA-BR-A4J1      TCGA-BR-A4J2 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-A4J4      TCGA-BR-A4J6      TCGA-BR-A4J7      TCGA-BR-A4J8 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-A4PD      TCGA-BR-A4PE      TCGA-BR-A4PF      TCGA-BR-A4QI 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-BR-A4QL      TCGA-BR-A4QM      TCGA-CD-5798      TCGA-CD-5799 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-CD-5800      TCGA-CD-5801      TCGA-CD-5802      TCGA-CD-5803 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-CD-5804      TCGA-CD-5813      TCGA-CD-8524      TCGA-CD-8525 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-CD-8526      TCGA-CD-8527      TCGA-CD-8528      TCGA-CD-8529 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-CD-8530      TCGA-CD-8531      TCGA-CD-8532      TCGA-CD-8534 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-CD-8535      TCGA-CD-8536      TCGA-CD-A486      TCGA-CD-A487 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-CD-A489      TCGA-CD-A48A      TCGA-CD-A48C      TCGA-CD-A4MG 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-CD-A4MH      TCGA-CD-A4MI      TCGA-CD-A4MJ      TCGA-D7-5577 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-D7-5578      TCGA-D7-5579      TCGA-D7-6518      TCGA-D7-6519 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-D7-6520      TCGA-D7-6521      TCGA-D7-6522      TCGA-D7-6524 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-D7-6525      TCGA-D7-6526      TCGA-D7-6527      TCGA-D7-6528 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-D7-6815      TCGA-D7-6817      TCGA-D7-6818      TCGA-D7-6820 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-D7-6822      TCGA-D7-8570      TCGA-D7-8572      TCGA-D7-8573 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-D7-8574      TCGA-D7-8575      TCGA-D7-8576      TCGA-D7-8578 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-D7-8579      TCGA-D7-A4YT      TCGA-D7-A4YU      TCGA-D7-A4YV 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-D7-A4YX      TCGA-D7-A4YY      TCGA-D7-A4Z0      TCGA-EQ-5647 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-EQ-8122      TCGA-EQ-A4SO      TCGA-F1-6177      TCGA-F1-6874 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-F1-6875      TCGA-F1-A448      TCGA-FP-7735      TCGA-FP-7829 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-FP-7916      TCGA-FP-7998      TCGA-FP-8099      TCGA-FP-8209 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-FP-8210      TCGA-FP-8211      TCGA-FP-8631      TCGA-FP-A4BE 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-FP-A4BF      TCGA-HJ-7597      TCGA-HU-8243      TCGA-HU-8245 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-HU-8249      TCGA-HU-8602      TCGA-HU-8604      TCGA-HU-8608 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-HU-8610      TCGA-HU-A4G2      TCGA-HU-A4G3      TCGA-HU-A4G6 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-HU-A4G8      TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-HU-A4GF      TCGA-HU-A4GH      TCGA-HU-A4GN      TCGA-HU-A4GP 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-HU-A4GQ      TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-HU-A4GY      TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-HU-A4H4      TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-HU-A4HD      TCGA-IN-7806      TCGA-IN-7808      TCGA-IN-8462 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 
     TCGA-IN-8663      TCGA-IP-7968 
"YIF1A WILD-TYPE" "YIF1A WILD-TYPE" 

Clustering(425) Variable = EGR1 MUTATION ANALYSIS
D425V1, survival
                sevent
clus2              0   1
  EGR1 MUTATED     7   3
  EGR1 WILD-TYPE 174  77
  EGR1 MUTATED EGR1 WILD-TYPE 
            10            251 
  EGR1 MUTATED EGR1 WILD-TYPE 
             3             77 
$`EGR1 MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5723 TCGA-CG-5733 
       34.68        12.26        15.95         1.02       105.07        21.07 
TCGA-F1-6874 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       14.47        29.98         0.10         6.51 

$`EGR1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       20.02         3.02        27.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  EGR1 MUTATED EGR1 WILD-TYPE 
           0.1            0.0 
  EGR1 MUTATED EGR1 WILD-TYPE 
        105.07          79.07 
  EGR1 MUTATED EGR1 WILD-TYPE 
         15.21          12.59 
[1] "0.1 - 105.1 (15.2)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.7"
D425V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EGR1 MUTATED         0        0        1        2         3         1
  EGR1 WILD-TYPE       1        9       26       24        28        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EGR1 MUTATED           0          1          0          1        1
  EGR1 WILD-TYPE         3         48         36         23       23
D425V3, multiclass
            clus
vv           EGR1 MUTATED EGR1 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              2             24
  STAGE IIA             3             28
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            1             23
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EGR1 MUTATED     0   5   3   2
  EGR1 WILD-TYPE  11  67 119  73
D425V4, multiclass
    clus
vv   EGR1 MUTATED EGR1 WILD-TYPE
  T1            0             11
  T2            5             67
  T3            3            119
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  EGR1 MUTATED    4  3  3  0
  EGR1 WILD-TYPE 89 78 47 53
D425V5, multiclass
    clus
vv   EGR1 MUTATED EGR1 WILD-TYPE
  N0            4             89
  N1            3             78
  N2            3             47
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D425V6, binary
                cls
clus               0   1
  EGR1 MUTATED     9   1
  EGR1 WILD-TYPE 248  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED      9    1
  EGR1 WILD-TYPE  248   17
   clus
vv  EGR1 MUTATED EGR1 WILD-TYPE
  0            9            248
  1            1             17
[1] 2 2
[1] FALSE
D425V7, binary
                cls
clus               0   1
  EGR1 MUTATED     4   6
  EGR1 WILD-TYPE 106 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED      4    6
  EGR1 WILD-TYPE  106  173
        clus
vv       EGR1 MUTATED EGR1 WILD-TYPE
  FEMALE            4            106
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  EGR1 MUTATED                                       0
  EGR1 WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EGR1 MUTATED                                                        5
  EGR1 WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EGR1 MUTATED                                                                   2
  EGR1 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  EGR1 MUTATED                                                  3
  EGR1 WILD-TYPE                                               35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  EGR1 MUTATED                                                          0
  EGR1 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  EGR1 MUTATED                                                           0
  EGR1 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  EGR1 MUTATED                                          0
  EGR1 WILD-TYPE                                        3
D425V8, multiclass
                                                                   clus
vv                                                                  EGR1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  EGR1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D425V9, binary
                cls
clus               0   1
  EGR1 MUTATED     0  10
  EGR1 WILD-TYPE   5 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED      0   10
  EGR1 WILD-TYPE    5  274
     clus
vv    EGR1 MUTATED EGR1 WILD-TYPE
  NO             0              5
  YES           10            274
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EGR1 MUTATED     9   0   1   0
  EGR1 WILD-TYPE 218  10   9  24
D425V10, multiclass
    clus
vv   EGR1 MUTATED EGR1 WILD-TYPE
  R0            9            218
  R1            0             10
  R2            1              9
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D425V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EGR1 MUTATED       3                         0     3
  EGR1 WILD-TYPE    73                         4   165
D425V12, multiclass
                           clus
vv                          EGR1 MUTATED EGR1 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                3            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(426) Variable = GTF3C4 MUTATION ANALYSIS
D426V1, survival
                  sevent
clus2                0   1
  GTF3C4 MUTATED    10   0
  GTF3C4 WILD-TYPE 171  80
  GTF3C4 MUTATED GTF3C4 WILD-TYPE 
              10              251 
  GTF3C4 MUTATED GTF3C4 WILD-TYPE 
               0               80 
$`GTF3C4 MUTATED`
TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-A4QL 
       34.68        20.55         4.31         1.12        13.45        11.57 
TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-A4YY TCGA-F1-6874 
      105.07        65.10        13.78        14.47 

$`GTF3C4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       17.49        14.43         0.69        12.26         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79        15.81         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         6.02         0.99        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 
       20.91        14.27        16.44         5.92        15.16        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        0.62         7.99        16.24        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  GTF3C4 MUTATED GTF3C4 WILD-TYPE 
            1.12             0.00 
  GTF3C4 MUTATED GTF3C4 WILD-TYPE 
          105.07            79.07 
  GTF3C4 MUTATED GTF3C4 WILD-TYPE 
          14.125           12.560 
[1] "1.1 - 105.1 (14.1)" "0.0 - 79.1 (12.6)" 
[1] "hr="   "3e+07"
D426V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GTF3C4 MUTATED         0        0        3        1         2         1
  GTF3C4 WILD-TYPE       1        9       24       25        29        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GTF3C4 MUTATED           0          0          2          1        0
  GTF3C4 WILD-TYPE         3         49         34         23       24
D426V3, multiclass
            clus
vv           GTF3C4 MUTATED GTF3C4 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                3               24
  STAGE II                1               25
  STAGE IIA               2               29
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              2               34
  STAGE IIIC              1               23
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GTF3C4 MUTATED     0   4   4   2
  GTF3C4 WILD-TYPE  11  68 118  73
D426V4, multiclass
    clus
vv   GTF3C4 MUTATED GTF3C4 WILD-TYPE
  T1              0               11
  T2              4               68
  T3              4              118
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  GTF3C4 MUTATED    6  2  0  3
  GTF3C4 WILD-TYPE 87 79 50 50
D426V5, multiclass
    clus
vv   GTF3C4 MUTATED GTF3C4 WILD-TYPE
  N0              6               87
  N1              2               79
  N2              0               50
  N3              3               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D426V6, binary
                  cls
clus                 0   1
  GTF3C4 MUTATED    12   0
  GTF3C4 WILD-TYPE 245  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C4 MUTATED     12    0
  GTF3C4 WILD-TYPE  245   18
   clus
vv  GTF3C4 MUTATED GTF3C4 WILD-TYPE
  0             12              245
  1              0               18
[1] 2 2
[1] FALSE
D426V7, binary
                  cls
clus                 0   1
  GTF3C4 MUTATED     7   5
  GTF3C4 WILD-TYPE 103 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C4 MUTATED      7    5
  GTF3C4 WILD-TYPE  103  174
        clus
vv       GTF3C4 MUTATED GTF3C4 WILD-TYPE
  FEMALE              7              103
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GTF3C4 MUTATED                                       0
  GTF3C4 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GTF3C4 MUTATED                                                       10
  GTF3C4 WILD-TYPE                                                    125
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GTF3C4 MUTATED                                                                   2
  GTF3C4 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GTF3C4 MUTATED                                                  0
  GTF3C4 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GTF3C4 MUTATED                                                          0
  GTF3C4 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GTF3C4 MUTATED                                                           0
  GTF3C4 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GTF3C4 MUTATED                                          0
  GTF3C4 WILD-TYPE                                        3
D426V8, multiclass
                                                                   clus
vv                                                                  GTF3C4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  GTF3C4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D426V9, binary
                  cls
clus                 0   1
  GTF3C4 MUTATED     0  12
  GTF3C4 WILD-TYPE   5 272
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C4 MUTATED      0   12
  GTF3C4 WILD-TYPE    5  272
     clus
vv    GTF3C4 MUTATED GTF3C4 WILD-TYPE
  NO               0                5
  YES             12              272
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GTF3C4 MUTATED    10   0   0   2
  GTF3C4 WILD-TYPE 217  10  10  22
D426V10, multiclass
    clus
vv   GTF3C4 MUTATED GTF3C4 WILD-TYPE
  R0             10              217
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D426V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GTF3C4 MUTATED       0                         0    10
  GTF3C4 WILD-TYPE    76                         4   158
D426V12, multiclass
                           clus
vv                          GTF3C4 MUTATED GTF3C4 WILD-TYPE
  ASIAN                                  0               76
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                 10              158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(427) Variable = ACTL6A MUTATION ANALYSIS
D427V1, survival
                  sevent
clus2                0   1
  ACTL6A MUTATED     5   2
  ACTL6A WILD-TYPE 176  78
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               7              254 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               2               78 
$`ACTL6A MUTATED`
TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8078 TCGA-BR-A4IY TCGA-BR-A4QL TCGA-CG-5726 
       34.68        24.76        12.26        12.89        11.57        28.96 
TCGA-HU-A4GQ 
        0.10 

$`ACTL6A WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        13.64         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  ACTL6A MUTATED ACTL6A WILD-TYPE 
             0.1              0.0 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
           34.68           105.07 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
          12.890           12.605 
[1] "0.1 - 34.7 (12.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D427V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ACTL6A MUTATED         0        2        0        1         1         2
  ACTL6A WILD-TYPE       1        7       27       25        30        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACTL6A MUTATED           0          0          1          1        0
  ACTL6A WILD-TYPE         3         49         35         23       24
D427V3, multiclass
            clus
vv           ACTL6A MUTATED ACTL6A WILD-TYPE
  STAGE I                 0                1
  STAGE IA                2                7
  STAGE IB                0               27
  STAGE II                1               25
  STAGE IIA               1               30
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              1               35
  STAGE IIIC              1               23
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ACTL6A MUTATED     2   1   2   3
  ACTL6A WILD-TYPE   9  71 120  72
D427V4, multiclass
    clus
vv   ACTL6A MUTATED ACTL6A WILD-TYPE
  T1              2                9
  T2              1               71
  T3              2              120
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ACTL6A MUTATED    5  1  1  1
  ACTL6A WILD-TYPE 88 80 49 52
D427V5, multiclass
    clus
vv   ACTL6A MUTATED ACTL6A WILD-TYPE
  N0              5               88
  N1              1               80
  N2              1               49
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D427V6, binary
                  cls
clus                 0   1
  ACTL6A MUTATED     8   0
  ACTL6A WILD-TYPE 249  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6A MUTATED      8    0
  ACTL6A WILD-TYPE  249   18
   clus
vv  ACTL6A MUTATED ACTL6A WILD-TYPE
  0              8              249
  1              0               18
[1] 2 2
[1] FALSE
D427V7, binary
                  cls
clus                 0   1
  ACTL6A MUTATED     3   5
  ACTL6A WILD-TYPE 107 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6A MUTATED      3    5
  ACTL6A WILD-TYPE  107  174
        clus
vv       ACTL6A MUTATED ACTL6A WILD-TYPE
  FEMALE              3              107
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ACTL6A MUTATED                                       0
  ACTL6A WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ACTL6A MUTATED                                                        4
  ACTL6A WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ACTL6A MUTATED                                                                   1
  ACTL6A WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ACTL6A MUTATED                                                  1
  ACTL6A WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ACTL6A MUTATED                                                          1
  ACTL6A WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ACTL6A MUTATED                                                           1
  ACTL6A WILD-TYPE                                                         5
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ACTL6A MUTATED                                          0
  ACTL6A WILD-TYPE                                        3
D427V8, multiclass
                                                                   clus
vv                                                                  ACTL6A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ACTL6A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D427V9, binary
                  cls
clus                 0   1
  ACTL6A MUTATED     1   7
  ACTL6A WILD-TYPE   4 277
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6A MUTATED      1    7
  ACTL6A WILD-TYPE    4  277
     clus
vv    ACTL6A MUTATED ACTL6A WILD-TYPE
  NO               1                4
  YES              7              277
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ACTL6A MUTATED     8   0   0   0
  ACTL6A WILD-TYPE 219  10  10  24
D427V10, multiclass
    clus
vv   ACTL6A MUTATED ACTL6A WILD-TYPE
  R0              8              219
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D427V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACTL6A MUTATED       2                         0     4
  ACTL6A WILD-TYPE    74                         4   164
D427V12, multiclass
                           clus
vv                          ACTL6A MUTATED ACTL6A WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(428) Variable = C7ORF49 MUTATION ANALYSIS
D428V1, survival
                   sevent
clus2                 0   1
  C7ORF49 MUTATED     6   1
  C7ORF49 WILD-TYPE 175  79
  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
                7               254 
  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
                1                79 
$`C7ORF49 MUTATED`
TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-A4MJ TCGA-D7-A4YV TCGA-HU-A4G9 
       12.26         1.12        13.45        12.62         5.92        24.20 
TCGA-HU-A4GU 
        6.25 

$`C7ORF49 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       16.44        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        11.84         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       11.77        29.98         8.98         0.10         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
             1.12              0.00 
  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
            24.20            105.07 
  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
            12.26             12.71 
[1] "1.1 - 24.2 (12.3)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.5"
D428V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C7ORF49 MUTATED         0        1        1        0         1         3
  C7ORF49 WILD-TYPE       1        8       26       26        30        41
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C7ORF49 MUTATED           0          0          0          1        0
  C7ORF49 WILD-TYPE         3         49         36         23       24
D428V3, multiclass
            clus
vv           C7ORF49 MUTATED C7ORF49 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 1                 8
  STAGE IB                 1                26
  STAGE II                 0                26
  STAGE IIA                1                30
  STAGE IIB                3                41
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               0                36
  STAGE IIIC               1                23
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C7ORF49 MUTATED     1   1   3   2
  C7ORF49 WILD-TYPE  10  71 119  73
D428V4, multiclass
    clus
vv   C7ORF49 MUTATED C7ORF49 WILD-TYPE
  T1               1                10
  T2               1                71
  T3               3               119
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  C7ORF49 MUTATED    4  2  0  1
  C7ORF49 WILD-TYPE 89 79 50 52
D428V5, multiclass
    clus
vv   C7ORF49 MUTATED C7ORF49 WILD-TYPE
  N0               4                89
  N1               2                79
  N2               0                50
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D428V6, binary
                   cls
clus                  0   1
  C7ORF49 MUTATED     7   0
  C7ORF49 WILD-TYPE 250  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF49 MUTATED      7    0
  C7ORF49 WILD-TYPE  250   18
   clus
vv  C7ORF49 MUTATED C7ORF49 WILD-TYPE
  0               7               250
  1               0                18
[1] 2 2
[1] FALSE
D428V7, binary
                   cls
clus                  0   1
  C7ORF49 MUTATED     4   3
  C7ORF49 WILD-TYPE 106 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF49 MUTATED      4    3
  C7ORF49 WILD-TYPE  106  176
        clus
vv       C7ORF49 MUTATED C7ORF49 WILD-TYPE
  FEMALE               4               106
  MALE                 3               176
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C7ORF49 MUTATED                                       1
  C7ORF49 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C7ORF49 MUTATED                                                        4
  C7ORF49 WILD-TYPE                                                    131
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C7ORF49 MUTATED                                                                   0
  C7ORF49 WILD-TYPE                                                                40
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C7ORF49 MUTATED                                                  2
  C7ORF49 WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C7ORF49 MUTATED                                                          0
  C7ORF49 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C7ORF49 MUTATED                                                           0
  C7ORF49 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C7ORF49 MUTATED                                          0
  C7ORF49 WILD-TYPE                                        3
D428V8, multiclass
                                                                   clus
vv                                                                  C7ORF49 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  C7ORF49 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D428V9, binary
                   cls
clus                  0   1
  C7ORF49 MUTATED     0   7
  C7ORF49 WILD-TYPE   5 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF49 MUTATED      0    7
  C7ORF49 WILD-TYPE    5  277
     clus
vv    C7ORF49 MUTATED C7ORF49 WILD-TYPE
  NO                0                 5
  YES               7               277
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C7ORF49 MUTATED     6   0   0   0
  C7ORF49 WILD-TYPE 221  10  10  24
D428V10, multiclass
    clus
vv   C7ORF49 MUTATED C7ORF49 WILD-TYPE
  R0               6               221
  R1               0                10
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D428V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C7ORF49 MUTATED       3                         0     4
  C7ORF49 WILD-TYPE    73                         4   164
D428V12, multiclass
                           clus
vv                          C7ORF49 MUTATED C7ORF49 WILD-TYPE
  ASIAN                                   3                73
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   4               164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(429) Variable = BEST3 MUTATION ANALYSIS
D429V1, survival
                 sevent
clus2               0   1
  BEST3 MUTATED     4   6
  BEST3 WILD-TYPE 177  74
  BEST3 MUTATED BEST3 WILD-TYPE 
             10             251 
  BEST3 MUTATED BEST3 WILD-TYPE 
              6              74 
$`BEST3 MUTATED`
TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4280 TCGA-BR-8371 TCGA-CG-4443 TCGA-CG-4449 
        6.97        18.35         6.61        11.80        29.98        19.07 
TCGA-HJ-7597 TCGA-HU-A4G8 TCGA-HU-A4GH TCGA-HU-A4GQ 
       26.47        11.84        11.77         0.10 

$`BEST3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
       26.70        11.70         6.61         4.64         7.43        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        47.05        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       11.08         5.52         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        22.75        25.81        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  BEST3 MUTATED BEST3 WILD-TYPE 
            0.1             0.0 
  BEST3 MUTATED BEST3 WILD-TYPE 
          29.98          105.07 
  BEST3 MUTATED BEST3 WILD-TYPE 
          11.82           12.66 
[1] "0.1 - 30.0 (11.8)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.9"
D429V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BEST3 MUTATED         0        2        1        1         0         1
  BEST3 WILD-TYPE       1        7       26       25        31        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BEST3 MUTATED           1          1          1          1        0
  BEST3 WILD-TYPE         2         48         35         23       24
D429V3, multiclass
            clus
vv           BEST3 MUTATED BEST3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               2               7
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              0              31
  STAGE IIB              1              43
  STAGE III              1               2
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BEST3 MUTATED     2   4   3   1
  BEST3 WILD-TYPE   9  68 119  74
D429V4, multiclass
    clus
vv   BEST3 MUTATED BEST3 WILD-TYPE
  T1             2               9
  T2             4              68
  T3             3             119
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  BEST3 MUTATED    3  5  1  1
  BEST3 WILD-TYPE 90 76 49 52
D429V5, multiclass
    clus
vv   BEST3 MUTATED BEST3 WILD-TYPE
  N0             3              90
  N1             5              76
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D429V6, binary
                 cls
clus                0   1
  BEST3 MUTATED     9   0
  BEST3 WILD-TYPE 248  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEST3 MUTATED      9    0
  BEST3 WILD-TYPE  248   18
   clus
vv  BEST3 MUTATED BEST3 WILD-TYPE
  0             9             248
  1             0              18
[1] 2 2
[1] FALSE
D429V7, binary
                 cls
clus                0   1
  BEST3 MUTATED     4   7
  BEST3 WILD-TYPE 106 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEST3 MUTATED      4    7
  BEST3 WILD-TYPE  106  172
        clus
vv       BEST3 MUTATED BEST3 WILD-TYPE
  FEMALE             4             106
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  BEST3 MUTATED                                       1
  BEST3 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BEST3 MUTATED                                                        5
  BEST3 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BEST3 MUTATED                                                                   1
  BEST3 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  BEST3 MUTATED                                                  2
  BEST3 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  BEST3 MUTATED                                                          1
  BEST3 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  BEST3 MUTATED                                                           0
  BEST3 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  BEST3 MUTATED                                          1
  BEST3 WILD-TYPE                                        2
D429V8, multiclass
                                                                   clus
vv                                                                  BEST3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  BEST3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D429V9, binary
                 cls
clus                0   1
  BEST3 MUTATED     0  11
  BEST3 WILD-TYPE   5 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEST3 MUTATED      0   11
  BEST3 WILD-TYPE    5  273
     clus
vv    BEST3 MUTATED BEST3 WILD-TYPE
  NO              0               5
  YES            11             273
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BEST3 MUTATED     6   0   0   4
  BEST3 WILD-TYPE 221  10  10  20
D429V10, multiclass
    clus
vv   BEST3 MUTATED BEST3 WILD-TYPE
  R0             6             221
  R1             0              10
  R2             0              10
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D429V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BEST3 MUTATED       3                         0     6
  BEST3 WILD-TYPE    73                         4   162
D429V12, multiclass
                           clus
vv                          BEST3 MUTATED BEST3 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(430) Variable = STX2 MUTATION ANALYSIS
D430V1, survival
                sevent
clus2              0   1
  STX2 MUTATED     4   2
  STX2 WILD-TYPE 177  78
  STX2 MUTATED STX2 WILD-TYPE 
             6            255 
  STX2 MUTATED STX2 WILD-TYPE 
             2             78 
$`STX2 MUTATED`
TCGA-BR-8680 TCGA-BR-A4CS TCGA-CG-4437 TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4H8 
       15.81         1.48         8.05        11.41         0.10         8.88 

$`STX2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU 
       12.56        13.87         7.53         6.08        22.26        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        11.77        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  STX2 MUTATED STX2 WILD-TYPE 
           0.1            0.0 
  STX2 MUTATED STX2 WILD-TYPE 
         15.81         105.07 
  STX2 MUTATED STX2 WILD-TYPE 
         8.465         12.760 
[1] "0.1 - 15.8 (8.5)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "2.1"
D430V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  STX2 MUTATED         0        0        1        1         0         1
  STX2 WILD-TYPE       1        9       26       25        31        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STX2 MUTATED           0          0          0          2        1
  STX2 WILD-TYPE         3         49         36         22       23
D430V3, multiclass
            clus
vv           STX2 MUTATED STX2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              1             25
  STAGE IIA             0             31
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            2             22
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  STX2 MUTATED     1   1   0   4
  STX2 WILD-TYPE  10  71 122  71
D430V4, multiclass
    clus
vv   STX2 MUTATED STX2 WILD-TYPE
  T1            1             10
  T2            1             71
  T3            0            122
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  STX2 MUTATED    1  2  2  1
  STX2 WILD-TYPE 92 79 48 52
D430V5, multiclass
    clus
vv   STX2 MUTATED STX2 WILD-TYPE
  N0            1             92
  N1            2             79
  N2            2             48
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D430V6, binary
                cls
clus               0   1
  STX2 MUTATED     5   1
  STX2 WILD-TYPE 252  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  STX2 MUTATED      5    1
  STX2 WILD-TYPE  252   17
   clus
vv  STX2 MUTATED STX2 WILD-TYPE
  0            5            252
  1            1             17
[1] 2 2
[1] FALSE
D430V7, binary
                cls
clus               0   1
  STX2 MUTATED     1   5
  STX2 WILD-TYPE 109 174
[1] "tbl2"
                cls
clus             [,1] [,2]
  STX2 MUTATED      1    5
  STX2 WILD-TYPE  109  174
        clus
vv       STX2 MUTATED STX2 WILD-TYPE
  FEMALE            1            109
  MALE              5            174
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  STX2 MUTATED                                       1
  STX2 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  STX2 MUTATED                                                        1
  STX2 WILD-TYPE                                                    134
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  STX2 MUTATED                                                                   1
  STX2 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  STX2 MUTATED                                                  3
  STX2 WILD-TYPE                                               35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  STX2 MUTATED                                                          0
  STX2 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  STX2 MUTATED                                                           0
  STX2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  STX2 MUTATED                                          0
  STX2 WILD-TYPE                                        3
D430V8, multiclass
                                                                   clus
vv                                                                  STX2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       1
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  STX2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D430V9, binary
                cls
clus               0   1
  STX2 MUTATED     0   6
  STX2 WILD-TYPE   5 278
[1] "tbl2"
                cls
clus             [,1] [,2]
  STX2 MUTATED      0    6
  STX2 WILD-TYPE    5  278
     clus
vv    STX2 MUTATED STX2 WILD-TYPE
  NO             0              5
  YES            6            278
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  STX2 MUTATED     6   0   0   0
  STX2 WILD-TYPE 221  10  10  24
D430V10, multiclass
    clus
vv   STX2 MUTATED STX2 WILD-TYPE
  R0            6            221
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D430V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STX2 MUTATED       4                         0     1
  STX2 WILD-TYPE    72                         4   167
D430V12, multiclass
                           clus
vv                          STX2 MUTATED STX2 WILD-TYPE
  ASIAN                                4             72
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                1            167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(431) Variable = ARHGEF5 MUTATION ANALYSIS
D431V1, survival
                   sevent
clus2                 0   1
  ARHGEF5 MUTATED     2   1
  ARHGEF5 WILD-TYPE 179  79
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
                3               258 
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
                1                79 
$`ARHGEF5 MUTATED`
TCGA-B7-5816 TCGA-CD-A4MJ TCGA-CG-4465 
       26.70        12.62         9.01 

$`ARHGEF5 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       19.07        12.03         0.00        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
             9.01              0.00 
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
            26.70            105.07 
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
           12.620            12.625 
[1] "9.0 - 26.7 (12.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D431V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARHGEF5 MUTATED         0        0        1        1         0         1
  ARHGEF5 WILD-TYPE       1        9       26       25        31        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGEF5 MUTATED           0          0          0          0        1
  ARHGEF5 WILD-TYPE         3         49         36         24       23
D431V3, multiclass
            clus
vv           ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 1                25
  STAGE IIA                0                31
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               0                36
  STAGE IIIC               0                24
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ARHGEF5 MUTATED     0   2   0   2
  ARHGEF5 WILD-TYPE  11  70 122  73
D431V4, multiclass
    clus
vv   ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  T1               0                11
  T2               2                70
  T3               0               122
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  ARHGEF5 MUTATED    2  2  0  1
  ARHGEF5 WILD-TYPE 91 79 50 52
D431V5, multiclass
    clus
vv   ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  N0               2                91
  N1               2                79
  N2               0                50
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D431V6, binary
                   cls
clus                  0   1
  ARHGEF5 MUTATED     4   1
  ARHGEF5 WILD-TYPE 253  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF5 MUTATED      4    1
  ARHGEF5 WILD-TYPE  253   17
   clus
vv  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  0               4               253
  1               1                17
[1] 2 2
[1] FALSE
D431V7, binary
                   cls
clus                  0   1
  ARHGEF5 MUTATED     2   3
  ARHGEF5 WILD-TYPE 108 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF5 MUTATED      2    3
  ARHGEF5 WILD-TYPE  108  176
        clus
vv       ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  FEMALE               2               108
  MALE                 3               176
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ARHGEF5 MUTATED                                       2
  ARHGEF5 WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ARHGEF5 MUTATED                                                        2
  ARHGEF5 WILD-TYPE                                                    133
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ARHGEF5 MUTATED                                                                   0
  ARHGEF5 WILD-TYPE                                                                40
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ARHGEF5 MUTATED                                                  0
  ARHGEF5 WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ARHGEF5 MUTATED                                                          1
  ARHGEF5 WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ARHGEF5 MUTATED                                                           0
  ARHGEF5 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ARHGEF5 MUTATED                                          0
  ARHGEF5 WILD-TYPE                                        3
D431V8, multiclass
                                                                   clus
vv                                                                  ARHGEF5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  ARHGEF5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D431V9, binary
                   cls
clus                  0   1
  ARHGEF5 MUTATED     1   4
  ARHGEF5 WILD-TYPE   4 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF5 MUTATED      1    4
  ARHGEF5 WILD-TYPE    4  280
     clus
vv    ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  NO                1                 4
  YES               4               280
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ARHGEF5 MUTATED     2   0   1   1
  ARHGEF5 WILD-TYPE 225  10   9  23
D431V10, multiclass
    clus
vv   ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  R0               2               225
  R1               0                10
  R2               1                 9
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D431V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARHGEF5 MUTATED       1                         0     2
  ARHGEF5 WILD-TYPE    75                         4   166
D431V12, multiclass
                           clus
vv                          ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  ASIAN                                   1                75
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   2               166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(432) Variable = FAM92B MUTATION ANALYSIS
D432V1, survival
                  sevent
clus2                0   1
  FAM92B MUTATED     3   0
  FAM92B WILD-TYPE 178  80
  FAM92B MUTATED FAM92B WILD-TYPE 
               3              258 
  FAM92B MUTATED FAM92B WILD-TYPE 
               0               80 
$`FAM92B MUTATED`
TCGA-BR-8078 TCGA-BR-8678 TCGA-HU-A4G9 
       12.26        11.54        24.20 

$`FAM92B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        13.45         6.28         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  FAM92B MUTATED FAM92B WILD-TYPE 
           11.54             0.00 
  FAM92B MUTATED FAM92B WILD-TYPE 
           24.20           105.07 
  FAM92B MUTATED FAM92B WILD-TYPE 
           12.26            12.64 
[1] "11.5 - 24.2 (12.3)" "0.0 - 105.1 (12.6)"
[1] "hr="     "9100000"
D432V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM92B MUTATED         0        1        1        0         0         1
  FAM92B WILD-TYPE       1        8       26       26        31        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM92B MUTATED           0          0          0          0        0
  FAM92B WILD-TYPE         3         49         36         24       24
D432V3, multiclass
            clus
vv           FAM92B MUTATED FAM92B WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               0               31
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM92B MUTATED     1   1   0   1
  FAM92B WILD-TYPE  10  71 122  74
D432V4, multiclass
    clus
vv   FAM92B MUTATED FAM92B WILD-TYPE
  T1              1               10
  T2              1               71
  T3              0              122
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  FAM92B MUTATED    3  0  0  0
  FAM92B WILD-TYPE 90 81 50 53
D432V5, multiclass
    clus
vv   FAM92B MUTATED FAM92B WILD-TYPE
  N0              3               90
  N1              0               81
  N2              0               50
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D432V6, binary
                  cls
clus                 0   1
  FAM92B MUTATED     3   0
  FAM92B WILD-TYPE 254  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM92B MUTATED      3    0
  FAM92B WILD-TYPE  254   18
   clus
vv  FAM92B MUTATED FAM92B WILD-TYPE
  0              3              254
  1              0               18
[1] 2 2
[1] FALSE
D432V7, binary
                  cls
clus                 0   1
  FAM92B MUTATED     2   1
  FAM92B WILD-TYPE 108 178
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM92B MUTATED      2    1
  FAM92B WILD-TYPE  108  178
        clus
vv       FAM92B MUTATED FAM92B WILD-TYPE
  FEMALE              2              108
  MALE                1              178
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FAM92B MUTATED                                       0
  FAM92B WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAM92B MUTATED                                                        2
  FAM92B WILD-TYPE                                                    133
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAM92B MUTATED                                                                   0
  FAM92B WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FAM92B MUTATED                                                  1
  FAM92B WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FAM92B MUTATED                                                          0
  FAM92B WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FAM92B MUTATED                                                           0
  FAM92B WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FAM92B MUTATED                                          0
  FAM92B WILD-TYPE                                        3
D432V8, multiclass
                                                                   clus
vv                                                                  FAM92B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  FAM92B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D432V9, binary
                  cls
clus                 0   1
  FAM92B MUTATED     0   3
  FAM92B WILD-TYPE   5 281
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM92B MUTATED      0    3
  FAM92B WILD-TYPE    5  281
     clus
vv    FAM92B MUTATED FAM92B WILD-TYPE
  NO               0                5
  YES              3              281
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FAM92B MUTATED     3   0   0   0
  FAM92B WILD-TYPE 224  10  10  24
D432V10, multiclass
    clus
vv   FAM92B MUTATED FAM92B WILD-TYPE
  R0              3              224
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D432V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM92B MUTATED       1                         0     2
  FAM92B WILD-TYPE    75                         4   166
D432V12, multiclass
                           clus
vv                          FAM92B MUTATED FAM92B WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  2              166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(433) Variable = BRSK1 MUTATION ANALYSIS
D433V1, survival
                 sevent
clus2               0   1
  BRSK1 MUTATED     8   2
  BRSK1 WILD-TYPE 173  78
  BRSK1 MUTATED BRSK1 WILD-TYPE 
             10             251 
  BRSK1 MUTATED BRSK1 WILD-TYPE 
              2              78 
$`BRSK1 MUTATED`
TCGA-BR-4280 TCGA-BR-8078 TCGA-BR-8382 TCGA-BR-8589 TCGA-BR-8680 TCGA-CD-5813 
        6.61        12.26        15.85        15.81        15.81         0.39 
TCGA-CD-A4MI TCGA-CG-5723 TCGA-D7-6525 TCGA-HU-A4GX 
        0.10       105.07        13.35        10.19 

$`BRSK1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        12.79         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         6.02         0.99        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  BRSK1 MUTATED BRSK1 WILD-TYPE 
            0.1             0.0 
  BRSK1 MUTATED BRSK1 WILD-TYPE 
         105.07           79.07 
  BRSK1 MUTATED BRSK1 WILD-TYPE 
         12.805          12.620 
[1] "0.1 - 105.1 (12.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.9"
D433V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BRSK1 MUTATED         1        0        0        2         0         1
  BRSK1 WILD-TYPE       0        9       27       24        31        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BRSK1 MUTATED           1          2          2          2        1
  BRSK1 WILD-TYPE         2         47         34         22       23
D433V3, multiclass
            clus
vv           BRSK1 MUTATED BRSK1 WILD-TYPE
  STAGE I                1               0
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               2              24
  STAGE IIA              0              31
  STAGE IIB              1              43
  STAGE III              1               2
  STAGE IIIA             2              47
  STAGE IIIB             2              34
  STAGE IIIC             2              22
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BRSK1 MUTATED     1   3   3   5
  BRSK1 WILD-TYPE  10  69 119  70
D433V4, multiclass
    clus
vv   BRSK1 MUTATED BRSK1 WILD-TYPE
  T1             1              10
  T2             3              69
  T3             3             119
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  BRSK1 MUTATED    2  6  3  1
  BRSK1 WILD-TYPE 91 75 47 52
D433V5, multiclass
    clus
vv   BRSK1 MUTATED BRSK1 WILD-TYPE
  N0             2              91
  N1             6              75
  N2             3              47
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D433V6, binary
                 cls
clus                0   1
  BRSK1 MUTATED    10   1
  BRSK1 WILD-TYPE 247  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRSK1 MUTATED     10    1
  BRSK1 WILD-TYPE  247   17
   clus
vv  BRSK1 MUTATED BRSK1 WILD-TYPE
  0            10             247
  1             1              17
[1] 2 2
[1] FALSE
D433V7, binary
                 cls
clus                0   1
  BRSK1 MUTATED     4   8
  BRSK1 WILD-TYPE 106 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRSK1 MUTATED      4    8
  BRSK1 WILD-TYPE  106  171
        clus
vv       BRSK1 MUTATED BRSK1 WILD-TYPE
  FEMALE             4             106
  MALE               8             171
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  BRSK1 MUTATED                                       2
  BRSK1 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BRSK1 MUTATED                                                        8
  BRSK1 WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BRSK1 MUTATED                                                                   0
  BRSK1 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  BRSK1 MUTATED                                                  1
  BRSK1 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  BRSK1 MUTATED                                                          1
  BRSK1 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  BRSK1 MUTATED                                                           0
  BRSK1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  BRSK1 MUTATED                                          0
  BRSK1 WILD-TYPE                                        3
D433V8, multiclass
                                                                   clus
vv                                                                  BRSK1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  BRSK1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D433V9, binary
                 cls
clus                0   1
  BRSK1 MUTATED     0  12
  BRSK1 WILD-TYPE   5 272
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRSK1 MUTATED      0   12
  BRSK1 WILD-TYPE    5  272
     clus
vv    BRSK1 MUTATED BRSK1 WILD-TYPE
  NO              0               5
  YES            12             272
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BRSK1 MUTATED     9   0   0   1
  BRSK1 WILD-TYPE 218  10  10  23
D433V10, multiclass
    clus
vv   BRSK1 MUTATED BRSK1 WILD-TYPE
  R0             9             218
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D433V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BRSK1 MUTATED       5                         1     5
  BRSK1 WILD-TYPE    71                         3   163
D433V12, multiclass
                           clus
vv                          BRSK1 MUTATED BRSK1 WILD-TYPE
  ASIAN                                 5              71
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(434) Variable = KIAA1804 MUTATION ANALYSIS
D434V1, survival
                    sevent
clus2                  0   1
  KIAA1804 MUTATED     3   3
  KIAA1804 WILD-TYPE 178  77
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 6                255 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 3                 77 
$`KIAA1804 MUTATED`
TCGA-BR-6458 TCGA-BR-8680 TCGA-CD-5813 TCGA-CG-4306 TCGA-D7-A4YV TCGA-HU-A4GT 
       19.33        15.81         0.39         1.02         5.92         6.51 

$`KIAA1804 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       16.44        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         0.10         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
              0.39               0.00 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
             19.33             105.07 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
             6.215             12.660 
[1] "0.4 - 19.3 (6.2)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "3"  
D434V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1804 MUTATED         0        0        1        1         1         2
  KIAA1804 WILD-TYPE       1        9       26       25        30        42
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1804 MUTATED           0          0          0          0        2
  KIAA1804 WILD-TYPE         3         49         36         24       22
D434V3, multiclass
            clus
vv           KIAA1804 MUTATED KIAA1804 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  1                 26
  STAGE II                  1                 25
  STAGE IIA                 1                 30
  STAGE IIB                 2                 42
  STAGE III                 0                  3
  STAGE IIIA                0                 49
  STAGE IIIB                0                 36
  STAGE IIIC                0                 24
  STAGE IV                  2                 22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1804 MUTATED     0   1   5   1
  KIAA1804 WILD-TYPE  11  71 117  74
D434V4, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  T1                0                 11
  T2                1                 71
  T3                5                117
  T4                1                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  KIAA1804 MUTATED    3  2  2  0
  KIAA1804 WILD-TYPE 90 79 48 53
D434V5, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  N0                3                 90
  N1                2                 79
  N2                2                 48
  N3                0                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D434V6, binary
                    cls
clus                   0   1
  KIAA1804 MUTATED     6   2
  KIAA1804 WILD-TYPE 251  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED      6    2
  KIAA1804 WILD-TYPE  251   16
   clus
vv  KIAA1804 MUTATED KIAA1804 WILD-TYPE
  0                6                251
  1                2                 16
[1] 2 2
[1] FALSE
D434V7, binary
                    cls
clus                   0   1
  KIAA1804 MUTATED     3   5
  KIAA1804 WILD-TYPE 107 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED      3    5
  KIAA1804 WILD-TYPE  107  174
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  FEMALE                3                107
  MALE                  5                174
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KIAA1804 MUTATED                                       0
  KIAA1804 WILD-TYPE                                    50
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA1804 MUTATED                                                        3
  KIAA1804 WILD-TYPE                                                    132
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA1804 MUTATED                                                                   1
  KIAA1804 WILD-TYPE                                                                39
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KIAA1804 MUTATED                                                  3
  KIAA1804 WILD-TYPE                                               35
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KIAA1804 MUTATED                                                          1
  KIAA1804 WILD-TYPE                                                       15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KIAA1804 MUTATED                                                           0
  KIAA1804 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KIAA1804 MUTATED                                          0
  KIAA1804 WILD-TYPE                                        3
D434V8, multiclass
                                                                   clus
vv                                                                  KIAA1804 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  KIAA1804 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D434V9, binary
                    cls
clus                   0   1
  KIAA1804 MUTATED     0   8
  KIAA1804 WILD-TYPE   5 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED      0    8
  KIAA1804 WILD-TYPE    5  276
     clus
vv    KIAA1804 MUTATED KIAA1804 WILD-TYPE
  NO                 0                  5
  YES                8                276
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA1804 MUTATED     5   0   1   1
  KIAA1804 WILD-TYPE 222  10   9  23
D434V10, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  R0                5                222
  R1                0                 10
  R2                1                  9
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D434V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA1804 MUTATED       3                         0     3
  KIAA1804 WILD-TYPE    73                         4   165
D434V12, multiclass
                           clus
vv                          KIAA1804 MUTATED KIAA1804 WILD-TYPE
  ASIAN                                    3                 73
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    3                165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(435) Variable = ZNF711 MUTATION ANALYSIS
D435V1, survival
                  sevent
clus2                0   1
  ZNF711 MUTATED     7   3
  ZNF711 WILD-TYPE 174  77
  ZNF711 MUTATED ZNF711 WILD-TYPE 
              10              251 
  ZNF711 MUTATED ZNF711 WILD-TYPE 
               3               77 
$`ZNF711 MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8589 TCGA-BR-A4CS 
        6.97         6.61        23.93        12.26        15.81         1.48 
TCGA-BR-A4QL TCGA-CG-5728 TCGA-D7-A4YT TCGA-HU-A4GU 
       11.57        65.10        14.27         6.25 

$`ZNF711 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
       22.26        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  ZNF711 MUTATED ZNF711 WILD-TYPE 
            1.48             0.00 
  ZNF711 MUTATED ZNF711 WILD-TYPE 
           65.10           105.07 
  ZNF711 MUTATED ZNF711 WILD-TYPE 
          11.915           12.660 
[1] "1.5 - 65.1 (11.9)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1"  
D435V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF711 MUTATED         0        0        2        1         0         2
  ZNF711 WILD-TYPE       1        9       25       25        31        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF711 MUTATED           1          2          2          1        0
  ZNF711 WILD-TYPE         2         47         34         23       24
D435V3, multiclass
            clus
vv           ZNF711 MUTATED ZNF711 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                2               25
  STAGE II                1               25
  STAGE IIA               0               31
  STAGE IIB               2               42
  STAGE III               1                2
  STAGE IIIA              2               47
  STAGE IIIB              2               34
  STAGE IIIC              1               23
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF711 MUTATED     0   5   3   3
  ZNF711 WILD-TYPE  11  67 119  72
D435V4, multiclass
    clus
vv   ZNF711 MUTATED ZNF711 WILD-TYPE
  T1              0               11
  T2              5               67
  T3              3              119
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZNF711 MUTATED    3  6  0  3
  ZNF711 WILD-TYPE 90 75 50 50
D435V5, multiclass
    clus
vv   ZNF711 MUTATED ZNF711 WILD-TYPE
  N0              3               90
  N1              6               75
  N2              0               50
  N3              3               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D435V6, binary
                  cls
clus                 0   1
  ZNF711 MUTATED    12   0
  ZNF711 WILD-TYPE 245  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF711 MUTATED     12    0
  ZNF711 WILD-TYPE  245   18
   clus
vv  ZNF711 MUTATED ZNF711 WILD-TYPE
  0             12              245
  1              0               18
[1] 2 2
[1] FALSE
D435V7, binary
                  cls
clus                 0   1
  ZNF711 MUTATED     7   6
  ZNF711 WILD-TYPE 103 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF711 MUTATED      7    6
  ZNF711 WILD-TYPE  103  173
        clus
vv       ZNF711 MUTATED ZNF711 WILD-TYPE
  FEMALE              7              103
  MALE                6              173
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZNF711 MUTATED                                       1
  ZNF711 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF711 MUTATED                                                        9
  ZNF711 WILD-TYPE                                                    126
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF711 MUTATED                                                                   1
  ZNF711 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZNF711 MUTATED                                                  1
  ZNF711 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZNF711 MUTATED                                                          1
  ZNF711 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZNF711 MUTATED                                                           0
  ZNF711 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZNF711 MUTATED                                          0
  ZNF711 WILD-TYPE                                        3
D435V8, multiclass
                                                                   clus
vv                                                                  ZNF711 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ZNF711 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D435V9, binary
                  cls
clus                 0   1
  ZNF711 MUTATED     1  12
  ZNF711 WILD-TYPE   4 272
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF711 MUTATED      1   12
  ZNF711 WILD-TYPE    4  272
     clus
vv    ZNF711 MUTATED ZNF711 WILD-TYPE
  NO               1                4
  YES             12              272
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF711 MUTATED     9   0   0   4
  ZNF711 WILD-TYPE 218  10  10  20
D435V10, multiclass
    clus
vv   ZNF711 MUTATED ZNF711 WILD-TYPE
  R0              9              218
  R1              0               10
  R2              0               10
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D435V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF711 MUTATED       1                         0    10
  ZNF711 WILD-TYPE    75                         4   158
D435V12, multiclass
                           clus
vv                          ZNF711 MUTATED ZNF711 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                 10              158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(436) Variable = HCRTR2 MUTATION ANALYSIS
D436V1, survival
                  sevent
clus2                0   1
  HCRTR2 MUTATED     6   2
  HCRTR2 WILD-TYPE 175  78
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
               8              253 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
               2               78 
$`HCRTR2 MUTATED`
TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8366 TCGA-CD-A4MG TCGA-CG-4466 TCGA-CG-5721 
       12.26         0.26         0.95         6.58        18.97         6.02 
TCGA-FP-A4BE TCGA-HU-A4GX 
       11.08        10.19 

$`HCRTR2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 
        7.40         6.18        19.50        22.19        17.52        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51         6.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
            0.26             0.00 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
           18.97           105.07 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
           8.385           12.790 
[1] "0.3 - 19.0 (8.4)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.5"
D436V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HCRTR2 MUTATED         0        0        2        0         3         1
  HCRTR2 WILD-TYPE       1        9       25       26        28        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HCRTR2 MUTATED           0          0          0          1        1
  HCRTR2 WILD-TYPE         3         49         36         23       23
D436V3, multiclass
            clus
vv           HCRTR2 MUTATED HCRTR2 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                2               25
  STAGE II                0               26
  STAGE IIA               3               28
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HCRTR2 MUTATED     0   2   3   3
  HCRTR2 WILD-TYPE  11  70 119  72
D436V4, multiclass
    clus
vv   HCRTR2 MUTATED HCRTR2 WILD-TYPE
  T1              0               11
  T2              2               70
  T3              3              119
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  HCRTR2 MUTATED    6  2  1  0
  HCRTR2 WILD-TYPE 87 79 49 53
D436V5, multiclass
    clus
vv   HCRTR2 MUTATED HCRTR2 WILD-TYPE
  N0              6               87
  N1              2               79
  N2              1               49
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D436V6, binary
                  cls
clus                 0   1
  HCRTR2 MUTATED     9   0
  HCRTR2 WILD-TYPE 248  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR2 MUTATED      9    0
  HCRTR2 WILD-TYPE  248   18
   clus
vv  HCRTR2 MUTATED HCRTR2 WILD-TYPE
  0              9              248
  1              0               18
[1] 2 2
[1] FALSE
D436V7, binary
                  cls
clus                 0   1
  HCRTR2 MUTATED     5   4
  HCRTR2 WILD-TYPE 105 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR2 MUTATED      5    4
  HCRTR2 WILD-TYPE  105  175
        clus
vv       HCRTR2 MUTATED HCRTR2 WILD-TYPE
  FEMALE              5              105
  MALE                4              175
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  HCRTR2 MUTATED                                       2
  HCRTR2 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HCRTR2 MUTATED                                                        5
  HCRTR2 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HCRTR2 MUTATED                                                                   2
  HCRTR2 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  HCRTR2 MUTATED                                                  0
  HCRTR2 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  HCRTR2 MUTATED                                                          0
  HCRTR2 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  HCRTR2 MUTATED                                                           0
  HCRTR2 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  HCRTR2 MUTATED                                          0
  HCRTR2 WILD-TYPE                                        3
D436V8, multiclass
                                                                   clus
vv                                                                  HCRTR2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  HCRTR2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D436V9, binary
                  cls
clus                 0   1
  HCRTR2 MUTATED     0   9
  HCRTR2 WILD-TYPE   5 275
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR2 MUTATED      0    9
  HCRTR2 WILD-TYPE    5  275
     clus
vv    HCRTR2 MUTATED HCRTR2 WILD-TYPE
  NO               0                5
  YES              9              275
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  HCRTR2 MUTATED     7   0   0   1
  HCRTR2 WILD-TYPE 220  10  10  23
D436V10, multiclass
    clus
vv   HCRTR2 MUTATED HCRTR2 WILD-TYPE
  R0              7              220
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D436V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HCRTR2 MUTATED       2                         1     4
  HCRTR2 WILD-TYPE    74                         3   164
D436V12, multiclass
                           clus
vv                          HCRTR2 MUTATED HCRTR2 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(437) Variable = OR51A7 MUTATION ANALYSIS
D437V1, survival
                  sevent
clus2                0   1
  OR51A7 MUTATED     2   4
  OR51A7 WILD-TYPE 179  76
  OR51A7 MUTATED OR51A7 WILD-TYPE 
               6              255 
  OR51A7 MUTATED OR51A7 WILD-TYPE 
               4               76 
$`OR51A7 MUTATED`
TCGA-BR-6453 TCGA-BR-6458 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-A452 TCGA-CD-5801 
       15.95        19.33        12.79         9.34         7.53        13.18 

$`OR51A7 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 
        9.21        20.22         1.12        15.81        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
       15.68         8.22        10.68        12.56        13.87         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        2.83         3.25        13.15         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  OR51A7 MUTATED OR51A7 WILD-TYPE 
            7.53             0.00 
  OR51A7 MUTATED OR51A7 WILD-TYPE 
           19.33           105.07 
  OR51A7 MUTATED OR51A7 WILD-TYPE 
          12.985           12.590 
[1] "7.5 - 19.3 (13.0)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.5"
D437V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OR51A7 MUTATED         0        0        0        0         1         2
  OR51A7 WILD-TYPE       1        9       27       26        30        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR51A7 MUTATED           0          2          0          1        0
  OR51A7 WILD-TYPE         3         47         36         23       24
D437V3, multiclass
            clus
vv           OR51A7 MUTATED OR51A7 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR51A7 MUTATED     0   1   2   3
  OR51A7 WILD-TYPE  11  71 120  72
D437V4, multiclass
    clus
vv   OR51A7 MUTATED OR51A7 WILD-TYPE
  T1              0               11
  T2              1               71
  T3              2              120
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  OR51A7 MUTATED    1  4  1  0
  OR51A7 WILD-TYPE 92 77 49 53
D437V5, multiclass
    clus
vv   OR51A7 MUTATED OR51A7 WILD-TYPE
  N0              1               92
  N1              4               77
  N2              1               49
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D437V6, binary
                  cls
clus                 0   1
  OR51A7 MUTATED     6   0
  OR51A7 WILD-TYPE 251  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51A7 MUTATED      6    0
  OR51A7 WILD-TYPE  251   18
   clus
vv  OR51A7 MUTATED OR51A7 WILD-TYPE
  0              6              251
  1              0               18
[1] 2 2
[1] FALSE
D437V7, binary
                  cls
clus                 0   1
  OR51A7 MUTATED     2   4
  OR51A7 WILD-TYPE 108 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51A7 MUTATED      2    4
  OR51A7 WILD-TYPE  108  175
        clus
vv       OR51A7 MUTATED OR51A7 WILD-TYPE
  FEMALE              2              108
  MALE                4              175
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  OR51A7 MUTATED                                       0
  OR51A7 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OR51A7 MUTATED                                                        5
  OR51A7 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OR51A7 MUTATED                                                                   0
  OR51A7 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  OR51A7 MUTATED                                                  1
  OR51A7 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  OR51A7 MUTATED                                                          0
  OR51A7 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  OR51A7 MUTATED                                                           0
  OR51A7 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  OR51A7 MUTATED                                          0
  OR51A7 WILD-TYPE                                        3
D437V8, multiclass
                                                                   clus
vv                                                                  OR51A7 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  OR51A7 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D437V9, binary
                  cls
clus                 0   1
  OR51A7 MUTATED     0   6
  OR51A7 WILD-TYPE   5 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51A7 MUTATED      0    6
  OR51A7 WILD-TYPE    5  278
     clus
vv    OR51A7 MUTATED OR51A7 WILD-TYPE
  NO               0                5
  YES              6              278
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR51A7 MUTATED     6   0   0   0
  OR51A7 WILD-TYPE 221  10  10  24
D437V10, multiclass
    clus
vv   OR51A7 MUTATED OR51A7 WILD-TYPE
  R0              6              221
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D437V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR51A7 MUTATED       2                         0     4
  OR51A7 WILD-TYPE    74                         4   164
D437V12, multiclass
                           clus
vv                          OR51A7 MUTATED OR51A7 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(438) Variable = C2ORF42 MUTATION ANALYSIS
D438V1, survival
                   sevent
clus2                 0   1
  C2ORF42 MUTATED     9   2
  C2ORF42 WILD-TYPE 172  78
  C2ORF42 MUTATED C2ORF42 WILD-TYPE 
               11               250 
  C2ORF42 MUTATED C2ORF42 WILD-TYPE 
                2                78 
$`C2ORF42 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7901 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8372 
       30.90        34.68         3.45        12.26        19.50        19.17 
TCGA-CD-A4MI TCGA-CG-4477 TCGA-FP-A4BE TCGA-HU-A4G9 TCGA-IN-7806 
        0.10        30.97        11.08        24.20        21.21 

$`C2ORF42 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       18.35         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
       16.31         2.20        15.58         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        22.98         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 
       59.54         5.03        13.58         0.56         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        11.84         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  C2ORF42 MUTATED C2ORF42 WILD-TYPE 
              0.1               0.0 
  C2ORF42 MUTATED C2ORF42 WILD-TYPE 
            34.68            105.07 
  C2ORF42 MUTATED C2ORF42 WILD-TYPE 
           19.500            12.575 
[1] "0.1 - 34.7 (19.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.6"
D438V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C2ORF42 MUTATED         0        1        1        0         2         3
  C2ORF42 WILD-TYPE       1        8       26       26        29        41
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C2ORF42 MUTATED           0          1          1          2        0
  C2ORF42 WILD-TYPE         3         48         35         22       24
D438V3, multiclass
            clus
vv           C2ORF42 MUTATED C2ORF42 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 1                 8
  STAGE IB                 1                26
  STAGE II                 0                26
  STAGE IIA                2                29
  STAGE IIB                3                41
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               1                35
  STAGE IIIC               2                22
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C2ORF42 MUTATED     2   2   6   4
  C2ORF42 WILD-TYPE   9  70 116  71
D438V4, multiclass
    clus
vv   C2ORF42 MUTATED C2ORF42 WILD-TYPE
  T1               2                 9
  T2               2                70
  T3               6               116
  T4               4                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  C2ORF42 MUTATED    6  3  1  1
  C2ORF42 WILD-TYPE 87 78 49 52
D438V5, multiclass
    clus
vv   C2ORF42 MUTATED C2ORF42 WILD-TYPE
  N0               6                87
  N1               3                78
  N2               1                49
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D438V6, binary
                   cls
clus                  0   1
  C2ORF42 MUTATED    13   0
  C2ORF42 WILD-TYPE 244  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF42 MUTATED     13    0
  C2ORF42 WILD-TYPE  244   18
   clus
vv  C2ORF42 MUTATED C2ORF42 WILD-TYPE
  0              13               244
  1               0                18
[1] 2 2
[1] FALSE
D438V7, binary
                   cls
clus                  0   1
  C2ORF42 MUTATED     9   5
  C2ORF42 WILD-TYPE 101 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF42 MUTATED      9    5
  C2ORF42 WILD-TYPE  101  174
        clus
vv       C2ORF42 MUTATED C2ORF42 WILD-TYPE
  FEMALE               9               101
  MALE                 5               174
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C2ORF42 MUTATED                                       1
  C2ORF42 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C2ORF42 MUTATED                                                       11
  C2ORF42 WILD-TYPE                                                    124
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C2ORF42 MUTATED                                                                   1
  C2ORF42 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C2ORF42 MUTATED                                                  1
  C2ORF42 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C2ORF42 MUTATED                                                          0
  C2ORF42 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C2ORF42 MUTATED                                                           0
  C2ORF42 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C2ORF42 MUTATED                                          0
  C2ORF42 WILD-TYPE                                        3
D438V8, multiclass
                                                                   clus
vv                                                                  C2ORF42 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  C2ORF42 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D438V9, binary
                   cls
clus                  0   1
  C2ORF42 MUTATED     0  14
  C2ORF42 WILD-TYPE   5 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF42 MUTATED      0   14
  C2ORF42 WILD-TYPE    5  270
     clus
vv    C2ORF42 MUTATED C2ORF42 WILD-TYPE
  NO                0                 5
  YES              14               270
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C2ORF42 MUTATED     9   0   0   4
  C2ORF42 WILD-TYPE 218  10  10  20
D438V10, multiclass
    clus
vv   C2ORF42 MUTATED C2ORF42 WILD-TYPE
  R0               9               218
  R1               0                10
  R2               0                10
  RX               4                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D438V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C2ORF42 MUTATED       2                         1    10
  C2ORF42 WILD-TYPE    74                         3   158
D438V12, multiclass
                           clus
vv                          C2ORF42 MUTATED C2ORF42 WILD-TYPE
  ASIAN                                   2                74
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                  10               158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(439) Variable = KCTD21 MUTATION ANALYSIS
D439V1, survival
                  sevent
clus2                0   1
  KCTD21 MUTATED     4   2
  KCTD21 WILD-TYPE 177  78
  KCTD21 MUTATED KCTD21 WILD-TYPE 
               6              255 
  KCTD21 MUTATED KCTD21 WILD-TYPE 
               2               78 
$`KCTD21 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-CD-A4MG TCGA-CG-5721 TCGA-D7-8570 TCGA-HU-A4GX 
       30.90        34.68         6.58         6.02        24.72        10.19 

$`KCTD21 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       18.35         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.55        11.31        12.33        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  KCTD21 MUTATED KCTD21 WILD-TYPE 
            6.02             0.00 
  KCTD21 MUTATED KCTD21 WILD-TYPE 
           34.68           105.07 
  KCTD21 MUTATED KCTD21 WILD-TYPE 
          17.455           12.620 
[1] "6.0 - 34.7 (17.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D439V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCTD21 MUTATED         0        0        0        0         2         0
  KCTD21 WILD-TYPE       1        9       27       26        29        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCTD21 MUTATED           0          0          1          1        2
  KCTD21 WILD-TYPE         3         49         35         23       22
D439V3, multiclass
            clus
vv           KCTD21 MUTATED KCTD21 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               2               29
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              1               35
  STAGE IIIC              1               23
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KCTD21 MUTATED     0   1   3   3
  KCTD21 WILD-TYPE  11  71 119  72
D439V4, multiclass
    clus
vv   KCTD21 MUTATED KCTD21 WILD-TYPE
  T1              0               11
  T2              1               71
  T3              3              119
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  KCTD21 MUTATED    2  1  2  1
  KCTD21 WILD-TYPE 91 80 48 52
D439V5, multiclass
    clus
vv   KCTD21 MUTATED KCTD21 WILD-TYPE
  N0              2               91
  N1              1               80
  N2              2               48
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D439V6, binary
                  cls
clus                 0   1
  KCTD21 MUTATED     7   0
  KCTD21 WILD-TYPE 250  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCTD21 MUTATED      7    0
  KCTD21 WILD-TYPE  250   18
   clus
vv  KCTD21 MUTATED KCTD21 WILD-TYPE
  0              7              250
  1              0               18
[1] 2 2
[1] FALSE
D439V7, binary
                  cls
clus                 0   1
  KCTD21 MUTATED     4   3
  KCTD21 WILD-TYPE 106 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCTD21 MUTATED      4    3
  KCTD21 WILD-TYPE  106  176
        clus
vv       KCTD21 MUTATED KCTD21 WILD-TYPE
  FEMALE              4              106
  MALE                3              176
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KCTD21 MUTATED                                       2
  KCTD21 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KCTD21 MUTATED                                                        3
  KCTD21 WILD-TYPE                                                    132
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KCTD21 MUTATED                                                                   1
  KCTD21 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KCTD21 MUTATED                                                  1
  KCTD21 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KCTD21 MUTATED                                                          0
  KCTD21 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KCTD21 MUTATED                                                           0
  KCTD21 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KCTD21 MUTATED                                          0
  KCTD21 WILD-TYPE                                        3
D439V8, multiclass
                                                                   clus
vv                                                                  KCTD21 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  KCTD21 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D439V9, binary
                  cls
clus                 0   1
  KCTD21 MUTATED     0   7
  KCTD21 WILD-TYPE   5 277
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCTD21 MUTATED      0    7
  KCTD21 WILD-TYPE    5  277
     clus
vv    KCTD21 MUTATED KCTD21 WILD-TYPE
  NO               0                5
  YES              7              277
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  KCTD21 MUTATED     4   0   0   2
  KCTD21 WILD-TYPE 223  10  10  22
D439V10, multiclass
    clus
vv   KCTD21 MUTATED KCTD21 WILD-TYPE
  R0              4              223
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D439V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KCTD21 MUTATED       2                         0     4
  KCTD21 WILD-TYPE    74                         4   164
D439V12, multiclass
                           clus
vv                          KCTD21 MUTATED KCTD21 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(440) Variable = SEZ6 MUTATION ANALYSIS
D440V1, survival
                sevent
clus2              0   1
  SEZ6 MUTATED     8   0
  SEZ6 WILD-TYPE 173  80
  SEZ6 MUTATED SEZ6 WILD-TYPE 
             8            253 
  SEZ6 MUTATED SEZ6 WILD-TYPE 
             0             80 
$`SEZ6 MUTATED`
TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-8382 TCGA-BR-A4QL TCGA-CD-A4MI TCGA-D7-A4YU 
       20.55         6.18        15.85        11.57         0.10        16.44 
TCGA-HU-A4G8 TCGA-HU-A4GN 
       11.84        29.98 

$`SEZ6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       18.21        14.66        21.14        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  SEZ6 MUTATED SEZ6 WILD-TYPE 
           0.1            0.0 
  SEZ6 MUTATED SEZ6 WILD-TYPE 
         29.98         105.07 
  SEZ6 MUTATED SEZ6 WILD-TYPE 
        13.845         12.620 
[1] "0.1 - 30.0 (13.8)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "2.6e+07"
D440V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SEZ6 MUTATED         1        0        1        0         2         2
  SEZ6 WILD-TYPE       0        9       26       26        29        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SEZ6 MUTATED           0          0          3          1        0
  SEZ6 WILD-TYPE         3         49         33         23       24
D440V3, multiclass
            clus
vv           SEZ6 MUTATED SEZ6 WILD-TYPE
  STAGE I               1              0
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             2             29
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            3             33
  STAGE IIIC            1             23
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SEZ6 MUTATED     1   2   5   2
  SEZ6 WILD-TYPE  10  70 117  73
D440V4, multiclass
    clus
vv   SEZ6 MUTATED SEZ6 WILD-TYPE
  T1            1             10
  T2            2             70
  T3            5            117
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  SEZ6 MUTATED    3  4  0  3
  SEZ6 WILD-TYPE 90 77 50 50
D440V5, multiclass
    clus
vv   SEZ6 MUTATED SEZ6 WILD-TYPE
  N0            3             90
  N1            4             77
  N2            0             50
  N3            3             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D440V6, binary
                cls
clus               0   1
  SEZ6 MUTATED     9   0
  SEZ6 WILD-TYPE 248  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  SEZ6 MUTATED      9    0
  SEZ6 WILD-TYPE  248   18
   clus
vv  SEZ6 MUTATED SEZ6 WILD-TYPE
  0            9            248
  1            0             18
[1] 2 2
[1] FALSE
D440V7, binary
                cls
clus               0   1
  SEZ6 MUTATED     4   6
  SEZ6 WILD-TYPE 106 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  SEZ6 MUTATED      4    6
  SEZ6 WILD-TYPE  106  173
        clus
vv       SEZ6 MUTATED SEZ6 WILD-TYPE
  FEMALE            4            106
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SEZ6 MUTATED                                       1
  SEZ6 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SEZ6 MUTATED                                                        5
  SEZ6 WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SEZ6 MUTATED                                                                   2
  SEZ6 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SEZ6 MUTATED                                                  2
  SEZ6 WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SEZ6 MUTATED                                                          0
  SEZ6 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SEZ6 MUTATED                                                           0
  SEZ6 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SEZ6 MUTATED                                          0
  SEZ6 WILD-TYPE                                        3
D440V8, multiclass
                                                                   clus
vv                                                                  SEZ6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  SEZ6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D440V9, binary
                cls
clus               0   1
  SEZ6 MUTATED     0  10
  SEZ6 WILD-TYPE   5 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  SEZ6 MUTATED      0   10
  SEZ6 WILD-TYPE    5  274
     clus
vv    SEZ6 MUTATED SEZ6 WILD-TYPE
  NO             0              5
  YES           10            274
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SEZ6 MUTATED     8   0   0   0
  SEZ6 WILD-TYPE 219  10  10  24
D440V10, multiclass
    clus
vv   SEZ6 MUTATED SEZ6 WILD-TYPE
  R0            8            219
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D440V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SEZ6 MUTATED       3                         1     5
  SEZ6 WILD-TYPE    73                         3   163
D440V12, multiclass
                           clus
vv                          SEZ6 MUTATED SEZ6 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                                5            163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(441) Variable = C7ORF58 MUTATION ANALYSIS
D441V1, survival
                   sevent
clus2                 0   1
  C7ORF58 MUTATED    12   3
  C7ORF58 WILD-TYPE 169  77
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               15               246 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
                3                77 
$`C7ORF58 MUTATED`
TCGA-BR-4184 TCGA-BR-7197 TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8487 TCGA-BR-8589 
        6.97         9.21        19.50        14.04         1.12        15.81 
TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-4466 TCGA-CG-5726 TCGA-CG-5728 
       13.45        15.81         6.58        18.97        28.96        65.10 
TCGA-D7-A4YY TCGA-FP-A4BE TCGA-HU-A4GX 
       13.78        11.08        10.19 

$`C7ORF58 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       21.11        30.90        31.20        32.94        12.82        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       12.79         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
       12.03         0.00         9.01         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
      105.07        12.03        79.07         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       15.16        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
             1.12              0.00 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
            65.10            105.07 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
           13.780            12.575 
[1] "1.1 - 65.1 (13.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.8"
D441V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C7ORF58 MUTATED         0        1        2        1         3         0
  C7ORF58 WILD-TYPE       1        8       25       25        28        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C7ORF58 MUTATED           0          1          3          3        1
  C7ORF58 WILD-TYPE         3         48         33         21       23
D441V3, multiclass
            clus
vv           C7ORF58 MUTATED C7ORF58 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 1                 8
  STAGE IB                 2                25
  STAGE II                 1                25
  STAGE IIA                3                28
  STAGE IIB                0                44
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               3                33
  STAGE IIIC               3                21
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C7ORF58 MUTATED     1   2   7   5
  C7ORF58 WILD-TYPE  10  70 115  70
D441V4, multiclass
    clus
vv   C7ORF58 MUTATED C7ORF58 WILD-TYPE
  T1               1                10
  T2               2                70
  T3               7               115
  T4               5                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  C7ORF58 MUTATED    7  2  3  3
  C7ORF58 WILD-TYPE 86 79 47 50
D441V5, multiclass
    clus
vv   C7ORF58 MUTATED C7ORF58 WILD-TYPE
  N0               7                86
  N1               2                79
  N2               3                47
  N3               3                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D441V6, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED    13   1
  C7ORF58 WILD-TYPE 244  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED     13    1
  C7ORF58 WILD-TYPE  244   17
   clus
vv  C7ORF58 MUTATED C7ORF58 WILD-TYPE
  0              13               244
  1               1                17
[1] 2 2
[1] FALSE
D441V7, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED     6   9
  C7ORF58 WILD-TYPE 104 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED      6    9
  C7ORF58 WILD-TYPE  104  170
        clus
vv       C7ORF58 MUTATED C7ORF58 WILD-TYPE
  FEMALE               6               104
  MALE                 9               170
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C7ORF58 MUTATED                                       2
  C7ORF58 WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C7ORF58 MUTATED                                                        9
  C7ORF58 WILD-TYPE                                                    126
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C7ORF58 MUTATED                                                                   3
  C7ORF58 WILD-TYPE                                                                37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C7ORF58 MUTATED                                                  1
  C7ORF58 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C7ORF58 MUTATED                                                          0
  C7ORF58 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C7ORF58 MUTATED                                                           0
  C7ORF58 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C7ORF58 MUTATED                                          0
  C7ORF58 WILD-TYPE                                        3
D441V8, multiclass
                                                                   clus
vv                                                                  C7ORF58 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  C7ORF58 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D441V9, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED     0  15
  C7ORF58 WILD-TYPE   5 269
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED      0   15
  C7ORF58 WILD-TYPE    5  269
     clus
vv    C7ORF58 MUTATED C7ORF58 WILD-TYPE
  NO                0                 5
  YES              15               269
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C7ORF58 MUTATED    13   0   0   1
  C7ORF58 WILD-TYPE 214  10  10  23
D441V10, multiclass
    clus
vv   C7ORF58 MUTATED C7ORF58 WILD-TYPE
  R0              13               214
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D441V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C7ORF58 MUTATED       3                         1     8
  C7ORF58 WILD-TYPE    73                         3   160
D441V12, multiclass
                           clus
vv                          C7ORF58 MUTATED C7ORF58 WILD-TYPE
  ASIAN                                   3                73
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   8               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(442) Variable = STK38 MUTATION ANALYSIS
D442V1, survival
                 sevent
clus2               0   1
  STK38 MUTATED     5   0
  STK38 WILD-TYPE 176  80
  STK38 MUTATED STK38 WILD-TYPE 
              5             256 
  STK38 MUTATED STK38 WILD-TYPE 
              0              80 
$`STK38 MUTATED`
TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8361 TCGA-CG-5721 TCGA-HU-A4GT 
       34.68        24.76        19.50         6.02         6.51 

$`STK38 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  STK38 MUTATED STK38 WILD-TYPE 
           6.02            0.00 
  STK38 MUTATED STK38 WILD-TYPE 
          34.68          105.07 
  STK38 MUTATED STK38 WILD-TYPE 
         19.500          12.605 
[1] "6.0 - 34.7 (19.5)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "2.5e+07"
D442V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  STK38 MUTATED         0        1        1        0         2         0
  STK38 WILD-TYPE       1        8       26       26        29        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STK38 MUTATED           0          0          0          1        1
  STK38 WILD-TYPE         3         49         36         23       23
D442V3, multiclass
            clus
vv           STK38 MUTATED STK38 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STK38 MUTATED     1   1   2   2
  STK38 WILD-TYPE  10  71 120  73
D442V4, multiclass
    clus
vv   STK38 MUTATED STK38 WILD-TYPE
  T1             1              10
  T2             1              71
  T3             2             120
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  STK38 MUTATED    4  1  1  0
  STK38 WILD-TYPE 89 80 49 53
D442V5, multiclass
    clus
vv   STK38 MUTATED STK38 WILD-TYPE
  N0             4              89
  N1             1              80
  N2             1              49
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D442V6, binary
                 cls
clus                0   1
  STK38 MUTATED     6   0
  STK38 WILD-TYPE 251  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK38 MUTATED      6    0
  STK38 WILD-TYPE  251   18
   clus
vv  STK38 MUTATED STK38 WILD-TYPE
  0             6             251
  1             0              18
[1] 2 2
[1] FALSE
D442V7, binary
                 cls
clus                0   1
  STK38 MUTATED     3   3
  STK38 WILD-TYPE 107 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK38 MUTATED      3    3
  STK38 WILD-TYPE  107  176
        clus
vv       STK38 MUTATED STK38 WILD-TYPE
  FEMALE             3             107
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  STK38 MUTATED                                       0
  STK38 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  STK38 MUTATED                                                        2
  STK38 WILD-TYPE                                                    133
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  STK38 MUTATED                                                                   2
  STK38 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  STK38 MUTATED                                                  1
  STK38 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  STK38 MUTATED                                                          0
  STK38 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  STK38 MUTATED                                                           1
  STK38 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  STK38 MUTATED                                          0
  STK38 WILD-TYPE                                        3
D442V8, multiclass
                                                                   clus
vv                                                                  STK38 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  STK38 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D442V9, binary
                 cls
clus                0   1
  STK38 MUTATED     0   6
  STK38 WILD-TYPE   5 278
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK38 MUTATED      0    6
  STK38 WILD-TYPE    5  278
     clus
vv    STK38 MUTATED STK38 WILD-TYPE
  NO              0               5
  YES             6             278
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  STK38 MUTATED     6   0   0   0
  STK38 WILD-TYPE 221  10  10  24
D442V10, multiclass
    clus
vv   STK38 MUTATED STK38 WILD-TYPE
  R0             6             221
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D442V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STK38 MUTATED       1                         0     3
  STK38 WILD-TYPE    75                         4   165
D442V12, multiclass
                           clus
vv                          STK38 MUTATED STK38 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(443) Variable = PTPN4 MUTATION ANALYSIS
D443V1, survival
                 sevent
clus2               0   1
  PTPN4 MUTATED     5   1
  PTPN4 WILD-TYPE 176  79
  PTPN4 MUTATED PTPN4 WILD-TYPE 
              6             255 
  PTPN4 MUTATED PTPN4 WILD-TYPE 
              1              79 
$`PTPN4 MUTATED`
TCGA-BR-4184 TCGA-BR-7851 TCGA-BR-8078 TCGA-BR-8680 TCGA-BR-A4QL TCGA-FP-A4BE 
        6.97        12.43        12.26        15.81        11.57        11.08 

$`PTPN4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        13.64         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  PTPN4 MUTATED PTPN4 WILD-TYPE 
           6.97            0.00 
  PTPN4 MUTATED PTPN4 WILD-TYPE 
          15.81          105.07 
  PTPN4 MUTATED PTPN4 WILD-TYPE 
         11.915          12.760 
[1] "7.0 - 15.8 (11.9)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.4"
D443V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTPN4 MUTATED         0        0        0        0         1         2
  PTPN4 WILD-TYPE       1        9       27       26        30        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPN4 MUTATED           0          2          1          0        2
  PTPN4 WILD-TYPE         3         47         35         24       22
D443V3, multiclass
            clus
vv           PTPN4 MUTATED PTPN4 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPN4 MUTATED     0   0   3   5
  PTPN4 WILD-TYPE  11  72 119  70
D443V4, multiclass
    clus
vv   PTPN4 MUTATED PTPN4 WILD-TYPE
  T1             0              11
  T2             0              72
  T3             3             119
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PTPN4 MUTATED    4  1  2  1
  PTPN4 WILD-TYPE 89 80 48 52
D443V5, multiclass
    clus
vv   PTPN4 MUTATED PTPN4 WILD-TYPE
  N0             4              89
  N1             1              80
  N2             2              48
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D443V6, binary
                 cls
clus                0   1
  PTPN4 MUTATED     7   1
  PTPN4 WILD-TYPE 250  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN4 MUTATED      7    1
  PTPN4 WILD-TYPE  250   17
   clus
vv  PTPN4 MUTATED PTPN4 WILD-TYPE
  0             7             250
  1             1              17
[1] 2 2
[1] FALSE
D443V7, binary
                 cls
clus                0   1
  PTPN4 MUTATED     5   4
  PTPN4 WILD-TYPE 105 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN4 MUTATED      5    4
  PTPN4 WILD-TYPE  105  175
        clus
vv       PTPN4 MUTATED PTPN4 WILD-TYPE
  FEMALE             5             105
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PTPN4 MUTATED                                       0
  PTPN4 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PTPN4 MUTATED                                                        7
  PTPN4 WILD-TYPE                                                    128
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PTPN4 MUTATED                                                                   1
  PTPN4 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PTPN4 MUTATED                                                  1
  PTPN4 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PTPN4 MUTATED                                                          0
  PTPN4 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PTPN4 MUTATED                                                           0
  PTPN4 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PTPN4 MUTATED                                          0
  PTPN4 WILD-TYPE                                        3
D443V8, multiclass
                                                                   clus
vv                                                                  PTPN4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  PTPN4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D443V9, binary
                 cls
clus                0   1
  PTPN4 MUTATED     0   9
  PTPN4 WILD-TYPE   5 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN4 MUTATED      0    9
  PTPN4 WILD-TYPE    5  275
     clus
vv    PTPN4 MUTATED PTPN4 WILD-TYPE
  NO              0               5
  YES             9             275
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PTPN4 MUTATED     5   0   0   4
  PTPN4 WILD-TYPE 222  10  10  20
D443V10, multiclass
    clus
vv   PTPN4 MUTATED PTPN4 WILD-TYPE
  R0             5             222
  R1             0              10
  R2             0              10
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D443V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTPN4 MUTATED       1                         1     7
  PTPN4 WILD-TYPE    75                         3   161
D443V12, multiclass
                           clus
vv                          PTPN4 MUTATED PTPN4 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 7             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(444) Variable = CTSD MUTATION ANALYSIS
D444V1, survival
                sevent
clus2              0   1
  CTSD MUTATED     6   1
  CTSD WILD-TYPE 175  79
  CTSD MUTATED CTSD WILD-TYPE 
             7            254 
  CTSD MUTATED CTSD WILD-TYPE 
             1             79 
$`CTSD MUTATED`
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8059 TCGA-BR-8368 TCGA-D7-6820 TCGA-HU-8602 
       34.68        32.78        14.43         4.31        11.31        11.41 
TCGA-HU-A4GN 
       29.98 

$`CTSD WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.55        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  CTSD MUTATED CTSD WILD-TYPE 
          4.31           0.00 
  CTSD MUTATED CTSD WILD-TYPE 
         34.68         105.07 
  CTSD MUTATED CTSD WILD-TYPE 
        14.430         12.605 
[1] "4.3 - 34.7 (14.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "3.4"
D444V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CTSD MUTATED         0        0        1        0         3         2
  CTSD WILD-TYPE       1        9       26       26        28        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTSD MUTATED           1          0          0          0        0
  CTSD WILD-TYPE         2         49         36         24       24
D444V3, multiclass
            clus
vv           CTSD MUTATED CTSD WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             3             28
  STAGE IIB             2             42
  STAGE III             1              2
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CTSD MUTATED     0   3   2   2
  CTSD WILD-TYPE  11  69 120  73
D444V4, multiclass
    clus
vv   CTSD MUTATED CTSD WILD-TYPE
  T1            0             11
  T2            3             69
  T3            2            120
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  CTSD MUTATED    4  3  0  0
  CTSD WILD-TYPE 89 78 50 53
D444V5, multiclass
    clus
vv   CTSD MUTATED CTSD WILD-TYPE
  N0            4             89
  N1            3             78
  N2            0             50
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D444V6, binary
                cls
clus               0   1
  CTSD MUTATED     7   0
  CTSD WILD-TYPE 250  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSD MUTATED      7    0
  CTSD WILD-TYPE  250   18
   clus
vv  CTSD MUTATED CTSD WILD-TYPE
  0            7            250
  1            0             18
[1] 2 2
[1] FALSE
D444V7, binary
                cls
clus               0   1
  CTSD MUTATED     4   3
  CTSD WILD-TYPE 106 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSD MUTATED      4    3
  CTSD WILD-TYPE  106  176
        clus
vv       CTSD MUTATED CTSD WILD-TYPE
  FEMALE            4            106
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CTSD MUTATED                                       1
  CTSD WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CTSD MUTATED                                                        3
  CTSD WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CTSD MUTATED                                                                   1
  CTSD WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CTSD MUTATED                                                  2
  CTSD WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CTSD MUTATED                                                          0
  CTSD WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CTSD MUTATED                                                           0
  CTSD WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CTSD MUTATED                                          0
  CTSD WILD-TYPE                                        3
D444V8, multiclass
                                                                   clus
vv                                                                  CTSD MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  CTSD WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D444V9, binary
                cls
clus               0   1
  CTSD MUTATED     0   7
  CTSD WILD-TYPE   5 277
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSD MUTATED      0    7
  CTSD WILD-TYPE    5  277
     clus
vv    CTSD MUTATED CTSD WILD-TYPE
  NO             0              5
  YES            7            277
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CTSD MUTATED     7   0   0   0
  CTSD WILD-TYPE 220  10  10  24
D444V10, multiclass
    clus
vv   CTSD MUTATED CTSD WILD-TYPE
  R0            7            220
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D444V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CTSD MUTATED       2                         0     5
  CTSD WILD-TYPE    74                         4   163
D444V12, multiclass
                           clus
vv                          CTSD MUTATED CTSD WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                5            163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(445) Variable = EOMES MUTATION ANALYSIS
D445V1, survival
                 sevent
clus2               0   1
  EOMES MUTATED     4   3
  EOMES WILD-TYPE 177  77
  EOMES MUTATED EOMES WILD-TYPE 
              7             254 
  EOMES MUTATED EOMES WILD-TYPE 
              3              77 
$`EOMES MUTATED`
TCGA-BR-4201 TCGA-BR-6706 TCGA-BR-8078 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MI 
       30.90        18.05        12.26        11.57         0.10         0.10 
TCGA-CG-4306 
        1.02 

$`EOMES WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        32.78        25.61        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  EOMES MUTATED EOMES WILD-TYPE 
            0.1             0.0 
  EOMES MUTATED EOMES WILD-TYPE 
          30.90          105.07 
  EOMES MUTATED EOMES WILD-TYPE 
          11.57           12.71 
[1] "0.1 - 30.9 (11.6)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.8"
D445V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EOMES MUTATED         0        0        0        1         0         1
  EOMES WILD-TYPE       1        9       27       25        31        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EOMES MUTATED           0          1          2          0        1
  EOMES WILD-TYPE         3         48         34         24       23
D445V3, multiclass
            clus
vv           EOMES MUTATED EOMES WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              0              31
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             2              34
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EOMES MUTATED     0   1   5   1
  EOMES WILD-TYPE  11  71 117  74
D445V4, multiclass
    clus
vv   EOMES MUTATED EOMES WILD-TYPE
  T1             0              11
  T2             1              71
  T3             5             117
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  EOMES MUTATED    2  3  1  1
  EOMES WILD-TYPE 91 78 49 52
D445V5, multiclass
    clus
vv   EOMES MUTATED EOMES WILD-TYPE
  N0             2              91
  N1             3              78
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D445V6, binary
                 cls
clus                0   1
  EOMES MUTATED     7   1
  EOMES WILD-TYPE 250  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED      7    1
  EOMES WILD-TYPE  250   17
   clus
vv  EOMES MUTATED EOMES WILD-TYPE
  0             7             250
  1             1              17
[1] 2 2
[1] FALSE
D445V7, binary
                 cls
clus                0   1
  EOMES MUTATED     3   5
  EOMES WILD-TYPE 107 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED      3    5
  EOMES WILD-TYPE  107  174
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  FEMALE             3             107
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  EOMES MUTATED                                       0
  EOMES WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EOMES MUTATED                                                        8
  EOMES WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EOMES MUTATED                                                                   0
  EOMES WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  EOMES MUTATED                                                  0
  EOMES WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  EOMES MUTATED                                                          0
  EOMES WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  EOMES MUTATED                                                           0
  EOMES WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  EOMES MUTATED                                          0
  EOMES WILD-TYPE                                        3
D445V8, multiclass
                                                                   clus
vv                                                                  EOMES MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  EOMES WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D445V9, binary
                 cls
clus                0   1
  EOMES MUTATED     0   8
  EOMES WILD-TYPE   5 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED      0    8
  EOMES WILD-TYPE    5  276
     clus
vv    EOMES MUTATED EOMES WILD-TYPE
  NO              0               5
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EOMES MUTATED     4   0   1   2
  EOMES WILD-TYPE 223  10   9  22
D445V10, multiclass
    clus
vv   EOMES MUTATED EOMES WILD-TYPE
  R0             4             223
  R1             0              10
  R2             1               9
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D445V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EOMES MUTATED       2                         0     5
  EOMES WILD-TYPE    74                         4   163
D445V12, multiclass
                           clus
vv                          EOMES MUTATED EOMES WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(446) Variable = AVPR1A MUTATION ANALYSIS
D446V1, survival
                  sevent
clus2                0   1
  AVPR1A MUTATED     6   4
  AVPR1A WILD-TYPE 175  76
  AVPR1A MUTATED AVPR1A WILD-TYPE 
              10              251 
  AVPR1A MUTATED AVPR1A WILD-TYPE 
               4               76 
$`AVPR1A MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8591 TCGA-BR-A4QL 
        6.97        34.68        30.90        32.94        13.45        11.57 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-EQ-8122 TCGA-HU-A4GQ 
        6.58         6.02         7.99         0.10 

$`AVPR1A WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       31.20        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        15.81         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
       14.76         0.62        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  AVPR1A MUTATED AVPR1A WILD-TYPE 
             0.1              0.0 
  AVPR1A MUTATED AVPR1A WILD-TYPE 
           34.68           105.07 
  AVPR1A MUTATED AVPR1A WILD-TYPE 
            9.78            12.66 
[1] "0.1 - 34.7 (9.8)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.2"
D446V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AVPR1A MUTATED         1        0        0        1         3         1
  AVPR1A WILD-TYPE       0        9       27       25        28        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AVPR1A MUTATED           0          2          1          2        1
  AVPR1A WILD-TYPE         3         47         35         22       23
D446V3, multiclass
            clus
vv           AVPR1A MUTATED AVPR1A WILD-TYPE
  STAGE I                 1                0
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                1               25
  STAGE IIA               3               28
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              1               35
  STAGE IIIC              2               22
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  AVPR1A MUTATED     1   1   7   3
  AVPR1A WILD-TYPE  10  71 115  72
D446V4, multiclass
    clus
vv   AVPR1A MUTATED AVPR1A WILD-TYPE
  T1              1               10
  T2              1               71
  T3              7              115
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  AVPR1A MUTATED    3  5  2  2
  AVPR1A WILD-TYPE 90 76 48 51
D446V5, multiclass
    clus
vv   AVPR1A MUTATED AVPR1A WILD-TYPE
  N0              3               90
  N1              5               76
  N2              2               48
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D446V6, binary
                  cls
clus                 0   1
  AVPR1A MUTATED     9   0
  AVPR1A WILD-TYPE 248  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AVPR1A MUTATED      9    0
  AVPR1A WILD-TYPE  248   18
   clus
vv  AVPR1A MUTATED AVPR1A WILD-TYPE
  0              9              248
  1              0               18
[1] 2 2
[1] FALSE
D446V7, binary
                  cls
clus                 0   1
  AVPR1A MUTATED     4   8
  AVPR1A WILD-TYPE 106 171
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AVPR1A MUTATED      4    8
  AVPR1A WILD-TYPE  106  171
        clus
vv       AVPR1A MUTATED AVPR1A WILD-TYPE
  FEMALE              4              106
  MALE                8              171
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AVPR1A MUTATED                                       1
  AVPR1A WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AVPR1A MUTATED                                                        7
  AVPR1A WILD-TYPE                                                    128
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AVPR1A MUTATED                                                                   2
  AVPR1A WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AVPR1A MUTATED                                                  1
  AVPR1A WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AVPR1A MUTATED                                                          1
  AVPR1A WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AVPR1A MUTATED                                                           0
  AVPR1A WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AVPR1A MUTATED                                          0
  AVPR1A WILD-TYPE                                        3
D446V8, multiclass
                                                                   clus
vv                                                                  AVPR1A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  AVPR1A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D446V9, binary
                  cls
clus                 0   1
  AVPR1A MUTATED     1  11
  AVPR1A WILD-TYPE   4 273
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AVPR1A MUTATED      1   11
  AVPR1A WILD-TYPE    4  273
     clus
vv    AVPR1A MUTATED AVPR1A WILD-TYPE
  NO               1                4
  YES             11              273
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  AVPR1A MUTATED     9   0   0   1
  AVPR1A WILD-TYPE 218  10  10  23
D446V10, multiclass
    clus
vv   AVPR1A MUTATED AVPR1A WILD-TYPE
  R0              9              218
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D446V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AVPR1A MUTATED       2                         1     7
  AVPR1A WILD-TYPE    74                         3   161
D446V12, multiclass
                           clus
vv                          AVPR1A MUTATED AVPR1A WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  7              161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(447) Variable = DDX43 MUTATION ANALYSIS
D447V1, survival
                 sevent
clus2               0   1
  DDX43 MUTATED     6   2
  DDX43 WILD-TYPE 175  78
  DDX43 MUTATED DDX43 WILD-TYPE 
              8             253 
  DDX43 MUTATED DDX43 WILD-TYPE 
              2              78 
$`DDX43 MUTATED`
TCGA-BR-8487 TCGA-BR-A4QL TCGA-CG-4306 TCGA-CG-4441 TCGA-D7-8572 TCGA-F1-A448 
        1.12        11.57         1.02        14.01        16.80        21.27 
TCGA-HU-A4G6 TCGA-IP-7968 
       12.30         2.53 

$`DDX43 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 
       10.55        11.31        12.33        24.72        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       16.24        14.47        72.23         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 
        3.39 

  DDX43 MUTATED DDX43 WILD-TYPE 
           1.02            0.00 
  DDX43 MUTATED DDX43 WILD-TYPE 
          21.27          105.07 
  DDX43 MUTATED DDX43 WILD-TYPE 
         11.935          12.660 
[1] "1.0 - 21.3 (11.9)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.2"
D447V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDX43 MUTATED         0        1        0        0         1         1
  DDX43 WILD-TYPE       1        8       27       26        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DDX43 MUTATED           0          1          3          0        1
  DDX43 WILD-TYPE         3         48         33         24       23
D447V3, multiclass
            clus
vv           DDX43 MUTATED DDX43 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             3              33
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDX43 MUTATED     1   2   6   0
  DDX43 WILD-TYPE  10  70 116  75
D447V4, multiclass
    clus
vv   DDX43 MUTATED DDX43 WILD-TYPE
  T1             1              10
  T2             2              70
  T3             6             116
  T4             0              75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  DDX43 MUTATED    2  1  4  2
  DDX43 WILD-TYPE 91 80 46 51
D447V5, multiclass
    clus
vv   DDX43 MUTATED DDX43 WILD-TYPE
  N0             2              91
  N1             1              80
  N2             4              46
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D447V6, binary
                 cls
clus                0   1
  DDX43 MUTATED     7   1
  DDX43 WILD-TYPE 250  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED      7    1
  DDX43 WILD-TYPE  250   17
   clus
vv  DDX43 MUTATED DDX43 WILD-TYPE
  0             7             250
  1             1              17
[1] 2 2
[1] FALSE
D447V7, binary
                 cls
clus                0   1
  DDX43 MUTATED     3   7
  DDX43 WILD-TYPE 107 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED      3    7
  DDX43 WILD-TYPE  107  172
        clus
vv       DDX43 MUTATED DDX43 WILD-TYPE
  FEMALE             3             107
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DDX43 MUTATED                                       0
  DDX43 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DDX43 MUTATED                                                        7
  DDX43 WILD-TYPE                                                    128
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DDX43 MUTATED                                                                   1
  DDX43 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DDX43 MUTATED                                                  0
  DDX43 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DDX43 MUTATED                                                          1
  DDX43 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DDX43 MUTATED                                                           1
  DDX43 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DDX43 MUTATED                                          0
  DDX43 WILD-TYPE                                        3
D447V8, multiclass
                                                                   clus
vv                                                                  DDX43 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  DDX43 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D447V9, binary
                 cls
clus                0   1
  DDX43 MUTATED     0  10
  DDX43 WILD-TYPE   5 274
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED      0   10
  DDX43 WILD-TYPE    5  274
     clus
vv    DDX43 MUTATED DDX43 WILD-TYPE
  NO              0               5
  YES            10             274
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DDX43 MUTATED     7   0   1   2
  DDX43 WILD-TYPE 220  10   9  22
D447V10, multiclass
    clus
vv   DDX43 MUTATED DDX43 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             1               9
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D447V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDX43 MUTATED       1                         0     7
  DDX43 WILD-TYPE    75                         4   161
D447V12, multiclass
                           clus
vv                          DDX43 MUTATED DDX43 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 7             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(448) Variable = OR4K5 MUTATION ANALYSIS
D448V1, survival
                 sevent
clus2               0   1
  OR4K5 MUTATED     8   4
  OR4K5 WILD-TYPE 173  76
  OR4K5 MUTATED OR4K5 WILD-TYPE 
             12             249 
  OR4K5 MUTATED OR4K5 WILD-TYPE 
              4              76 
$`OR4K5 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8289 TCGA-BR-8589 TCGA-BR-8680 TCGA-D7-6527 
        6.97        34.68         2.66        15.81        15.81        10.26 
TCGA-F1-6874 TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4GU TCGA-HU-A4GX 
       14.47        11.08        26.47        11.41         6.25        10.19 

$`OR4K5 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       12.95        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        12.79         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  OR4K5 MUTATED OR4K5 WILD-TYPE 
           2.66            0.00 
  OR4K5 MUTATED OR4K5 WILD-TYPE 
          34.68          105.07 
  OR4K5 MUTATED OR4K5 WILD-TYPE 
         11.245          12.660 
[1] "2.7 - 34.7 (11.2)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.1"
D448V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OR4K5 MUTATED         0        0        2        1         2         2
  OR4K5 WILD-TYPE       1        9       25       25        29        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR4K5 MUTATED           0          1          1          1        2
  OR4K5 WILD-TYPE         3         48         35         23       22
D448V3, multiclass
            clus
vv           OR4K5 MUTATED OR4K5 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               1              25
  STAGE IIA              2              29
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR4K5 MUTATED     0   3   4   5
  OR4K5 WILD-TYPE  11  69 118  70
D448V4, multiclass
    clus
vv   OR4K5 MUTATED OR4K5 WILD-TYPE
  T1             0              11
  T2             3              69
  T3             4             118
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  OR4K5 MUTATED    5  4  2  1
  OR4K5 WILD-TYPE 88 77 48 52
D448V5, multiclass
    clus
vv   OR4K5 MUTATED OR4K5 WILD-TYPE
  N0             5              88
  N1             4              77
  N2             2              48
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D448V6, binary
                 cls
clus                0   1
  OR4K5 MUTATED     8   2
  OR4K5 WILD-TYPE 249  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4K5 MUTATED      8    2
  OR4K5 WILD-TYPE  249   16
   clus
vv  OR4K5 MUTATED OR4K5 WILD-TYPE
  0             8             249
  1             2              16
[1] 2 2
[1] FALSE
D448V7, binary
                 cls
clus                0   1
  OR4K5 MUTATED     4   8
  OR4K5 WILD-TYPE 106 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4K5 MUTATED      4    8
  OR4K5 WILD-TYPE  106  171
        clus
vv       OR4K5 MUTATED OR4K5 WILD-TYPE
  FEMALE             4             106
  MALE               8             171
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  OR4K5 MUTATED                                       3
  OR4K5 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OR4K5 MUTATED                                                        4
  OR4K5 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OR4K5 MUTATED                                                                   2
  OR4K5 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  OR4K5 MUTATED                                                  1
  OR4K5 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  OR4K5 MUTATED                                                          0
  OR4K5 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  OR4K5 MUTATED                                                           1
  OR4K5 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  OR4K5 MUTATED                                          1
  OR4K5 WILD-TYPE                                        2
D448V8, multiclass
                                                                   clus
vv                                                                  OR4K5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  OR4K5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D448V9, binary
                 cls
clus                0   1
  OR4K5 MUTATED     0  12
  OR4K5 WILD-TYPE   5 272
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4K5 MUTATED      0   12
  OR4K5 WILD-TYPE    5  272
     clus
vv    OR4K5 MUTATED OR4K5 WILD-TYPE
  NO              0               5
  YES            12             272
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR4K5 MUTATED    11   0   0   1
  OR4K5 WILD-TYPE 216  10  10  23
D448V10, multiclass
    clus
vv   OR4K5 MUTATED OR4K5 WILD-TYPE
  R0            11             216
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D448V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR4K5 MUTATED       4                         1     7
  OR4K5 WILD-TYPE    72                         3   161
D448V12, multiclass
                           clus
vv                          OR4K5 MUTATED OR4K5 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 7             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(449) Variable = GPR124 MUTATION ANALYSIS
D449V1, survival
                  sevent
clus2                0   1
  GPR124 MUTATED     8   3
  GPR124 WILD-TYPE 173  77
  GPR124 MUTATED GPR124 WILD-TYPE 
              11              250 
  GPR124 MUTATED GPR124 WILD-TYPE 
               3               77 
$`GPR124 MUTATED`
TCGA-BR-4280 TCGA-BR-6458 TCGA-BR-8360 TCGA-BR-8372 TCGA-BR-A4PF TCGA-CD-8531 
        6.61        19.33         6.18        19.17         1.15         0.10 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5723 TCGA-F1-6874 TCGA-F1-A448 
        6.58         6.02       105.07        14.47        21.27 

$`GPR124 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51        20.65        20.42        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.13         0.16         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99         0.99        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        0.62         7.99        16.24        72.23         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  GPR124 MUTATED GPR124 WILD-TYPE 
             0.1              0.0 
  GPR124 MUTATED GPR124 WILD-TYPE 
          105.07            79.07 
  GPR124 MUTATED GPR124 WILD-TYPE 
            6.61            12.64 
[1] "0.1 - 105.1 (6.6)" "0.0 - 79.1 (12.6)"
[1] "hr=" "1.3"
D449V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPR124 MUTATED         0        0        1        1         2         1
  GPR124 WILD-TYPE       1        9       26       25        29        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR124 MUTATED           1          2          2          1        1
  GPR124 WILD-TYPE         2         47         34         23       23
D449V3, multiclass
            clus
vv           GPR124 MUTATED GPR124 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                1               25
  STAGE IIA               2               29
  STAGE IIB               1               43
  STAGE III               1                2
  STAGE IIIA              2               47
  STAGE IIIB              2               34
  STAGE IIIC              1               23
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR124 MUTATED     1   3   5   4
  GPR124 WILD-TYPE  10  69 117  71
D449V4, multiclass
    clus
vv   GPR124 MUTATED GPR124 WILD-TYPE
  T1              1               10
  T2              3               69
  T3              5              117
  T4              4               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  GPR124 MUTATED    4  5  1  2
  GPR124 WILD-TYPE 89 76 49 51
D449V5, multiclass
    clus
vv   GPR124 MUTATED GPR124 WILD-TYPE
  N0              4               89
  N1              5               76
  N2              1               49
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D449V6, binary
                  cls
clus                 0   1
  GPR124 MUTATED    13   0
  GPR124 WILD-TYPE 244  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR124 MUTATED     13    0
  GPR124 WILD-TYPE  244   18
   clus
vv  GPR124 MUTATED GPR124 WILD-TYPE
  0             13              244
  1              0               18
[1] 2 2
[1] FALSE
D449V7, binary
                  cls
clus                 0   1
  GPR124 MUTATED     5   8
  GPR124 WILD-TYPE 105 171
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR124 MUTATED      5    8
  GPR124 WILD-TYPE  105  171
        clus
vv       GPR124 MUTATED GPR124 WILD-TYPE
  FEMALE              5              105
  MALE                8              171
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GPR124 MUTATED                                       2
  GPR124 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPR124 MUTATED                                                        7
  GPR124 WILD-TYPE                                                    128
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPR124 MUTATED                                                                   3
  GPR124 WILD-TYPE                                                                37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GPR124 MUTATED                                                  0
  GPR124 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GPR124 MUTATED                                                          1
  GPR124 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GPR124 MUTATED                                                           0
  GPR124 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GPR124 MUTATED                                          0
  GPR124 WILD-TYPE                                        3
D449V8, multiclass
                                                                   clus
vv                                                                  GPR124 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  GPR124 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D449V9, binary
                  cls
clus                 0   1
  GPR124 MUTATED     0  13
  GPR124 WILD-TYPE   5 271
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR124 MUTATED      0   13
  GPR124 WILD-TYPE    5  271
     clus
vv    GPR124 MUTATED GPR124 WILD-TYPE
  NO               0                5
  YES             13              271
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GPR124 MUTATED     9   0   0   3
  GPR124 WILD-TYPE 218  10  10  21
D449V10, multiclass
    clus
vv   GPR124 MUTATED GPR124 WILD-TYPE
  R0              9              218
  R1              0               10
  R2              0               10
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D449V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPR124 MUTATED       2                         0     9
  GPR124 WILD-TYPE    74                         4   159
D449V12, multiclass
                           clus
vv                          GPR124 MUTATED GPR124 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  9              159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(450) Variable = FAAH MUTATION ANALYSIS
D450V1, survival
                sevent
clus2              0   1
  FAAH MUTATED     2   1
  FAAH WILD-TYPE 179  79
  FAAH MUTATED FAAH WILD-TYPE 
             3            258 
  FAAH MUTATED FAAH WILD-TYPE 
             1             79 
$`FAAH MUTATED`
TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-A4QL 
       14.43        20.55        11.57 

$`FAAH WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       18.71        17.49         0.69        12.26         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  FAAH MUTATED FAAH WILD-TYPE 
         11.57           0.00 
  FAAH MUTATED FAAH WILD-TYPE 
         20.55         105.07 
  FAAH MUTATED FAAH WILD-TYPE 
        14.430         12.605 
[1] "11.6 - 20.6 (14.4)" "0.0 - 105.1 (12.6)"
[1] "hr=" "1"  
D450V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAAH MUTATED         0        0        0        0         0         1
  FAAH WILD-TYPE       1        9       27       26        31        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAAH MUTATED           1          0          1          0        0
  FAAH WILD-TYPE         2         49         35         24       24
D450V3, multiclass
            clus
vv           FAAH MUTATED FAAH WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              0             26
  STAGE IIA             0             31
  STAGE IIB             1             43
  STAGE III             1              2
  STAGE IIIA            0             49
  STAGE IIIB            1             35
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FAAH MUTATED     0   0   1   2
  FAAH WILD-TYPE  11  72 121  73
D450V4, multiclass
    clus
vv   FAAH MUTATED FAAH WILD-TYPE
  T1            0             11
  T2            0             72
  T3            1            121
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  FAAH MUTATED    1  2  0  1
  FAAH WILD-TYPE 92 79 50 52
D450V5, multiclass
    clus
vv   FAAH MUTATED FAAH WILD-TYPE
  N0            1             92
  N1            2             79
  N2            0             50
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D450V6, binary
                cls
clus               0   1
  FAAH MUTATED     4   0
  FAAH WILD-TYPE 253  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAAH MUTATED      4    0
  FAAH WILD-TYPE  253   18
   clus
vv  FAAH MUTATED FAAH WILD-TYPE
  0            4            253
  1            0             18
[1] 2 2
[1] FALSE
D450V7, binary
                cls
clus               0   1
  FAAH MUTATED     2   2
  FAAH WILD-TYPE 108 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAAH MUTATED      2    2
  FAAH WILD-TYPE  108  177
        clus
vv       FAAH MUTATED FAAH WILD-TYPE
  FEMALE            2            108
  MALE              2            177
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FAAH MUTATED                                       0
  FAAH WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAAH MUTATED                                                        3
  FAAH WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAAH MUTATED                                                                   1
  FAAH WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FAAH MUTATED                                                  0
  FAAH WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FAAH MUTATED                                                          0
  FAAH WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FAAH MUTATED                                                           0
  FAAH WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FAAH MUTATED                                          0
  FAAH WILD-TYPE                                        3
D450V8, multiclass
                                                                   clus
vv                                                                  FAAH MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  FAAH WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D450V9, binary
                cls
clus               0   1
  FAAH MUTATED     0   4
  FAAH WILD-TYPE   5 280
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAAH MUTATED      0    4
  FAAH WILD-TYPE    5  280
     clus
vv    FAAH MUTATED FAAH WILD-TYPE
  NO             0              5
  YES            4            280
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FAAH MUTATED     3   0   0   1
  FAAH WILD-TYPE 224  10  10  23
D450V10, multiclass
    clus
vv   FAAH MUTATED FAAH WILD-TYPE
  R0            3            224
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D450V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAAH MUTATED       0                         0     4
  FAAH WILD-TYPE    76                         4   164
D450V12, multiclass
                           clus
vv                          FAAH MUTATED FAAH WILD-TYPE
  ASIAN                                0             76
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                4            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(451) Variable = EYA4 MUTATION ANALYSIS
D451V1, survival
                sevent
clus2              0   1
  EYA4 MUTATED    10   5
  EYA4 WILD-TYPE 171  75
  EYA4 MUTATED EYA4 WILD-TYPE 
            15            246 
  EYA4 MUTATED EYA4 WILD-TYPE 
             5             75 
$`EYA4 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7716 TCGA-BR-7901 TCGA-BR-8366 
        6.97        30.90        34.68        28.01         3.45         0.95 
TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-4444 TCGA-CG-5726 TCGA-D7-6817 TCGA-D7-8579 
        1.12        15.81        47.05        28.96        12.79        20.91 
TCGA-HJ-7597 TCGA-HU-A4GN TCGA-HU-A4HD 
       26.47        29.98        27.42 

$`EYA4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 
       15.42        18.15        15.32        28.73        12.43         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        20.55         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
       13.35        17.19        10.26        15.22        15.98        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        14.66        21.14        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       11.08         5.52         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        8.88        21.21         3.45        18.81         3.39         2.53 

  EYA4 MUTATED EYA4 WILD-TYPE 
          0.95           0.00 
  EYA4 MUTATED EYA4 WILD-TYPE 
         47.05         105.07 
  EYA4 MUTATED EYA4 WILD-TYPE 
         26.47          12.43 
[1] "0.9 - 47.0 (26.5)"  "0.0 - 105.1 (12.4)"
[1] "hr=" "1.6"
D451V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EYA4 MUTATED         0        1        1        0         4         3
  EYA4 WILD-TYPE       1        8       26       26        27        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EYA4 MUTATED           0          4          0          0        1
  EYA4 WILD-TYPE         3         45         36         24       23
D451V3, multiclass
            clus
vv           EYA4 MUTATED EYA4 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             4             27
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            4             45
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EYA4 MUTATED     1   6   7   1
  EYA4 WILD-TYPE  10  66 115  74
D451V4, multiclass
    clus
vv   EYA4 MUTATED EYA4 WILD-TYPE
  T1            1             10
  T2            6             66
  T3            7            115
  T4            1             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  EYA4 MUTATED    5  4  4  1
  EYA4 WILD-TYPE 88 77 46 52
D451V5, multiclass
    clus
vv   EYA4 MUTATED EYA4 WILD-TYPE
  N0            5             88
  N1            4             77
  N2            4             46
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D451V6, binary
                cls
clus               0   1
  EYA4 MUTATED    12   1
  EYA4 WILD-TYPE 245  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  EYA4 MUTATED     12    1
  EYA4 WILD-TYPE  245   17
   clus
vv  EYA4 MUTATED EYA4 WILD-TYPE
  0           12            245
  1            1             17
[1] 2 2
[1] FALSE
D451V7, binary
                cls
clus               0   1
  EYA4 MUTATED     7   8
  EYA4 WILD-TYPE 103 171
[1] "tbl2"
                cls
clus             [,1] [,2]
  EYA4 MUTATED      7    8
  EYA4 WILD-TYPE  103  171
        clus
vv       EYA4 MUTATED EYA4 WILD-TYPE
  FEMALE            7            103
  MALE              8            171
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  EYA4 MUTATED                                       1
  EYA4 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EYA4 MUTATED                                                        7
  EYA4 WILD-TYPE                                                    128
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EYA4 MUTATED                                                                   2
  EYA4 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  EYA4 MUTATED                                                  4
  EYA4 WILD-TYPE                                               34
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  EYA4 MUTATED                                                          0
  EYA4 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  EYA4 MUTATED                                                           0
  EYA4 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  EYA4 MUTATED                                          1
  EYA4 WILD-TYPE                                        2
D451V8, multiclass
                                                                   clus
vv                                                                  EYA4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  EYA4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D451V9, binary
                cls
clus               0   1
  EYA4 MUTATED     1  14
  EYA4 WILD-TYPE   4 270
[1] "tbl2"
                cls
clus             [,1] [,2]
  EYA4 MUTATED      1   14
  EYA4 WILD-TYPE    4  270
     clus
vv    EYA4 MUTATED EYA4 WILD-TYPE
  NO             1              4
  YES           14            270
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EYA4 MUTATED    13   0   0   2
  EYA4 WILD-TYPE 214  10  10  22
D451V10, multiclass
    clus
vv   EYA4 MUTATED EYA4 WILD-TYPE
  R0           13            214
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D451V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EYA4 MUTATED       3                         0    10
  EYA4 WILD-TYPE    73                         4   158
D451V12, multiclass
                           clus
vv                          EYA4 MUTATED EYA4 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               10            158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(452) Variable = ZNF701 MUTATION ANALYSIS
D452V1, survival
                  sevent
clus2                0   1
  ZNF701 MUTATED     4   4
  ZNF701 WILD-TYPE 177  76
  ZNF701 MUTATED ZNF701 WILD-TYPE 
               8              253 
  ZNF701 MUTATED ZNF701 WILD-TYPE 
               4               76 
$`ZNF701 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8059 TCGA-BR-8363 TCGA-BR-8680 TCGA-BR-A4J1 
        6.97        34.68        14.43         0.26        15.81         0.72 
TCGA-CD-A4MI TCGA-CG-5727 
        0.10        79.07 

$`ZNF701 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       19.50        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  ZNF701 MUTATED ZNF701 WILD-TYPE 
             0.1              0.0 
  ZNF701 MUTATED ZNF701 WILD-TYPE 
           79.07           105.07 
  ZNF701 MUTATED ZNF701 WILD-TYPE 
           10.70            12.62 
[1] "0.1 - 79.1 (10.7)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D452V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF701 MUTATED         0        0        1        1         1         0
  ZNF701 WILD-TYPE       1        9       26       25        30        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF701 MUTATED           1          2          1          0        1
  ZNF701 WILD-TYPE         2         47         35         24       23
D452V3, multiclass
            clus
vv           ZNF701 MUTATED ZNF701 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                1               25
  STAGE IIA               1               30
  STAGE IIB               0               44
  STAGE III               1                2
  STAGE IIIA              2               47
  STAGE IIIB              1               35
  STAGE IIIC              0               24
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF701 MUTATED     0   1   4   3
  ZNF701 WILD-TYPE  11  71 118  72
D452V4, multiclass
    clus
vv   ZNF701 MUTATED ZNF701 WILD-TYPE
  T1              0               11
  T2              1               71
  T3              4              118
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZNF701 MUTATED    3  4  1  0
  ZNF701 WILD-TYPE 90 77 49 53
D452V5, multiclass
    clus
vv   ZNF701 MUTATED ZNF701 WILD-TYPE
  N0              3               90
  N1              4               77
  N2              1               49
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D452V6, binary
                  cls
clus                 0   1
  ZNF701 MUTATED     6   1
  ZNF701 WILD-TYPE 251  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF701 MUTATED      6    1
  ZNF701 WILD-TYPE  251   17
   clus
vv  ZNF701 MUTATED ZNF701 WILD-TYPE
  0              6              251
  1              1               17
[1] 2 2
[1] FALSE
D452V7, binary
                  cls
clus                 0   1
  ZNF701 MUTATED     2   6
  ZNF701 WILD-TYPE 108 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF701 MUTATED      2    6
  ZNF701 WILD-TYPE  108  173
        clus
vv       ZNF701 MUTATED ZNF701 WILD-TYPE
  FEMALE              2              108
  MALE                6              173
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZNF701 MUTATED                                       0
  ZNF701 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF701 MUTATED                                                        5
  ZNF701 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF701 MUTATED                                                                   2
  ZNF701 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZNF701 MUTATED                                                  1
  ZNF701 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZNF701 MUTATED                                                          0
  ZNF701 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZNF701 MUTATED                                                           0
  ZNF701 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZNF701 MUTATED                                          0
  ZNF701 WILD-TYPE                                        3
D452V8, multiclass
                                                                   clus
vv                                                                  ZNF701 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ZNF701 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D452V9, binary
                  cls
clus                 0   1
  ZNF701 MUTATED     0   8
  ZNF701 WILD-TYPE   5 276
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF701 MUTATED      0    8
  ZNF701 WILD-TYPE    5  276
     clus
vv    ZNF701 MUTATED ZNF701 WILD-TYPE
  NO               0                5
  YES              8              276
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF701 MUTATED     6   0   0   1
  ZNF701 WILD-TYPE 221  10  10  23
D452V10, multiclass
    clus
vv   ZNF701 MUTATED ZNF701 WILD-TYPE
  R0              6              221
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D452V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF701 MUTATED       3                         0     4
  ZNF701 WILD-TYPE    73                         4   164
D452V12, multiclass
                           clus
vv                          ZNF701 MUTATED ZNF701 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(453) Variable = OR2J3 MUTATION ANALYSIS
D453V1, survival
                 sevent
clus2               0   1
  OR2J3 MUTATED     4   1
  OR2J3 WILD-TYPE 177  79
  OR2J3 MUTATED OR2J3 WILD-TYPE 
              5             256 
  OR2J3 MUTATED OR2J3 WILD-TYPE 
              1              79 
$`OR2J3 MUTATED`
TCGA-BR-4187 TCGA-BR-6452 TCGA-CD-8536 TCGA-D7-6822 TCGA-D7-A4Z0 
        4.64        34.68         0.10        12.33        14.76 

$`OR2J3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         6.97         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        10.55        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-EQ-5647 TCGA-EQ-8122 
       16.44         5.92        15.16        13.78         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  OR2J3 MUTATED OR2J3 WILD-TYPE 
            0.1             0.0 
  OR2J3 MUTATED OR2J3 WILD-TYPE 
          34.68          105.07 
  OR2J3 MUTATED OR2J3 WILD-TYPE 
          12.33           12.64 
[1] "0.1 - 34.7 (12.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.5"
D453V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OR2J3 MUTATED         1        0        1        1         1         1
  OR2J3 WILD-TYPE       0        9       26       25        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR2J3 MUTATED           0          0          0          0        0
  OR2J3 WILD-TYPE         3         49         36         24       24
D453V3, multiclass
            clus
vv           OR2J3 MUTATED OR2J3 WILD-TYPE
  STAGE I                1               0
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR2J3 MUTATED     1   2   2   0
  OR2J3 WILD-TYPE  10  70 120  75
D453V4, multiclass
    clus
vv   OR2J3 MUTATED OR2J3 WILD-TYPE
  T1             1              10
  T2             2              70
  T3             2             120
  T4             0              75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  OR2J3 MUTATED    3  1  1  0
  OR2J3 WILD-TYPE 90 80 49 53
D453V5, multiclass
    clus
vv   OR2J3 MUTATED OR2J3 WILD-TYPE
  N0             3              90
  N1             1              80
  N2             1              49
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D453V6, binary
                 cls
clus                0   1
  OR2J3 MUTATED     5   0
  OR2J3 WILD-TYPE 252  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2J3 MUTATED      5    0
  OR2J3 WILD-TYPE  252   18
   clus
vv  OR2J3 MUTATED OR2J3 WILD-TYPE
  0             5             252
  1             0              18
[1] 2 2
[1] FALSE
D453V7, binary
                 cls
clus                0   1
  OR2J3 MUTATED     2   4
  OR2J3 WILD-TYPE 108 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2J3 MUTATED      2    4
  OR2J3 WILD-TYPE  108  175
        clus
vv       OR2J3 MUTATED OR2J3 WILD-TYPE
  FEMALE             2             108
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  OR2J3 MUTATED                                       0
  OR2J3 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OR2J3 MUTATED                                                        4
  OR2J3 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OR2J3 MUTATED                                                                   0
  OR2J3 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  OR2J3 MUTATED                                                  1
  OR2J3 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  OR2J3 MUTATED                                                          1
  OR2J3 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  OR2J3 MUTATED                                                           0
  OR2J3 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  OR2J3 MUTATED                                          0
  OR2J3 WILD-TYPE                                        3
D453V8, multiclass
                                                                   clus
vv                                                                  OR2J3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  OR2J3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D453V9, binary
                 cls
clus                0   1
  OR2J3 MUTATED     0   6
  OR2J3 WILD-TYPE   5 278
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2J3 MUTATED      0    6
  OR2J3 WILD-TYPE    5  278
     clus
vv    OR2J3 MUTATED OR2J3 WILD-TYPE
  NO              0               5
  YES             6             278
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR2J3 MUTATED     5   0   0   1
  OR2J3 WILD-TYPE 222  10  10  23
D453V10, multiclass
    clus
vv   OR2J3 MUTATED OR2J3 WILD-TYPE
  R0             5             222
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D453V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR2J3 MUTATED       1                         1     4
  OR2J3 WILD-TYPE    75                         3   164
D453V12, multiclass
                           clus
vv                          OR2J3 MUTATED OR2J3 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(454) Variable = MPRIP MUTATION ANALYSIS
D454V1, survival
                 sevent
clus2               0   1
  MPRIP MUTATED     7   5
  MPRIP WILD-TYPE 174  75
  MPRIP MUTATED MPRIP WILD-TYPE 
             12             249 
  MPRIP MUTATED MPRIP WILD-TYPE 
              5              75 
$`MPRIP MUTATED`
TCGA-BR-4184 TCGA-BR-6566 TCGA-BR-8360 TCGA-BR-8368 TCGA-BR-8590 TCGA-BR-8591 
        6.97        32.78         6.18         4.31         9.34        13.45 
TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4465 TCGA-CG-5726 TCGA-D7-6818 TCGA-HU-A4H8 
       11.57         6.58         9.01        28.96        10.55         8.88 

$`MPRIP WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
        1.12        12.79        15.81         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       19.07        12.03         0.00        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  MPRIP MUTATED MPRIP WILD-TYPE 
           4.31            0.00 
  MPRIP MUTATED MPRIP WILD-TYPE 
          32.78          105.07 
  MPRIP MUTATED MPRIP WILD-TYPE 
          9.175          12.790 
[1] "4.3 - 32.8 (9.2)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.6"
D454V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MPRIP MUTATED         0        1        2        0         3         0
  MPRIP WILD-TYPE       1        8       25       26        28        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MPRIP MUTATED           0          2          1          2        1
  MPRIP WILD-TYPE         3         47         35         22       23
D454V3, multiclass
            clus
vv           MPRIP MUTATED MPRIP WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              3              28
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             1              35
  STAGE IIIC             2              22
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MPRIP MUTATED     3   2   6   3
  MPRIP WILD-TYPE   8  70 116  72
D454V4, multiclass
    clus
vv   MPRIP MUTATED MPRIP WILD-TYPE
  T1             3               8
  T2             2              70
  T3             6             116
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  MPRIP MUTATED    5  2  1  4
  MPRIP WILD-TYPE 88 79 49 49
D454V5, multiclass
    clus
vv   MPRIP MUTATED MPRIP WILD-TYPE
  N0             5              88
  N1             2              79
  N2             1              49
  N3             4              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D454V6, binary
                 cls
clus                0   1
  MPRIP MUTATED    11   1
  MPRIP WILD-TYPE 246  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MPRIP MUTATED     11    1
  MPRIP WILD-TYPE  246   17
   clus
vv  MPRIP MUTATED MPRIP WILD-TYPE
  0            11             246
  1             1              17
[1] 2 2
[1] FALSE
D454V7, binary
                 cls
clus                0   1
  MPRIP MUTATED     6   8
  MPRIP WILD-TYPE 104 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MPRIP MUTATED      6    8
  MPRIP WILD-TYPE  104  171
        clus
vv       MPRIP MUTATED MPRIP WILD-TYPE
  FEMALE             6             104
  MALE               8             171
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MPRIP MUTATED                                       3
  MPRIP WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MPRIP MUTATED                                                        8
  MPRIP WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MPRIP MUTATED                                                                   2
  MPRIP WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MPRIP MUTATED                                                  1
  MPRIP WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MPRIP MUTATED                                                          0
  MPRIP WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MPRIP MUTATED                                                           0
  MPRIP WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MPRIP MUTATED                                          0
  MPRIP WILD-TYPE                                        3
D454V8, multiclass
                                                                   clus
vv                                                                  MPRIP MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  MPRIP WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D454V9, binary
                 cls
clus                0   1
  MPRIP MUTATED     1  13
  MPRIP WILD-TYPE   4 271
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MPRIP MUTATED      1   13
  MPRIP WILD-TYPE    4  271
     clus
vv    MPRIP MUTATED MPRIP WILD-TYPE
  NO              1               4
  YES            13             271
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MPRIP MUTATED     9   0   1   3
  MPRIP WILD-TYPE 218  10   9  21
D454V10, multiclass
    clus
vv   MPRIP MUTATED MPRIP WILD-TYPE
  R0             9             218
  R1             0              10
  R2             1               9
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D454V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MPRIP MUTATED       2                         0    10
  MPRIP WILD-TYPE    74                         4   158
D454V12, multiclass
                           clus
vv                          MPRIP MUTATED MPRIP WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                10             158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(455) Variable = SYNJ2 MUTATION ANALYSIS
D455V1, survival
                 sevent
clus2               0   1
  SYNJ2 MUTATED    10   3
  SYNJ2 WILD-TYPE 171  77
  SYNJ2 MUTATED SYNJ2 WILD-TYPE 
             13             248 
  SYNJ2 MUTATED SYNJ2 WILD-TYPE 
              3              77 
$`SYNJ2 MUTATED`
TCGA-BR-4201 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-8081 TCGA-BR-8361 TCGA-CG-5721 
       30.90        39.12        32.78        20.55        19.50         6.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-F1-A448 TCGA-HU-A4GN TCGA-HU-A4GX 
       28.96        65.10        21.07        21.27        29.98        10.19 
TCGA-HU-A4H2 
       12.95 

$`SYNJ2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        19.33        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69        12.26         9.60         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
       16.31         2.20        15.58         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       79.07         4.01        69.04         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        0.62         7.99        16.24        14.47        72.23         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       22.75        25.81        11.77         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.25         0.26         2.10        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  SYNJ2 MUTATED SYNJ2 WILD-TYPE 
           6.02            0.00 
  SYNJ2 MUTATED SYNJ2 WILD-TYPE 
          65.10          105.07 
  SYNJ2 MUTATED SYNJ2 WILD-TYPE 
         21.270          12.395 
[1] "6.0 - 65.1 (21.3)"  "0.0 - 105.1 (12.4)"
[1] "hr=" "2.8"
D455V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SYNJ2 MUTATED         1        1        1        0         2         2
  SYNJ2 WILD-TYPE       0        8       26       26        29        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SYNJ2 MUTATED           0          2          2          2        1
  SYNJ2 WILD-TYPE         3         47         34         22       23
D455V3, multiclass
            clus
vv           SYNJ2 MUTATED SYNJ2 WILD-TYPE
  STAGE I                1               0
  STAGE IA               1               8
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             2              34
  STAGE IIIC             2              22
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SYNJ2 MUTATED     3   4   4   5
  SYNJ2 WILD-TYPE   8  68 118  70
D455V4, multiclass
    clus
vv   SYNJ2 MUTATED SYNJ2 WILD-TYPE
  T1             3               8
  T2             4              68
  T3             4             118
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  SYNJ2 MUTATED    5  4  3  2
  SYNJ2 WILD-TYPE 88 77 47 51
D455V5, multiclass
    clus
vv   SYNJ2 MUTATED SYNJ2 WILD-TYPE
  N0             5              88
  N1             4              77
  N2             3              47
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D455V6, binary
                 cls
clus                0   1
  SYNJ2 MUTATED    15   0
  SYNJ2 WILD-TYPE 242  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNJ2 MUTATED     15    0
  SYNJ2 WILD-TYPE  242   18
   clus
vv  SYNJ2 MUTATED SYNJ2 WILD-TYPE
  0            15             242
  1             0              18
[1] 2 2
[1] FALSE
D455V7, binary
                 cls
clus                0   1
  SYNJ2 MUTATED    10   6
  SYNJ2 WILD-TYPE 100 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNJ2 MUTATED     10    6
  SYNJ2 WILD-TYPE  100  173
        clus
vv       SYNJ2 MUTATED SYNJ2 WILD-TYPE
  FEMALE            10             100
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SYNJ2 MUTATED                                       1
  SYNJ2 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SYNJ2 MUTATED                                                        8
  SYNJ2 WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SYNJ2 MUTATED                                                                   4
  SYNJ2 WILD-TYPE                                                                36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SYNJ2 MUTATED                                                  2
  SYNJ2 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SYNJ2 MUTATED                                                          1
  SYNJ2 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SYNJ2 MUTATED                                                           0
  SYNJ2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SYNJ2 MUTATED                                          0
  SYNJ2 WILD-TYPE                                        3
D455V8, multiclass
                                                                   clus
vv                                                                  SYNJ2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  SYNJ2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D455V9, binary
                 cls
clus                0   1
  SYNJ2 MUTATED     0  16
  SYNJ2 WILD-TYPE   5 268
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNJ2 MUTATED      0   16
  SYNJ2 WILD-TYPE    5  268
     clus
vv    SYNJ2 MUTATED SYNJ2 WILD-TYPE
  NO              0               5
  YES            16             268
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SYNJ2 MUTATED    13   0   0   3
  SYNJ2 WILD-TYPE 214  10  10  21
D455V10, multiclass
    clus
vv   SYNJ2 MUTATED SYNJ2 WILD-TYPE
  R0            13             214
  R1             0              10
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D455V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SYNJ2 MUTATED       3                         1     8
  SYNJ2 WILD-TYPE    73                         3   160
D455V12, multiclass
                           clus
vv                          SYNJ2 MUTATED SYNJ2 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 8             160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(456) Variable = KIAA1324L MUTATION ANALYSIS
D456V1, survival
                     sevent
clus2                   0   1
  KIAA1324L MUTATED    14   4
  KIAA1324L WILD-TYPE 167  76
  KIAA1324L MUTATED KIAA1324L WILD-TYPE 
                 18                 243 
  KIAA1324L MUTATED KIAA1324L WILD-TYPE 
                  4                  76 
$`KIAA1324L MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8368 TCGA-BR-8680 TCGA-BR-8683 
        6.97         6.61        34.68         4.31        15.81         9.86 
TCGA-BR-A4PD TCGA-BR-A4QL TCGA-CD-8528 TCGA-CD-A487 TCGA-CG-4444 TCGA-CG-5728 
       20.65        11.57         0.10         9.34        47.05        65.10 
TCGA-D7-6528 TCGA-D7-A4YV TCGA-F1-6874 TCGA-HU-8602 TCGA-HU-A4GU TCGA-HU-A4GX 
       15.22         5.92        14.47        11.41         6.25        10.19 

$`KIAA1324L WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       30.90         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 
        7.53         0.49        11.54        16.44        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE 
       14.17         0.53         0.66        19.36        13.51        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         0.10         3.42        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        79.07         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 
       14.76         0.62         7.99        16.24        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  KIAA1324L MUTATED KIAA1324L WILD-TYPE 
                0.1                 0.0 
  KIAA1324L MUTATED KIAA1324L WILD-TYPE 
              65.10              105.07 
  KIAA1324L MUTATED KIAA1324L WILD-TYPE 
              10.80               12.76 
[1] "0.1 - 65.1 (10.8)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.5"
D456V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1324L MUTATED         1        0        4        0         1         5
  KIAA1324L WILD-TYPE       0        9       23       26        30        39
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1324L MUTATED           1          3          2          1        2
  KIAA1324L WILD-TYPE         2         46         34         23       22
D456V3, multiclass
            clus
vv           KIAA1324L MUTATED KIAA1324L WILD-TYPE
  STAGE I                    1                   0
  STAGE IA                   0                   9
  STAGE IB                   4                  23
  STAGE II                   0                  26
  STAGE IIA                  1                  30
  STAGE IIB                  5                  39
  STAGE III                  1                   2
  STAGE IIIA                 3                  46
  STAGE IIIB                 2                  34
  STAGE IIIC                 1                  23
  STAGE IV                   2                  22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  KIAA1324L MUTATED     2   6   6   7
  KIAA1324L WILD-TYPE   9  66 116  68
D456V4, multiclass
    clus
vv   KIAA1324L MUTATED KIAA1324L WILD-TYPE
  T1                 2                   9
  T2                 6                  66
  T3                 6                 116
  T4                 7                  68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  N0 N1 N2 N3
  KIAA1324L MUTATED    8  6  5  1
  KIAA1324L WILD-TYPE 85 75 45 52
D456V5, multiclass
    clus
vv   KIAA1324L MUTATED KIAA1324L WILD-TYPE
  N0                 8                  85
  N1                 6                  75
  N2                 5                  45
  N3                 1                  52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D456V6, binary
                     cls
clus                    0   1
  KIAA1324L MUTATED    17   2
  KIAA1324L WILD-TYPE 240  16
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIAA1324L MUTATED     17    2
  KIAA1324L WILD-TYPE  240   16
   clus
vv  KIAA1324L MUTATED KIAA1324L WILD-TYPE
  0                17                 240
  1                 2                  16
[1] 2 2
[1] FALSE
D456V7, binary
                     cls
clus                    0   1
  KIAA1324L MUTATED    13   8
  KIAA1324L WILD-TYPE  97 171
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIAA1324L MUTATED     13    8
  KIAA1324L WILD-TYPE   97  171
        clus
vv       KIAA1324L MUTATED KIAA1324L WILD-TYPE
  FEMALE                13                  97
  MALE                   8                 171
[1] 2 2
[1] FALSE
                     vv
clus                  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KIAA1324L MUTATED                                       6
  KIAA1324L WILD-TYPE                                    44
                     vv
clus                  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA1324L MUTATED                                                        9
  KIAA1324L WILD-TYPE                                                    126
                     vv
clus                  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA1324L MUTATED                                                                   2
  KIAA1324L WILD-TYPE                                                                38
                     vv
clus                  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KIAA1324L MUTATED                                                  4
  KIAA1324L WILD-TYPE                                               34
                     vv
clus                  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KIAA1324L MUTATED                                                          0
  KIAA1324L WILD-TYPE                                                       16
                     vv
clus                  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KIAA1324L MUTATED                                                           0
  KIAA1324L WILD-TYPE                                                         6
                     vv
clus                  STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KIAA1324L MUTATED                                          0
  KIAA1324L WILD-TYPE                                        3
D456V8, multiclass
                                                                   clus
vv                                                                  KIAA1324L MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          0
                                                                   clus
vv                                                                  KIAA1324L WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                              44
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                   34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                           16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                           6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                            3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D456V9, binary
                     cls
clus                    0   1
  KIAA1324L MUTATED     0  21
  KIAA1324L WILD-TYPE   5 263
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIAA1324L MUTATED      0   21
  KIAA1324L WILD-TYPE    5  263
     clus
vv    KIAA1324L MUTATED KIAA1324L WILD-TYPE
  NO                  0                   5
  YES                21                 263
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  KIAA1324L MUTATED    17   0   1   3
  KIAA1324L WILD-TYPE 210  10   9  21
D456V10, multiclass
    clus
vv   KIAA1324L MUTATED KIAA1324L WILD-TYPE
  R0                17                 210
  R1                 0                  10
  R2                 1                   9
  RX                 3                  21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D456V11, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA1324L MUTATED       7                         1    10
  KIAA1324L WILD-TYPE    69                         3   158
D456V12, multiclass
                           clus
vv                          KIAA1324L MUTATED KIAA1324L WILD-TYPE
  ASIAN                                     7                  69
  BLACK OR AFRICAN AMERICAN                 1                   3
  WHITE                                    10                 158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(457) Variable = GPR141 MUTATION ANALYSIS
D457V1, survival
                  sevent
clus2                0   1
  GPR141 MUTATED     5   4
  GPR141 WILD-TYPE 176  76
  GPR141 MUTATED GPR141 WILD-TYPE 
               9              252 
  GPR141 MUTATED GPR141 WILD-TYPE 
               4               76 
$`GPR141 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-7957 TCGA-BR-8363 TCGA-BR-8372 TCGA-D7-6525 
       26.70         6.97         9.07         0.26        19.17        13.35 
TCGA-D7-A4YY TCGA-F1-A448 TCGA-HU-A4GU 
       13.78        21.27         6.25 

$`GPR141 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         3.45        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       19.50        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
       20.55        18.84        18.54        18.61        17.85        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       15.16        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  GPR141 MUTATED GPR141 WILD-TYPE 
            0.26             0.00 
  GPR141 MUTATED GPR141 WILD-TYPE 
           26.70           105.07 
  GPR141 MUTATED GPR141 WILD-TYPE 
          13.350           12.605 
[1] "0.3 - 26.7 (13.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.6"
D457V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPR141 MUTATED         0        0        1        0         0         2
  GPR141 WILD-TYPE       1        9       26       26        31        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR141 MUTATED           0          2          2          1        1
  GPR141 WILD-TYPE         3         47         34         23       23
D457V3, multiclass
            clus
vv           GPR141 MUTATED GPR141 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               0               31
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              2               34
  STAGE IIIC              1               23
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR141 MUTATED     0   2   5   2
  GPR141 WILD-TYPE  11  70 117  73
D457V4, multiclass
    clus
vv   GPR141 MUTATED GPR141 WILD-TYPE
  T1              0               11
  T2              2               70
  T3              5              117
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  GPR141 MUTATED    2  2  1  4
  GPR141 WILD-TYPE 91 79 49 49
D457V5, multiclass
    clus
vv   GPR141 MUTATED GPR141 WILD-TYPE
  N0              2               91
  N1              2               79
  N2              1               49
  N3              4               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D457V6, binary
                  cls
clus                 0   1
  GPR141 MUTATED     7   1
  GPR141 WILD-TYPE 250  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR141 MUTATED      7    1
  GPR141 WILD-TYPE  250   17
   clus
vv  GPR141 MUTATED GPR141 WILD-TYPE
  0              7              250
  1              1               17
[1] 2 2
[1] FALSE
D457V7, binary
                  cls
clus                 0   1
  GPR141 MUTATED     3   6
  GPR141 WILD-TYPE 107 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR141 MUTATED      3    6
  GPR141 WILD-TYPE  107  173
        clus
vv       GPR141 MUTATED GPR141 WILD-TYPE
  FEMALE              3              107
  MALE                6              173
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GPR141 MUTATED                                       3
  GPR141 WILD-TYPE                                    47
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPR141 MUTATED                                                        4
  GPR141 WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPR141 MUTATED                                                                   1
  GPR141 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GPR141 MUTATED                                                  0
  GPR141 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GPR141 MUTATED                                                          1
  GPR141 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GPR141 MUTATED                                                           0
  GPR141 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GPR141 MUTATED                                          0
  GPR141 WILD-TYPE                                        3
D457V8, multiclass
                                                                   clus
vv                                                                  GPR141 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  GPR141 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D457V9, binary
                  cls
clus                 0   1
  GPR141 MUTATED     0   9
  GPR141 WILD-TYPE   5 275
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR141 MUTATED      0    9
  GPR141 WILD-TYPE    5  275
     clus
vv    GPR141 MUTATED GPR141 WILD-TYPE
  NO               0                5
  YES              9              275
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GPR141 MUTATED     8   0   0   1
  GPR141 WILD-TYPE 219  10  10  23
D457V10, multiclass
    clus
vv   GPR141 MUTATED GPR141 WILD-TYPE
  R0              8              219
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D457V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPR141 MUTATED       1                         0     8
  GPR141 WILD-TYPE    75                         4   160
D457V12, multiclass
                           clus
vv                          GPR141 MUTATED GPR141 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  8              160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(458) Variable = TLR4 MUTATION ANALYSIS
D458V1, survival
                sevent
clus2              0   1
  TLR4 MUTATED    12   7
  TLR4 WILD-TYPE 169  73
  TLR4 MUTATED TLR4 WILD-TYPE 
            19            242 
  TLR4 MUTATED TLR4 WILD-TYPE 
             7             73 
$`TLR4 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6706 TCGA-BR-7723 TCGA-BR-7851 
        6.97        34.68        15.95        18.05        28.73        12.43 
TCGA-BR-8297 TCGA-BR-8487 TCGA-BR-8690 TCGA-CD-8524 TCGA-CG-4466 TCGA-CG-4469 
        7.40         1.12        10.68         0.07        18.97         7.07 
TCGA-CG-5724 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6822 TCGA-F1-6875 TCGA-F1-A448 
       12.03        17.19        10.26        12.33        72.23        21.27 
TCGA-HU-A4H4 
       23.84 

$`TLR4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6455 TCGA-BR-6456 
       30.90         6.18         9.57         6.61        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       25.61        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       28.01        18.15        15.32         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         9.86        15.68         8.22        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00         9.01        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 
        1.02         0.99         6.02         0.99       105.07        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 
       18.54        18.61        17.85        13.35        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        10.55        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        7.99        16.24        14.47         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        19.36        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  TLR4 MUTATED TLR4 WILD-TYPE 
          0.07           0.00 
  TLR4 MUTATED TLR4 WILD-TYPE 
         72.23         105.07 
  TLR4 MUTATED TLR4 WILD-TYPE 
         12.43          12.64 
[1] "0.1 - 72.2 (12.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D458V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TLR4 MUTATED         0        1        3        2         3         2
  TLR4 WILD-TYPE       1        8       24       24        28        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TLR4 MUTATED           0          3          3          1        2
  TLR4 WILD-TYPE         3         46         33         23       22
D458V3, multiclass
            clus
vv           TLR4 MUTATED TLR4 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              3             24
  STAGE II              2             24
  STAGE IIA             3             28
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            3             46
  STAGE IIIB            3             33
  STAGE IIIC            1             23
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TLR4 MUTATED     0   7  11   2
  TLR4 WILD-TYPE  11  65 111  73
D458V4, multiclass
    clus
vv   TLR4 MUTATED TLR4 WILD-TYPE
  T1            0             11
  T2            7             65
  T3           11            111
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  TLR4 MUTATED    8  4  2  6
  TLR4 WILD-TYPE 85 77 48 47
D458V5, multiclass
    clus
vv   TLR4 MUTATED TLR4 WILD-TYPE
  N0            8             85
  N1            4             77
  N2            2             48
  N3            6             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D458V6, binary
                cls
clus               0   1
  TLR4 MUTATED    19   1
  TLR4 WILD-TYPE 238  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR4 MUTATED     19    1
  TLR4 WILD-TYPE  238   17
   clus
vv  TLR4 MUTATED TLR4 WILD-TYPE
  0           19            238
  1            1             17
[1] 2 2
[1] FALSE
D458V7, binary
                cls
clus               0   1
  TLR4 MUTATED     8  13
  TLR4 WILD-TYPE 102 166
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR4 MUTATED      8   13
  TLR4 WILD-TYPE  102  166
        clus
vv       TLR4 MUTATED TLR4 WILD-TYPE
  FEMALE            8            102
  MALE             13            166
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TLR4 MUTATED                                       2
  TLR4 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TLR4 MUTATED                                                       10
  TLR4 WILD-TYPE                                                    125
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TLR4 MUTATED                                                                   4
  TLR4 WILD-TYPE                                                                36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TLR4 MUTATED                                                  3
  TLR4 WILD-TYPE                                               35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TLR4 MUTATED                                                          1
  TLR4 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TLR4 MUTATED                                                           1
  TLR4 WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TLR4 MUTATED                                          0
  TLR4 WILD-TYPE                                        3
D458V8, multiclass
                                                                   clus
vv                                                                  TLR4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  TLR4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D458V9, binary
                cls
clus               0   1
  TLR4 MUTATED     0  21
  TLR4 WILD-TYPE   5 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR4 MUTATED      0   21
  TLR4 WILD-TYPE    5  263
     clus
vv    TLR4 MUTATED TLR4 WILD-TYPE
  NO             0              5
  YES           21            263
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TLR4 MUTATED    17   1   1   2
  TLR4 WILD-TYPE 210   9   9  22
D458V10, multiclass
    clus
vv   TLR4 MUTATED TLR4 WILD-TYPE
  R0           17            210
  R1            1              9
  R2            1              9
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D458V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TLR4 MUTATED       2                         1    15
  TLR4 WILD-TYPE    74                         3   153
D458V12, multiclass
                           clus
vv                          TLR4 MUTATED TLR4 WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                               15            153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(459) Variable = LYSMD3 MUTATION ANALYSIS
D459V1, survival
                  sevent
clus2                0   1
  LYSMD3 MUTATED     4   4
  LYSMD3 WILD-TYPE 177  76
  LYSMD3 MUTATED LYSMD3 WILD-TYPE 
               8              253 
  LYSMD3 MUTATED LYSMD3 WILD-TYPE 
               4               76 
$`LYSMD3 MUTATED`
TCGA-BR-8059 TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-A489 TCGA-CG-5726 
       14.43         0.26         1.12        15.81        11.31        28.96 
TCGA-HU-A4G8 TCGA-HU-A4H3 
       11.84        19.36 

$`LYSMD3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        19.50        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         3.42         9.34        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  LYSMD3 MUTATED LYSMD3 WILD-TYPE 
            0.26             0.00 
  LYSMD3 MUTATED LYSMD3 WILD-TYPE 
           28.96           105.07 
  LYSMD3 MUTATED LYSMD3 WILD-TYPE 
          13.135           12.620 
[1] "0.3 - 29.0 (13.1)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.7"
D459V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LYSMD3 MUTATED         0        1        1        1         2         1
  LYSMD3 WILD-TYPE       1        8       26       25        29        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LYSMD3 MUTATED           1          1          0          1        1
  LYSMD3 WILD-TYPE         2         48         36         23       23
D459V3, multiclass
            clus
vv           LYSMD3 MUTATED LYSMD3 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                1               26
  STAGE II                1               25
  STAGE IIA               2               29
  STAGE IIB               1               43
  STAGE III               1                2
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LYSMD3 MUTATED     1   2   3   4
  LYSMD3 WILD-TYPE  10  70 119  71
D459V4, multiclass
    clus
vv   LYSMD3 MUTATED LYSMD3 WILD-TYPE
  T1              1               10
  T2              2               70
  T3              3              119
  T4              4               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  LYSMD3 MUTATED    5  3  1  1
  LYSMD3 WILD-TYPE 88 78 49 52
D459V5, multiclass
    clus
vv   LYSMD3 MUTATED LYSMD3 WILD-TYPE
  N0              5               88
  N1              3               78
  N2              1               49
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D459V6, binary
                  cls
clus                 0   1
  LYSMD3 MUTATED     9   1
  LYSMD3 WILD-TYPE 248  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LYSMD3 MUTATED      9    1
  LYSMD3 WILD-TYPE  248   17
   clus
vv  LYSMD3 MUTATED LYSMD3 WILD-TYPE
  0              9              248
  1              1               17
[1] 2 2
[1] FALSE
D459V7, binary
                  cls
clus                 0   1
  LYSMD3 MUTATED     5   5
  LYSMD3 WILD-TYPE 105 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LYSMD3 MUTATED      5    5
  LYSMD3 WILD-TYPE  105  174
        clus
vv       LYSMD3 MUTATED LYSMD3 WILD-TYPE
  FEMALE              5              105
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  LYSMD3 MUTATED                                       3
  LYSMD3 WILD-TYPE                                    47
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LYSMD3 MUTATED                                                        3
  LYSMD3 WILD-TYPE                                                    132
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LYSMD3 MUTATED                                                                   2
  LYSMD3 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  LYSMD3 MUTATED                                                  1
  LYSMD3 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  LYSMD3 MUTATED                                                          1
  LYSMD3 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  LYSMD3 MUTATED                                                           0
  LYSMD3 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  LYSMD3 MUTATED                                          0
  LYSMD3 WILD-TYPE                                        3
D459V8, multiclass
                                                                   clus
vv                                                                  LYSMD3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  LYSMD3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D459V9, binary
                  cls
clus                 0   1
  LYSMD3 MUTATED     1   9
  LYSMD3 WILD-TYPE   4 275
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LYSMD3 MUTATED      1    9
  LYSMD3 WILD-TYPE    4  275
     clus
vv    LYSMD3 MUTATED LYSMD3 WILD-TYPE
  NO               1                4
  YES              9              275
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  LYSMD3 MUTATED     7   0   0   1
  LYSMD3 WILD-TYPE 220  10  10  23
D459V10, multiclass
    clus
vv   LYSMD3 MUTATED LYSMD3 WILD-TYPE
  R0              7              220
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D459V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LYSMD3 MUTATED       4                         0     4
  LYSMD3 WILD-TYPE    72                         4   164
D459V12, multiclass
                           clus
vv                          LYSMD3 MUTATED LYSMD3 WILD-TYPE
  ASIAN                                  4               72
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(460) Variable = LIAS MUTATION ANALYSIS
D460V1, survival
                sevent
clus2              0   1
  LIAS MUTATED     4   0
  LIAS WILD-TYPE 177  80
  LIAS MUTATED LIAS WILD-TYPE 
             4            257 
  LIAS MUTATED LIAS WILD-TYPE 
             0             80 
$`LIAS MUTATED`
TCGA-BR-6452 TCGA-BR-6566 TCGA-CD-A4MJ TCGA-HU-A4G8 
       34.68        32.78        12.62        11.84 

$`LIAS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 
       12.43        11.61         6.58        12.20         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  LIAS MUTATED LIAS WILD-TYPE 
         11.84           0.00 
  LIAS MUTATED LIAS WILD-TYPE 
         34.68         105.07 
  LIAS MUTATED LIAS WILD-TYPE 
         22.70          12.59 
[1] "11.8 - 34.7 (22.7)" "0.0 - 105.1 (12.6)"
[1] "hr="     "2.6e+07"
D460V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LIAS MUTATED         1        0        1        0         2         1
  LIAS WILD-TYPE       0        9       26       26        29        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LIAS MUTATED           0          0          0          0        0
  LIAS WILD-TYPE         3         49         36         24       24
D460V3, multiclass
            clus
vv           LIAS MUTATED LIAS WILD-TYPE
  STAGE I               1              0
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             2             29
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LIAS MUTATED     1   1   3   0
  LIAS WILD-TYPE  10  71 119  75
D460V4, multiclass
    clus
vv   LIAS MUTATED LIAS WILD-TYPE
  T1            1             10
  T2            1             71
  T3            3            119
  T4            0             75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  LIAS MUTATED    3  2  0  0
  LIAS WILD-TYPE 90 79 50 53
D460V5, multiclass
    clus
vv   LIAS MUTATED LIAS WILD-TYPE
  N0            3             90
  N1            2             79
  N2            0             50
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D460V6, binary
                cls
clus               0   1
  LIAS MUTATED     4   0
  LIAS WILD-TYPE 253  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIAS MUTATED      4    0
  LIAS WILD-TYPE  253   18
   clus
vv  LIAS MUTATED LIAS WILD-TYPE
  0            4            253
  1            0             18
[1] 2 2
[1] FALSE
D460V7, binary
                cls
clus               0   1
  LIAS MUTATED     3   2
  LIAS WILD-TYPE 107 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIAS MUTATED      3    2
  LIAS WILD-TYPE  107  177
        clus
vv       LIAS MUTATED LIAS WILD-TYPE
  FEMALE            3            107
  MALE              2            177
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  LIAS MUTATED                                       1
  LIAS WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LIAS MUTATED                                                        4
  LIAS WILD-TYPE                                                    131
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LIAS MUTATED                                                                   0
  LIAS WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  LIAS MUTATED                                                  0
  LIAS WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  LIAS MUTATED                                                          0
  LIAS WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  LIAS MUTATED                                                           0
  LIAS WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  LIAS MUTATED                                          0
  LIAS WILD-TYPE                                        3
D460V8, multiclass
                                                                   clus
vv                                                                  LIAS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  LIAS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D460V9, binary
                cls
clus               0   1
  LIAS MUTATED     0   5
  LIAS WILD-TYPE   5 279
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIAS MUTATED      0    5
  LIAS WILD-TYPE    5  279
     clus
vv    LIAS MUTATED LIAS WILD-TYPE
  NO             0              5
  YES            5            279
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LIAS MUTATED     3   0   0   0
  LIAS WILD-TYPE 224  10  10  24
D460V10, multiclass
    clus
vv   LIAS MUTATED LIAS WILD-TYPE
  R0            3            224
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D460V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LIAS MUTATED       2                         1     2
  LIAS WILD-TYPE    74                         3   166
D460V12, multiclass
                           clus
vv                          LIAS MUTATED LIAS WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                                2            166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(461) Variable = MAP7D3 MUTATION ANALYSIS
D461V1, survival
                  sevent
clus2                0   1
  MAP7D3 MUTATED    11   1
  MAP7D3 WILD-TYPE 170  79
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
              12              249 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
               1               79 
$`MAP7D3 MUTATED`
TCGA-BR-6566 TCGA-BR-8077 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-8591 
       32.78         0.69        20.55         0.26         1.12        13.45 
TCGA-BR-8680 TCGA-BR-A4IY TCGA-BR-A4QL TCGA-CD-A4MJ TCGA-HU-8602 TCGA-HU-A4GX 
       15.81        12.89        11.57        12.62        11.41        10.19 

$`MAP7D3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 
       17.49        14.43        12.26         9.60         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       19.50        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        15.81         9.34         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
            0.26             0.00 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
           32.78           105.07 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
          12.095           12.660 
[1] "0.3 - 32.8 (12.1)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "3.3"
D461V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAP7D3 MUTATED         0        0        3        0         2         3
  MAP7D3 WILD-TYPE       1        9       24       26        29        41
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP7D3 MUTATED           0          1          2          2        2
  MAP7D3 WILD-TYPE         3         48         34         22       22
D461V3, multiclass
            clus
vv           MAP7D3 MUTATED MAP7D3 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                3               24
  STAGE II                0               26
  STAGE IIA               2               29
  STAGE IIB               3               41
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              2               34
  STAGE IIIC              2               22
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAP7D3 MUTATED     0   3   3   9
  MAP7D3 WILD-TYPE  11  69 119  66
D461V4, multiclass
    clus
vv   MAP7D3 MUTATED MAP7D3 WILD-TYPE
  T1              0               11
  T2              3               69
  T3              3              119
  T4              9               66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  MAP7D3 MUTATED    9  1  3  2
  MAP7D3 WILD-TYPE 84 80 47 51
D461V5, multiclass
    clus
vv   MAP7D3 MUTATED MAP7D3 WILD-TYPE
  N0              9               84
  N1              1               80
  N2              3               47
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D461V6, binary
                  cls
clus                 0   1
  MAP7D3 MUTATED    15   1
  MAP7D3 WILD-TYPE 242  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED     15    1
  MAP7D3 WILD-TYPE  242   17
   clus
vv  MAP7D3 MUTATED MAP7D3 WILD-TYPE
  0             15              242
  1              1               17
[1] 2 2
[1] FALSE
D461V7, binary
                  cls
clus                 0   1
  MAP7D3 MUTATED    11   5
  MAP7D3 WILD-TYPE  99 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED     11    5
  MAP7D3 WILD-TYPE   99  174
        clus
vv       MAP7D3 MUTATED MAP7D3 WILD-TYPE
  FEMALE             11               99
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MAP7D3 MUTATED                                       2
  MAP7D3 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MAP7D3 MUTATED                                                       11
  MAP7D3 WILD-TYPE                                                    124
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MAP7D3 MUTATED                                                                   2
  MAP7D3 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MAP7D3 MUTATED                                                  1
  MAP7D3 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MAP7D3 MUTATED                                                          0
  MAP7D3 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MAP7D3 MUTATED                                                           0
  MAP7D3 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MAP7D3 MUTATED                                          0
  MAP7D3 WILD-TYPE                                        3
D461V8, multiclass
                                                                   clus
vv                                                                  MAP7D3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  MAP7D3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D461V9, binary
                  cls
clus                 0   1
  MAP7D3 MUTATED     0  16
  MAP7D3 WILD-TYPE   5 268
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED      0   16
  MAP7D3 WILD-TYPE    5  268
     clus
vv    MAP7D3 MUTATED MAP7D3 WILD-TYPE
  NO               0                5
  YES             16              268
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MAP7D3 MUTATED    12   0   0   3
  MAP7D3 WILD-TYPE 215  10  10  21
D461V10, multiclass
    clus
vv   MAP7D3 MUTATED MAP7D3 WILD-TYPE
  R0             12              215
  R1              0               10
  R2              0               10
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D461V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAP7D3 MUTATED       5                         0    10
  MAP7D3 WILD-TYPE    71                         4   158
D461V12, multiclass
                           clus
vv                          MAP7D3 MUTATED MAP7D3 WILD-TYPE
  ASIAN                                  5               71
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                 10              158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(462) Variable = ERN2 MUTATION ANALYSIS
D462V1, survival
                sevent
clus2              0   1
  ERN2 MUTATED     6   2
  ERN2 WILD-TYPE 175  78
  ERN2 MUTATED ERN2 WILD-TYPE 
             8            253 
  ERN2 MUTATED ERN2 WILD-TYPE 
             2             78 
$`ERN2 MUTATED`
TCGA-B7-5816 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-A4MI TCGA-CG-5721 TCGA-CG-5732 
       26.70        13.45        11.57         0.10         6.02        69.04 
TCGA-F1-A448 TCGA-HU-8243 
       21.27         5.92 

$`ERN2 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 
       12.03        28.96        79.07        65.10         4.01        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        72.23         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.52        26.47        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  ERN2 MUTATED ERN2 WILD-TYPE 
           0.1            0.0 
  ERN2 MUTATED ERN2 WILD-TYPE 
         69.04         105.07 
  ERN2 MUTATED ERN2 WILD-TYPE 
         12.51          12.62 
[1] "0.1 - 69.0 (12.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.6"
D462V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ERN2 MUTATED         0        0        1        0         0         1
  ERN2 WILD-TYPE       1        9       26       26        31        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ERN2 MUTATED           0          0          3          2        2
  ERN2 WILD-TYPE         3         49         33         22       22
D462V3, multiclass
            clus
vv           ERN2 MUTATED ERN2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             0             31
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            3             33
  STAGE IIIC            2             22
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ERN2 MUTATED     0   2   3   4
  ERN2 WILD-TYPE  11  70 119  71
D462V4, multiclass
    clus
vv   ERN2 MUTATED ERN2 WILD-TYPE
  T1            0             11
  T2            2             70
  T3            3            119
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  ERN2 MUTATED    2  4  0  5
  ERN2 WILD-TYPE 91 77 50 48
D462V5, multiclass
    clus
vv   ERN2 MUTATED ERN2 WILD-TYPE
  N0            2             91
  N1            4             77
  N2            0             50
  N3            5             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D462V6, binary
                cls
clus               0   1
  ERN2 MUTATED    11   0
  ERN2 WILD-TYPE 246  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN2 MUTATED     11    0
  ERN2 WILD-TYPE  246   18
   clus
vv  ERN2 MUTATED ERN2 WILD-TYPE
  0           11            246
  1            0             18
[1] 2 2
[1] FALSE
D462V7, binary
                cls
clus               0   1
  ERN2 MUTATED     3   8
  ERN2 WILD-TYPE 107 171
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN2 MUTATED      3    8
  ERN2 WILD-TYPE  107  171
        clus
vv       ERN2 MUTATED ERN2 WILD-TYPE
  FEMALE            3            107
  MALE              8            171
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ERN2 MUTATED                                       1
  ERN2 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ERN2 MUTATED                                                        5
  ERN2 WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ERN2 MUTATED                                                                   3
  ERN2 WILD-TYPE                                                                37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ERN2 MUTATED                                                  1
  ERN2 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ERN2 MUTATED                                                          1
  ERN2 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ERN2 MUTATED                                                           0
  ERN2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ERN2 MUTATED                                          0
  ERN2 WILD-TYPE                                        3
D462V8, multiclass
                                                                   clus
vv                                                                  ERN2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  ERN2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D462V9, binary
                cls
clus               0   1
  ERN2 MUTATED     0  11
  ERN2 WILD-TYPE   5 273
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN2 MUTATED      0   11
  ERN2 WILD-TYPE    5  273
     clus
vv    ERN2 MUTATED ERN2 WILD-TYPE
  NO             0              5
  YES           11            273
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ERN2 MUTATED     8   0   0   2
  ERN2 WILD-TYPE 219  10  10  22
D462V10, multiclass
    clus
vv   ERN2 MUTATED ERN2 WILD-TYPE
  R0            8            219
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D462V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERN2 MUTATED       2                         0     6
  ERN2 WILD-TYPE    74                         4   162
D462V12, multiclass
                           clus
vv                          ERN2 MUTATED ERN2 WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                6            162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(463) Variable = DSTN MUTATION ANALYSIS
D463V1, survival
                sevent
clus2              0   1
  DSTN MUTATED     3   1
  DSTN WILD-TYPE 178  79
  DSTN MUTATED DSTN WILD-TYPE 
             4            257 
  DSTN MUTATED DSTN WILD-TYPE 
             1             79 
$`DSTN MUTATED`
TCGA-BR-A4QL TCGA-CG-5721 TCGA-CG-5733 TCGA-FP-A4BE 
       11.57         6.02        21.07        11.08 

$`DSTN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
        5.03        13.58         0.56         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  DSTN MUTATED DSTN WILD-TYPE 
          6.02           0.00 
  DSTN MUTATED DSTN WILD-TYPE 
         21.07         105.07 
  DSTN MUTATED DSTN WILD-TYPE 
        11.325         12.660 
[1] "6.0 - 21.1 (11.3)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1"  
D463V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DSTN MUTATED         0        0        0        0         1         0
  DSTN WILD-TYPE       1        9       27       26        30        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DSTN MUTATED           0          2          1          0        1
  DSTN WILD-TYPE         3         47         35         24       23
D463V3, multiclass
            clus
vv           DSTN MUTATED DSTN WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              0             26
  STAGE IIA             1             30
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            1             35
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DSTN MUTATED     0   1   2   2
  DSTN WILD-TYPE  11  71 120  73
D463V4, multiclass
    clus
vv   DSTN MUTATED DSTN WILD-TYPE
  T1            0             11
  T2            1             71
  T3            2            120
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  DSTN MUTATED    2  1  1  1
  DSTN WILD-TYPE 91 80 49 52
D463V5, multiclass
    clus
vv   DSTN MUTATED DSTN WILD-TYPE
  N0            2             91
  N1            1             80
  N2            1             49
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D463V6, binary
                cls
clus               0   1
  DSTN MUTATED     5   0
  DSTN WILD-TYPE 252  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSTN MUTATED      5    0
  DSTN WILD-TYPE  252   18
   clus
vv  DSTN MUTATED DSTN WILD-TYPE
  0            5            252
  1            0             18
[1] 2 2
[1] FALSE
D463V7, binary
                cls
clus               0   1
  DSTN MUTATED     3   2
  DSTN WILD-TYPE 107 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSTN MUTATED      3    2
  DSTN WILD-TYPE  107  177
        clus
vv       DSTN MUTATED DSTN WILD-TYPE
  FEMALE            3            107
  MALE              2            177
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DSTN MUTATED                                       0
  DSTN WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DSTN MUTATED                                                        3
  DSTN WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DSTN MUTATED                                                                   2
  DSTN WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DSTN MUTATED                                                  0
  DSTN WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DSTN MUTATED                                                          0
  DSTN WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DSTN MUTATED                                                           0
  DSTN WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DSTN MUTATED                                          0
  DSTN WILD-TYPE                                        3
D463V8, multiclass
                                                                   clus
vv                                                                  DSTN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  DSTN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D463V9, binary
                cls
clus               0   1
  DSTN MUTATED     0   5
  DSTN WILD-TYPE   5 279
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSTN MUTATED      0    5
  DSTN WILD-TYPE    5  279
     clus
vv    DSTN MUTATED DSTN WILD-TYPE
  NO             0              5
  YES            5            279
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DSTN MUTATED     4   0   0   1
  DSTN WILD-TYPE 223  10  10  23
D463V10, multiclass
    clus
vv   DSTN MUTATED DSTN WILD-TYPE
  R0            4            223
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D463V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DSTN MUTATED       0                         1     2
  DSTN WILD-TYPE    76                         3   166
D463V12, multiclass
                           clus
vv                          DSTN MUTATED DSTN WILD-TYPE
  ASIAN                                0             76
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                                2            166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(464) Variable = PTPDC1 MUTATION ANALYSIS
D464V1, survival
                  sevent
clus2                0   1
  PTPDC1 MUTATED     4   3
  PTPDC1 WILD-TYPE 177  77
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
               7              254 
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
               3               77 
$`PTPDC1 MUTATED`
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6706 TCGA-BR-6802 TCGA-EQ-A4SO TCGA-HU-A4GH 
        6.61        34.68        18.05        30.90        16.24        11.77 
TCGA-IN-7808 
        3.45 

$`PTPDC1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
       18.35        30.90         6.18         9.57        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       32.78        25.61        19.89         8.98        21.11        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
       12.30         9.67         8.88        27.42        21.21        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
            3.45             0.00 
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
           34.68           105.07 
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
          16.240           12.605 
[1] "3.5 - 34.7 (16.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D464V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTPDC1 MUTATED         1        1        0        0         1         0
  PTPDC1 WILD-TYPE       0        8       27       26        30        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPDC1 MUTATED           2          2          1          0        0
  PTPDC1 WILD-TYPE         1         47         35         24       24
D464V3, multiclass
            clus
vv           PTPDC1 MUTATED PTPDC1 WILD-TYPE
  STAGE I                 1                0
  STAGE IA                1                8
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               0               44
  STAGE III               2                1
  STAGE IIIA              2               47
  STAGE IIIB              1               35
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PTPDC1 MUTATED     2   1   4   1
  PTPDC1 WILD-TYPE   9  71 118  74
D464V4, multiclass
    clus
vv   PTPDC1 MUTATED PTPDC1 WILD-TYPE
  T1              2                9
  T2              1               71
  T3              4              118
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  PTPDC1 MUTATED    2  4  1  1
  PTPDC1 WILD-TYPE 91 77 49 52
D464V5, multiclass
    clus
vv   PTPDC1 MUTATED PTPDC1 WILD-TYPE
  N0              2               91
  N1              4               77
  N2              1               49
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D464V6, binary
                  cls
clus                 0   1
  PTPDC1 MUTATED     5   1
  PTPDC1 WILD-TYPE 252  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPDC1 MUTATED      5    1
  PTPDC1 WILD-TYPE  252   17
   clus
vv  PTPDC1 MUTATED PTPDC1 WILD-TYPE
  0              5              252
  1              1               17
[1] 2 2
[1] FALSE
D464V7, binary
                  cls
clus                 0   1
  PTPDC1 MUTATED     2   6
  PTPDC1 WILD-TYPE 108 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPDC1 MUTATED      2    6
  PTPDC1 WILD-TYPE  108  173
        clus
vv       PTPDC1 MUTATED PTPDC1 WILD-TYPE
  FEMALE              2              108
  MALE                6              173
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PTPDC1 MUTATED                                       1
  PTPDC1 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PTPDC1 MUTATED                                                        6
  PTPDC1 WILD-TYPE                                                    129
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PTPDC1 MUTATED                                                                   0
  PTPDC1 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PTPDC1 MUTATED                                                  1
  PTPDC1 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PTPDC1 MUTATED                                                          0
  PTPDC1 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PTPDC1 MUTATED                                                           0
  PTPDC1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PTPDC1 MUTATED                                          0
  PTPDC1 WILD-TYPE                                        3
D464V8, multiclass
                                                                   clus
vv                                                                  PTPDC1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  PTPDC1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D464V9, binary
                  cls
clus                 0   1
  PTPDC1 MUTATED     0   8
  PTPDC1 WILD-TYPE   5 276
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPDC1 MUTATED      0    8
  PTPDC1 WILD-TYPE    5  276
     clus
vv    PTPDC1 MUTATED PTPDC1 WILD-TYPE
  NO               0                5
  YES              8              276
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PTPDC1 MUTATED     6   0   0   1
  PTPDC1 WILD-TYPE 221  10  10  23
D464V10, multiclass
    clus
vv   PTPDC1 MUTATED PTPDC1 WILD-TYPE
  R0              6              221
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D464V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTPDC1 MUTATED       1                         1     6
  PTPDC1 WILD-TYPE    75                         3   162
D464V12, multiclass
                           clus
vv                          PTPDC1 MUTATED PTPDC1 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(465) Variable = FYB MUTATION ANALYSIS
D465V1, survival
               sevent
clus2             0   1
  FYB MUTATED     8   1
  FYB WILD-TYPE 173  79
  FYB MUTATED FYB WILD-TYPE 
            9           252 
  FYB MUTATED FYB WILD-TYPE 
            1            79 
$`FYB MUTATED`
TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-7703 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8680 
       34.68        13.87        24.76        19.50         1.12        15.81 
TCGA-D7-6526 TCGA-HU-8602 TCGA-HU-A4H3 
       17.19        11.41        19.36 

$`FYB WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 
       30.90        31.20        32.94        12.82         9.21        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       18.84        18.54        18.61        17.85        13.35        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        5.52        26.47         5.92        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  FYB MUTATED FYB WILD-TYPE 
         1.12          0.00 
  FYB MUTATED FYB WILD-TYPE 
        34.68        105.07 
  FYB MUTATED FYB WILD-TYPE 
       17.190        12.495 
[1] "1.1 - 34.7 (17.2)"  "0.0 - 105.1 (12.5)"
[1] "hr=" "3.6"
D465V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FYB MUTATED         0        1        0        0         2         2
  FYB WILD-TYPE       1        8       27       26        29        42
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FYB MUTATED           0          1          0          2        1
  FYB WILD-TYPE         3         48         36         22       23
D465V3, multiclass
            clus
vv           FYB MUTATED FYB WILD-TYPE
  STAGE I              0             1
  STAGE IA             1             8
  STAGE IB             0            27
  STAGE II             0            26
  STAGE IIA            2            29
  STAGE IIB            2            42
  STAGE III            0             3
  STAGE IIIA           1            48
  STAGE IIIB           0            36
  STAGE IIIC           2            22
  STAGE IV             1            23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  FYB MUTATED     2   0   4   4
  FYB WILD-TYPE   9  72 118  71
D465V4, multiclass
    clus
vv   FYB MUTATED FYB WILD-TYPE
  T1           2             9
  T2           0            72
  T3           4           118
  T4           4            71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  FYB MUTATED    4  2  3  1
  FYB WILD-TYPE 89 79 47 52
D465V5, multiclass
    clus
vv   FYB MUTATED FYB WILD-TYPE
  N0           4            89
  N1           2            79
  N2           3            47
  N3           1            52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D465V6, binary
               cls
clus              0   1
  FYB MUTATED    10   1
  FYB WILD-TYPE 247  17
[1] "tbl2"
               cls
clus            [,1] [,2]
  FYB MUTATED     10    1
  FYB WILD-TYPE  247   17
   clus
vv  FYB MUTATED FYB WILD-TYPE
  0          10           247
  1           1            17
[1] 2 2
[1] FALSE
D465V7, binary
               cls
clus              0   1
  FYB MUTATED     8   3
  FYB WILD-TYPE 102 176
[1] "tbl2"
               cls
clus            [,1] [,2]
  FYB MUTATED      8    3
  FYB WILD-TYPE  102  176
        clus
vv       FYB MUTATED FYB WILD-TYPE
  FEMALE           8           102
  MALE             3           176
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FYB MUTATED                                       2
  FYB WILD-TYPE                                    48
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FYB MUTATED                                                        6
  FYB WILD-TYPE                                                    129
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FYB MUTATED                                                                   0
  FYB WILD-TYPE                                                                40
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FYB MUTATED                                                  2
  FYB WILD-TYPE                                               36
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FYB MUTATED                                                          0
  FYB WILD-TYPE                                                       16
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FYB MUTATED                                                           1
  FYB WILD-TYPE                                                         5
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FYB MUTATED                                          0
  FYB WILD-TYPE                                        3
D465V8, multiclass
                                                                   clus
vv                                                                  FYB MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  FYB WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D465V9, binary
               cls
clus              0   1
  FYB MUTATED     0  11
  FYB WILD-TYPE   5 273
[1] "tbl2"
               cls
clus            [,1] [,2]
  FYB MUTATED      0   11
  FYB WILD-TYPE    5  273
     clus
vv    FYB MUTATED FYB WILD-TYPE
  NO            0             5
  YES          11           273
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  FYB MUTATED     9   0   0   2
  FYB WILD-TYPE 218  10  10  22
D465V10, multiclass
    clus
vv   FYB MUTATED FYB WILD-TYPE
  R0           9           218
  R1           0            10
  R2           0            10
  RX           2            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D465V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FYB MUTATED       3                         0     8
  FYB WILD-TYPE    73                         4   160
D465V12, multiclass
                           clus
vv                          FYB MUTATED FYB WILD-TYPE
  ASIAN                               3            73
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                               8           160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(466) Variable = NDST2 MUTATION ANALYSIS
D466V1, survival
                 sevent
clus2               0   1
  NDST2 MUTATED     7   0
  NDST2 WILD-TYPE 174  80
  NDST2 MUTATED NDST2 WILD-TYPE 
              7             254 
  NDST2 MUTATED NDST2 WILD-TYPE 
              0              80 
$`NDST2 MUTATED`
TCGA-B7-5816 TCGA-BR-8372 TCGA-CG-4305 TCGA-CG-4449 TCGA-CG-5721 TCGA-HU-8602 
       26.70        19.17        15.95        19.07         6.02        11.41 
TCGA-HU-A4G8 
       11.84 

$`NDST2 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        47.05        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  NDST2 MUTATED NDST2 WILD-TYPE 
           6.02            0.00 
  NDST2 MUTATED NDST2 WILD-TYPE 
          26.70          105.07 
  NDST2 MUTATED NDST2 WILD-TYPE 
         15.950          12.605 
[1] "6.0 - 26.7 (15.9)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "2.6e+07"
D466V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NDST2 MUTATED         0        0        1        2         0         3
  NDST2 WILD-TYPE       1        9       26       24        31        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NDST2 MUTATED           0          0          0          1        1
  NDST2 WILD-TYPE         3         49         36         23       23
D466V3, multiclass
            clus
vv           NDST2 MUTATED NDST2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               2              24
  STAGE IIA              0              31
  STAGE IIB              3              41
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NDST2 MUTATED     0   3   1   4
  NDST2 WILD-TYPE  11  69 121  71
D466V4, multiclass
    clus
vv   NDST2 MUTATED NDST2 WILD-TYPE
  T1             0              11
  T2             3              69
  T3             1             121
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  NDST2 MUTATED    3  4  0  1
  NDST2 WILD-TYPE 90 77 50 52
D466V5, multiclass
    clus
vv   NDST2 MUTATED NDST2 WILD-TYPE
  N0             3              90
  N1             4              77
  N2             0              50
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D466V6, binary
                 cls
clus                0   1
  NDST2 MUTATED     8   0
  NDST2 WILD-TYPE 249  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDST2 MUTATED      8    0
  NDST2 WILD-TYPE  249   18
   clus
vv  NDST2 MUTATED NDST2 WILD-TYPE
  0             8             249
  1             0              18
[1] 2 2
[1] FALSE
D466V7, binary
                 cls
clus                0   1
  NDST2 MUTATED     3   5
  NDST2 WILD-TYPE 107 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDST2 MUTATED      3    5
  NDST2 WILD-TYPE  107  174
        clus
vv       NDST2 MUTATED NDST2 WILD-TYPE
  FEMALE             3             107
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NDST2 MUTATED                                       3
  NDST2 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NDST2 MUTATED                                                        2
  NDST2 WILD-TYPE                                                    133
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NDST2 MUTATED                                                                   2
  NDST2 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NDST2 MUTATED                                                  0
  NDST2 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NDST2 MUTATED                                                          1
  NDST2 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NDST2 MUTATED                                                           0
  NDST2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NDST2 MUTATED                                          0
  NDST2 WILD-TYPE                                        3
D466V8, multiclass
                                                                   clus
vv                                                                  NDST2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  NDST2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D466V9, binary
                 cls
clus                0   1
  NDST2 MUTATED     0   8
  NDST2 WILD-TYPE   5 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDST2 MUTATED      0    8
  NDST2 WILD-TYPE    5  276
     clus
vv    NDST2 MUTATED NDST2 WILD-TYPE
  NO              0               5
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NDST2 MUTATED     7   0   0   0
  NDST2 WILD-TYPE 220  10  10  24
D466V10, multiclass
    clus
vv   NDST2 MUTATED NDST2 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D466V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NDST2 MUTATED       2                         0     2
  NDST2 WILD-TYPE    74                         4   166
D466V12, multiclass
                           clus
vv                          NDST2 MUTATED NDST2 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 2             166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(467) Variable = TAF7L MUTATION ANALYSIS
D467V1, survival
                 sevent
clus2               0   1
  TAF7L MUTATED     6   1
  TAF7L WILD-TYPE 175  79
  TAF7L MUTATED TAF7L WILD-TYPE 
              7             254 
  TAF7L MUTATED TAF7L WILD-TYPE 
              1              79 
$`TAF7L MUTATED`
TCGA-BR-6852 TCGA-BR-8363 TCGA-BR-8382 TCGA-BR-8589 TCGA-CD-A4MJ TCGA-CG-5721 
       32.94         0.26        15.85        15.81        12.62         6.02 
TCGA-D7-6524 
       17.85 

$`TAF7L WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        30.90        31.20        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        19.50        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        12.79         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.84        18.54        18.61        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  TAF7L MUTATED TAF7L WILD-TYPE 
           0.26            0.00 
  TAF7L MUTATED TAF7L WILD-TYPE 
          32.94          105.07 
  TAF7L MUTATED TAF7L WILD-TYPE 
         15.810          12.575 
[1] "0.3 - 32.9 (15.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.3"
D467V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TAF7L MUTATED         0        0        2        1         1         0
  TAF7L WILD-TYPE       1        9       25       25        30        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TAF7L MUTATED           0          0          1          1        1
  TAF7L WILD-TYPE         3         49         35         23       23
D467V3, multiclass
            clus
vv           TAF7L MUTATED TAF7L WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TAF7L MUTATED     0   3   1   3
  TAF7L WILD-TYPE  11  69 121  72
D467V4, multiclass
    clus
vv   TAF7L MUTATED TAF7L WILD-TYPE
  T1             0              11
  T2             3              69
  T3             1             121
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  TAF7L MUTATED    3  3  0  1
  TAF7L WILD-TYPE 90 78 50 52
D467V5, multiclass
    clus
vv   TAF7L MUTATED TAF7L WILD-TYPE
  N0             3              90
  N1             3              78
  N2             0              50
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D467V6, binary
                 cls
clus                0   1
  TAF7L MUTATED     7   0
  TAF7L WILD-TYPE 250  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF7L MUTATED      7    0
  TAF7L WILD-TYPE  250   18
   clus
vv  TAF7L MUTATED TAF7L WILD-TYPE
  0             7             250
  1             0              18
[1] 2 2
[1] FALSE
D467V7, binary
                 cls
clus                0   1
  TAF7L MUTATED     3   4
  TAF7L WILD-TYPE 107 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF7L MUTATED      3    4
  TAF7L WILD-TYPE  107  175
        clus
vv       TAF7L MUTATED TAF7L WILD-TYPE
  FEMALE             3             107
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TAF7L MUTATED                                       1
  TAF7L WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TAF7L MUTATED                                                        5
  TAF7L WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TAF7L MUTATED                                                                   1
  TAF7L WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TAF7L MUTATED                                                  0
  TAF7L WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TAF7L MUTATED                                                          0
  TAF7L WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TAF7L MUTATED                                                           0
  TAF7L WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TAF7L MUTATED                                          0
  TAF7L WILD-TYPE                                        3
D467V8, multiclass
                                                                   clus
vv                                                                  TAF7L MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  TAF7L WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D467V9, binary
                 cls
clus                0   1
  TAF7L MUTATED     0   7
  TAF7L WILD-TYPE   5 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF7L MUTATED      0    7
  TAF7L WILD-TYPE    5  277
     clus
vv    TAF7L MUTATED TAF7L WILD-TYPE
  NO              0               5
  YES             7             277
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TAF7L MUTATED     5   1   0   0
  TAF7L WILD-TYPE 222   9  10  24
D467V10, multiclass
    clus
vv   TAF7L MUTATED TAF7L WILD-TYPE
  R0             5             222
  R1             1               9
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D467V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TAF7L MUTATED       1                         0     5
  TAF7L WILD-TYPE    75                         4   163
D467V12, multiclass
                           clus
vv                          TAF7L MUTATED TAF7L WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(468) Variable = SAP130 MUTATION ANALYSIS
D468V1, survival
                  sevent
clus2                0   1
  SAP130 MUTATED     8   0
  SAP130 WILD-TYPE 173  80
  SAP130 MUTATED SAP130 WILD-TYPE 
               8              253 
  SAP130 MUTATED SAP130 WILD-TYPE 
               0               80 
$`SAP130 MUTATED`
TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8487 TCGA-BR-8589 TCGA-CD-8536 
       34.68        24.76        23.93         1.12        15.81         0.10 
TCGA-HU-A4G8 TCGA-HU-A4H3 
       11.84        19.36 

$`SAP130 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 
        0.13         0.16         0.10         0.10         0.13         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  SAP130 MUTATED SAP130 WILD-TYPE 
             0.1              0.0 
  SAP130 MUTATED SAP130 WILD-TYPE 
           34.68           105.07 
  SAP130 MUTATED SAP130 WILD-TYPE 
          17.585           12.590 
[1] "0.1 - 34.7 (17.6)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "2.6e+07"
D468V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SAP130 MUTATED         0        1        1        1         2         1
  SAP130 WILD-TYPE       1        8       26       25        29        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SAP130 MUTATED           0          1          1          1        1
  SAP130 WILD-TYPE         3         48         35         23       23
D468V3, multiclass
            clus
vv           SAP130 MUTATED SAP130 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                1               26
  STAGE II                1               25
  STAGE IIA               2               29
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              1               23
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SAP130 MUTATED     1   1   4   4
  SAP130 WILD-TYPE  10  71 118  71
D468V4, multiclass
    clus
vv   SAP130 MUTATED SAP130 WILD-TYPE
  T1              1               10
  T2              1               71
  T3              4              118
  T4              4               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  SAP130 MUTATED    6  3  1  1
  SAP130 WILD-TYPE 87 78 49 52
D468V5, multiclass
    clus
vv   SAP130 MUTATED SAP130 WILD-TYPE
  N0              6               87
  N1              3               78
  N2              1               49
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D468V6, binary
                  cls
clus                 0   1
  SAP130 MUTATED    11   0
  SAP130 WILD-TYPE 246  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAP130 MUTATED     11    0
  SAP130 WILD-TYPE  246   18
   clus
vv  SAP130 MUTATED SAP130 WILD-TYPE
  0             11              246
  1              0               18
[1] 2 2
[1] FALSE
D468V7, binary
                  cls
clus                 0   1
  SAP130 MUTATED     8   3
  SAP130 WILD-TYPE 102 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAP130 MUTATED      8    3
  SAP130 WILD-TYPE  102  176
        clus
vv       SAP130 MUTATED SAP130 WILD-TYPE
  FEMALE              8              102
  MALE                3              176
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SAP130 MUTATED                                       2
  SAP130 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SAP130 MUTATED                                                        8
  SAP130 WILD-TYPE                                                    127
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SAP130 MUTATED                                                                   0
  SAP130 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SAP130 MUTATED                                                  0
  SAP130 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SAP130 MUTATED                                                          0
  SAP130 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SAP130 MUTATED                                                           1
  SAP130 WILD-TYPE                                                         5
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SAP130 MUTATED                                          0
  SAP130 WILD-TYPE                                        3
D468V8, multiclass
                                                                   clus
vv                                                                  SAP130 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  SAP130 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D468V9, binary
                  cls
clus                 0   1
  SAP130 MUTATED     0  11
  SAP130 WILD-TYPE   5 273
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAP130 MUTATED      0   11
  SAP130 WILD-TYPE    5  273
     clus
vv    SAP130 MUTATED SAP130 WILD-TYPE
  NO               0                5
  YES             11              273
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SAP130 MUTATED     7   0   0   3
  SAP130 WILD-TYPE 220  10  10  21
D468V10, multiclass
    clus
vv   SAP130 MUTATED SAP130 WILD-TYPE
  R0              7              220
  R1              0               10
  R2              0               10
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D468V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SAP130 MUTATED       3                         0     8
  SAP130 WILD-TYPE    73                         4   160
D468V12, multiclass
                           clus
vv                          SAP130 MUTATED SAP130 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  8              160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(469) Variable = SMARCB1 MUTATION ANALYSIS
D469V1, survival
                   sevent
clus2                 0   1
  SMARCB1 MUTATED     8   3
  SMARCB1 WILD-TYPE 173  77
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
               11               250 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                3                77 
$`SMARCB1 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7851 TCGA-BR-8368 TCGA-CD-A4MI 
        6.97        30.90        34.68        12.43         4.31         0.10 
TCGA-CG-4305 TCGA-HU-8245 TCGA-HU-A4GQ TCGA-HU-A4H3 TCGA-HU-A4H8 
       15.95        12.59         0.10        19.36         8.88 

$`SMARCB1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       15.42        28.01        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       12.20        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.52        26.47         5.92        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
       12.95        23.84        12.30         9.67        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
              0.1               0.0 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
            34.68            105.07 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
            12.43             12.71 
[1] "0.1 - 34.7 (12.4)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.1"
D469V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMARCB1 MUTATED         0        0        2        1         2         1
  SMARCB1 WILD-TYPE       1        9       25       25        29        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMARCB1 MUTATED           0          1          1          2        0
  SMARCB1 WILD-TYPE         3         48         35         22       24
D469V3, multiclass
            clus
vv           SMARCB1 MUTATED SMARCB1 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 2                25
  STAGE II                 1                25
  STAGE IIA                2                29
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               1                35
  STAGE IIIC               2                22
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SMARCB1 MUTATED     1   3   4   3
  SMARCB1 WILD-TYPE  10  69 118  72
D469V4, multiclass
    clus
vv   SMARCB1 MUTATED SMARCB1 WILD-TYPE
  T1               1                10
  T2               3                69
  T3               4               118
  T4               3                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  SMARCB1 MUTATED    4  4  1  1
  SMARCB1 WILD-TYPE 89 77 49 52
D469V5, multiclass
    clus
vv   SMARCB1 MUTATED SMARCB1 WILD-TYPE
  N0               4                89
  N1               4                77
  N2               1                49
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D469V6, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED    10   0
  SMARCB1 WILD-TYPE 247  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED     10    0
  SMARCB1 WILD-TYPE  247   18
   clus
vv  SMARCB1 MUTATED SMARCB1 WILD-TYPE
  0              10               247
  1               0                18
[1] 2 2
[1] FALSE
D469V7, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED     4   7
  SMARCB1 WILD-TYPE 106 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      4    7
  SMARCB1 WILD-TYPE  106  172
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  FEMALE               4               106
  MALE                 7               172
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SMARCB1 MUTATED                                       1
  SMARCB1 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SMARCB1 MUTATED                                                        6
  SMARCB1 WILD-TYPE                                                    129
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SMARCB1 MUTATED                                                                   1
  SMARCB1 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SMARCB1 MUTATED                                                  2
  SMARCB1 WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SMARCB1 MUTATED                                                          0
  SMARCB1 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SMARCB1 MUTATED                                                           1
  SMARCB1 WILD-TYPE                                                         5
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SMARCB1 MUTATED                                          0
  SMARCB1 WILD-TYPE                                        3
D469V8, multiclass
                                                                   clus
vv                                                                  SMARCB1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  SMARCB1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D469V9, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED     0  11
  SMARCB1 WILD-TYPE   5 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      0   11
  SMARCB1 WILD-TYPE    5  273
     clus
vv    SMARCB1 MUTATED SMARCB1 WILD-TYPE
  NO                0                 5
  YES              11               273
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SMARCB1 MUTATED     8   0   0   2
  SMARCB1 WILD-TYPE 219  10  10  22
D469V10, multiclass
    clus
vv   SMARCB1 MUTATED SMARCB1 WILD-TYPE
  R0               8               219
  R1               0                10
  R2               0                10
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D469V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMARCB1 MUTATED       5                         0     5
  SMARCB1 WILD-TYPE    71                         4   163
D469V12, multiclass
                           clus
vv                          SMARCB1 MUTATED SMARCB1 WILD-TYPE
  ASIAN                                   5                71
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   5               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(470) Variable = EPHA5 MUTATION ANALYSIS
D470V1, survival
                 sevent
clus2               0   1
  EPHA5 MUTATED    22   4
  EPHA5 WILD-TYPE 159  76
  EPHA5 MUTATED EPHA5 WILD-TYPE 
             26             235 
  EPHA5 MUTATED EPHA5 WILD-TYPE 
              4              76 
$`EPHA5 MUTATED`
TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-7851 TCGA-BR-8296 TCGA-BR-8372 
       11.70        34.68        24.76        12.43        15.58        19.17 
TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-5800 TCGA-CG-4305 TCGA-CG-4306 
       13.45        15.81        11.57        13.15        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-6526 
        7.99         4.01        47.05         6.02        65.10        17.19 
TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-A4GC 
        5.92        11.08        12.59        14.17        11.41         3.25 
TCGA-HU-A4GN TCGA-HU-A4H3 
       29.98        19.36 

$`EPHA5 WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 
       30.90        31.20        32.94        12.82         9.21        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       15.42        28.01        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       16.31         2.20         7.40         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       15.81         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 
       13.64         5.13         2.83         3.25        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
       27.02         8.05        54.08        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        28.96        79.07         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       26.47         5.92        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        11.84        24.20        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  EPHA5 MUTATED EPHA5 WILD-TYPE 
           1.02            0.00 
  EPHA5 MUTATED EPHA5 WILD-TYPE 
          65.10          105.07 
  EPHA5 MUTATED EPHA5 WILD-TYPE 
          13.30           12.56 
[1] "1.0 - 65.1 (13.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.5"
D470V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPHA5 MUTATED         0        1        3        2         4         3
  EPHA5 WILD-TYPE       1        8       24       24        27        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EPHA5 MUTATED           0          3          2          4        4
  EPHA5 WILD-TYPE         3         46         34         20       20
D470V3, multiclass
            clus
vv           EPHA5 MUTATED EPHA5 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               3              24
  STAGE II               2              24
  STAGE IIA              4              27
  STAGE IIB              3              41
  STAGE III              0               3
  STAGE IIIA             3              46
  STAGE IIIB             2              34
  STAGE IIIC             4              20
  STAGE IV               4              20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EPHA5 MUTATED     1   6  10   9
  EPHA5 WILD-TYPE  10  66 112  66
D470V4, multiclass
    clus
vv   EPHA5 MUTATED EPHA5 WILD-TYPE
  T1             1              10
  T2             6              66
  T3            10             112
  T4             9              66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  EPHA5 MUTATED   10  4  7  5
  EPHA5 WILD-TYPE 83 77 43 48
D470V5, multiclass
    clus
vv   EPHA5 MUTATED EPHA5 WILD-TYPE
  N0            10              83
  N1             4              77
  N2             7              43
  N3             5              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D470V6, binary
                 cls
clus                0   1
  EPHA5 MUTATED    23   3
  EPHA5 WILD-TYPE 234  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA5 MUTATED     23    3
  EPHA5 WILD-TYPE  234   15
   clus
vv  EPHA5 MUTATED EPHA5 WILD-TYPE
  0            23             234
  1             3              15
[1] 2 2
[1] FALSE
D470V7, binary
                 cls
clus                0   1
  EPHA5 MUTATED    10  16
  EPHA5 WILD-TYPE 100 163
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA5 MUTATED     10   16
  EPHA5 WILD-TYPE  100  163
        clus
vv       EPHA5 MUTATED EPHA5 WILD-TYPE
  FEMALE            10             100
  MALE              16             163
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  EPHA5 MUTATED                                       5
  EPHA5 WILD-TYPE                                    45
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EPHA5 MUTATED                                                        7
  EPHA5 WILD-TYPE                                                    128
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EPHA5 MUTATED                                                                   6
  EPHA5 WILD-TYPE                                                                34
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  EPHA5 MUTATED                                                  5
  EPHA5 WILD-TYPE                                               33
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  EPHA5 MUTATED                                                          0
  EPHA5 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  EPHA5 MUTATED                                                           3
  EPHA5 WILD-TYPE                                                         3
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  EPHA5 MUTATED                                          0
  EPHA5 WILD-TYPE                                        3
D470V8, multiclass
                                                                   clus
vv                                                                  EPHA5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  EPHA5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D470V9, binary
                 cls
clus                0   1
  EPHA5 MUTATED     0  26
  EPHA5 WILD-TYPE   5 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA5 MUTATED      0   26
  EPHA5 WILD-TYPE    5  258
     clus
vv    EPHA5 MUTATED EPHA5 WILD-TYPE
  NO              0               5
  YES            26             258
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EPHA5 MUTATED    24   0   2   0
  EPHA5 WILD-TYPE 203  10   8  24
D470V10, multiclass
    clus
vv   EPHA5 MUTATED EPHA5 WILD-TYPE
  R0            24             203
  R1             0              10
  R2             2               8
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D470V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EPHA5 MUTATED       8                         1    10
  EPHA5 WILD-TYPE    68                         3   158
D470V12, multiclass
                           clus
vv                          EPHA5 MUTATED EPHA5 WILD-TYPE
  ASIAN                                 8              68
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                10             158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(471) Variable = WAPAL MUTATION ANALYSIS
D471V1, survival
                 sevent
clus2               0   1
  WAPAL MUTATED    10   2
  WAPAL WILD-TYPE 171  78
  WAPAL MUTATED WAPAL WILD-TYPE 
             12             249 
  WAPAL MUTATED WAPAL WILD-TYPE 
              2              78 
$`WAPAL MUTATED`
TCGA-B7-5818 TCGA-BR-6457 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8361 TCGA-BR-8487 
       11.70        13.68        30.90        32.94        19.50         1.12 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5726 
        6.58         0.10        12.62        15.95         6.02        28.96 

$`WAPAL WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       31.20        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
       16.31         2.20        15.58         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 
        9.34        11.31        12.43        11.61        12.20        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  WAPAL MUTATED WAPAL WILD-TYPE 
            0.1             0.0 
  WAPAL MUTATED WAPAL WILD-TYPE 
          32.94          105.07 
  WAPAL MUTATED WAPAL WILD-TYPE 
          13.15           12.59 
[1] "0.1 - 32.9 (13.1)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.2"
D471V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WAPAL MUTATED         0        1        2        1         4         0
  WAPAL WILD-TYPE       1        8       25       25        27        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WAPAL MUTATED           0          1          1          1        1
  WAPAL WILD-TYPE         3         48         35         23       23
D471V3, multiclass
            clus
vv           WAPAL MUTATED WAPAL WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               2              25
  STAGE II               1              25
  STAGE IIA              4              27
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WAPAL MUTATED     1   3   7   2
  WAPAL WILD-TYPE  10  69 115  73
D471V4, multiclass
    clus
vv   WAPAL MUTATED WAPAL WILD-TYPE
  T1             1              10
  T2             3              69
  T3             7             115
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  WAPAL MUTATED    7  3  2  0
  WAPAL WILD-TYPE 86 78 48 53
D471V5, multiclass
    clus
vv   WAPAL MUTATED WAPAL WILD-TYPE
  N0             7              86
  N1             3              78
  N2             2              48
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D471V6, binary
                 cls
clus                0   1
  WAPAL MUTATED    12   0
  WAPAL WILD-TYPE 245  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WAPAL MUTATED     12    0
  WAPAL WILD-TYPE  245   18
   clus
vv  WAPAL MUTATED WAPAL WILD-TYPE
  0            12             245
  1             0              18
[1] 2 2
[1] FALSE
D471V7, binary
                 cls
clus                0   1
  WAPAL MUTATED     4   9
  WAPAL WILD-TYPE 106 170
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WAPAL MUTATED      4    9
  WAPAL WILD-TYPE  106  170
        clus
vv       WAPAL MUTATED WAPAL WILD-TYPE
  FEMALE             4             106
  MALE               9             170
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  WAPAL MUTATED                                       2
  WAPAL WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WAPAL MUTATED                                                        9
  WAPAL WILD-TYPE                                                    126
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WAPAL MUTATED                                                                   2
  WAPAL WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  WAPAL MUTATED                                                  0
  WAPAL WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  WAPAL MUTATED                                                          0
  WAPAL WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  WAPAL MUTATED                                                           0
  WAPAL WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  WAPAL MUTATED                                          0
  WAPAL WILD-TYPE                                        3
D471V8, multiclass
                                                                   clus
vv                                                                  WAPAL MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  WAPAL WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D471V9, binary
                 cls
clus                0   1
  WAPAL MUTATED     0  13
  WAPAL WILD-TYPE   5 271
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WAPAL MUTATED      0   13
  WAPAL WILD-TYPE    5  271
     clus
vv    WAPAL MUTATED WAPAL WILD-TYPE
  NO              0               5
  YES            13             271
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  WAPAL MUTATED     9   0   0   1
  WAPAL WILD-TYPE 218  10  10  23
D471V10, multiclass
    clus
vv   WAPAL MUTATED WAPAL WILD-TYPE
  R0             9             218
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D471V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WAPAL MUTATED       3                         0     7
  WAPAL WILD-TYPE    73                         4   161
D471V12, multiclass
                           clus
vv                          WAPAL MUTATED WAPAL WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 7             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(472) Variable = CEP120 MUTATION ANALYSIS
D472V1, survival
                  sevent
clus2                0   1
  CEP120 MUTATED     5   4
  CEP120 WILD-TYPE 176  76
  CEP120 MUTATED CEP120 WILD-TYPE 
               9              252 
  CEP120 MUTATED CEP120 WILD-TYPE 
               4               76 
$`CEP120 MUTATED`
TCGA-BR-4184 TCGA-BR-6705 TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-5721 
        6.97        25.61        12.26         1.12        15.81         6.02 
TCGA-CG-5726 TCGA-CG-5733 TCGA-HU-8602 
       28.96        21.07        11.41 

$`CEP120 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        32.78        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10         4.01        69.04         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       26.47         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  CEP120 MUTATED CEP120 WILD-TYPE 
            1.12             0.00 
  CEP120 MUTATED CEP120 WILD-TYPE 
           28.96           105.07 
  CEP120 MUTATED CEP120 WILD-TYPE 
           12.26            12.64 
[1] "1.1 - 29.0 (12.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D472V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CEP120 MUTATED         0        1        0        0         1         2
  CEP120 WILD-TYPE       1        8       27       26        30        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEP120 MUTATED           0          3          1          0        2
  CEP120 WILD-TYPE         3         46         35         24       22
D472V3, multiclass
            clus
vv           CEP120 MUTATED CEP120 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              3               46
  STAGE IIIB              1               35
  STAGE IIIC              0               24
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CEP120 MUTATED     1   1   3   5
  CEP120 WILD-TYPE  10  71 119  70
D472V4, multiclass
    clus
vv   CEP120 MUTATED CEP120 WILD-TYPE
  T1              1               10
  T2              1               71
  T3              3              119
  T4              5               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CEP120 MUTATED    5  2  2  1
  CEP120 WILD-TYPE 88 79 48 52
D472V5, multiclass
    clus
vv   CEP120 MUTATED CEP120 WILD-TYPE
  N0              5               88
  N1              2               79
  N2              2               48
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D472V6, binary
                  cls
clus                 0   1
  CEP120 MUTATED     8   1
  CEP120 WILD-TYPE 249  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP120 MUTATED      8    1
  CEP120 WILD-TYPE  249   17
   clus
vv  CEP120 MUTATED CEP120 WILD-TYPE
  0              8              249
  1              1               17
[1] 2 2
[1] FALSE
D472V7, binary
                  cls
clus                 0   1
  CEP120 MUTATED     6   4
  CEP120 WILD-TYPE 104 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP120 MUTATED      6    4
  CEP120 WILD-TYPE  104  175
        clus
vv       CEP120 MUTATED CEP120 WILD-TYPE
  FEMALE              6              104
  MALE                4              175
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CEP120 MUTATED                                       1
  CEP120 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CEP120 MUTATED                                                        5
  CEP120 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CEP120 MUTATED                                                                   3
  CEP120 WILD-TYPE                                                                37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CEP120 MUTATED                                                  1
  CEP120 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CEP120 MUTATED                                                          0
  CEP120 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CEP120 MUTATED                                                           0
  CEP120 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CEP120 MUTATED                                          0
  CEP120 WILD-TYPE                                        3
D472V8, multiclass
                                                                   clus
vv                                                                  CEP120 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  CEP120 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D472V9, binary
                  cls
clus                 0   1
  CEP120 MUTATED     0  10
  CEP120 WILD-TYPE   5 274
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP120 MUTATED      0   10
  CEP120 WILD-TYPE    5  274
     clus
vv    CEP120 MUTATED CEP120 WILD-TYPE
  NO               0                5
  YES             10              274
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CEP120 MUTATED     8   0   0   2
  CEP120 WILD-TYPE 219  10  10  22
D472V10, multiclass
    clus
vv   CEP120 MUTATED CEP120 WILD-TYPE
  R0              8              219
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D472V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CEP120 MUTATED       2                         0     5
  CEP120 WILD-TYPE    74                         4   163
D472V12, multiclass
                           clus
vv                          CEP120 MUTATED CEP120 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  5              163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(473) Variable = RDX MUTATION ANALYSIS
D473V1, survival
               sevent
clus2             0   1
  RDX MUTATED     5   1
  RDX WILD-TYPE 176  79
  RDX MUTATED RDX WILD-TYPE 
            6           255 
  RDX MUTATED RDX WILD-TYPE 
            1            79 
$`RDX MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-8382 TCGA-BR-8591 TCGA-CD-8535 TCGA-HU-A4GD 
       26.70         6.97        15.85        13.45         0.13        22.75 

$`RDX WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 
        0.10         0.13         0.16         0.10         0.10         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.59        12.30        11.84        24.20         3.25        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  RDX MUTATED RDX WILD-TYPE 
         0.13          0.00 
  RDX MUTATED RDX WILD-TYPE 
        26.70        105.07 
  RDX MUTATED RDX WILD-TYPE 
        14.65         12.59 
[1] "0.1 - 26.7 (14.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2"  
D473V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RDX MUTATED         0        0        0        0         0         2
  RDX WILD-TYPE       1        9       27       26        31        42
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RDX MUTATED           0          2          0          2        0
  RDX WILD-TYPE         3         47         36         22       24
D473V3, multiclass
            clus
vv           RDX MUTATED RDX WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             9
  STAGE IB             0            27
  STAGE II             0            26
  STAGE IIA            0            31
  STAGE IIB            2            42
  STAGE III            0             3
  STAGE IIIA           2            47
  STAGE IIIB           0            36
  STAGE IIIC           2            22
  STAGE IV             0            24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  RDX MUTATED     1   0   3   3
  RDX WILD-TYPE  10  72 119  72
D473V4, multiclass
    clus
vv   RDX MUTATED RDX WILD-TYPE
  T1           1            10
  T2           0            72
  T3           3           119
  T4           3            72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  RDX MUTATED    1  3  0  2
  RDX WILD-TYPE 92 78 50 51
D473V5, multiclass
    clus
vv   RDX MUTATED RDX WILD-TYPE
  N0           1            92
  N1           3            78
  N2           0            50
  N3           2            51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D473V6, binary
               cls
clus              0   1
  RDX MUTATED     6   0
  RDX WILD-TYPE 251  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  RDX MUTATED      6    0
  RDX WILD-TYPE  251   18
   clus
vv  RDX MUTATED RDX WILD-TYPE
  0           6           251
  1           0            18
[1] 2 2
[1] FALSE
D473V7, binary
               cls
clus              0   1
  RDX MUTATED     3   4
  RDX WILD-TYPE 107 175
[1] "tbl2"
               cls
clus            [,1] [,2]
  RDX MUTATED      3    4
  RDX WILD-TYPE  107  175
        clus
vv       RDX MUTATED RDX WILD-TYPE
  FEMALE           3           107
  MALE             4           175
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RDX MUTATED                                       1
  RDX WILD-TYPE                                    49
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RDX MUTATED                                                        5
  RDX WILD-TYPE                                                    130
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RDX MUTATED                                                                   0
  RDX WILD-TYPE                                                                40
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RDX MUTATED                                                  1
  RDX WILD-TYPE                                               37
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RDX MUTATED                                                          0
  RDX WILD-TYPE                                                       16
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RDX MUTATED                                                           0
  RDX WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RDX MUTATED                                          0
  RDX WILD-TYPE                                        3
D473V8, multiclass
                                                                   clus
vv                                                                  RDX MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  RDX WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D473V9, binary
               cls
clus              0   1
  RDX MUTATED     0   7
  RDX WILD-TYPE   5 277
[1] "tbl2"
               cls
clus            [,1] [,2]
  RDX MUTATED      0    7
  RDX WILD-TYPE    5  277
     clus
vv    RDX MUTATED RDX WILD-TYPE
  NO            0             5
  YES           7           277
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  RDX MUTATED     5   0   0   2
  RDX WILD-TYPE 222  10  10  22
D473V10, multiclass
    clus
vv   RDX MUTATED RDX WILD-TYPE
  R0           5           222
  R1           0            10
  R2           0            10
  RX           2            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D473V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RDX MUTATED       2                         0     5
  RDX WILD-TYPE    74                         4   163
D473V12, multiclass
                           clus
vv                          RDX MUTATED RDX WILD-TYPE
  ASIAN                               2            74
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                               5           163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(474) Variable = SPATA5L1 MUTATION ANALYSIS
D474V1, survival
                    sevent
clus2                  0   1
  SPATA5L1 MUTATED     6   1
  SPATA5L1 WILD-TYPE 175  79
  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE 
                 7                254 
  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE 
                 1                 79 
$`SPATA5L1 MUTATED`
TCGA-B7-5816 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8680 TCGA-CG-5728 TCGA-HU-A4GQ 
       26.70        32.94        12.26        15.81        65.10         0.10 
TCGA-HU-A4H0 
        2.10 

$`SPATA5L1 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        28.96        79.07         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE 
               0.1                0.0 
  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE 
             65.10             105.07 
  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE 
            15.810             12.605 
[1] "0.1 - 65.1 (15.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "3.4"
D474V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPATA5L1 MUTATED         0        0        1        0         1         2
  SPATA5L1 WILD-TYPE       1        9       26       26        30        42
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPATA5L1 MUTATED           0          0          0          2        1
  SPATA5L1 WILD-TYPE         3         49         36         22       23
D474V3, multiclass
            clus
vv           SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  1                 26
  STAGE II                  0                 26
  STAGE IIA                 1                 30
  STAGE IIB                 2                 42
  STAGE III                 0                  3
  STAGE IIIA                0                 49
  STAGE IIIB                0                 36
  STAGE IIIC                2                 22
  STAGE IV                  1                 23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SPATA5L1 MUTATED     0   1   1   5
  SPATA5L1 WILD-TYPE  11  71 121  70
D474V4, multiclass
    clus
vv   SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  T1                0                 11
  T2                1                 71
  T3                1                121
  T4                5                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  SPATA5L1 MUTATED    4  0  2  1
  SPATA5L1 WILD-TYPE 89 81 48 52
D474V5, multiclass
    clus
vv   SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  N0                4                 89
  N1                0                 81
  N2                2                 48
  N3                1                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D474V6, binary
                    cls
clus                   0   1
  SPATA5L1 MUTATED     6   1
  SPATA5L1 WILD-TYPE 251  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SPATA5L1 MUTATED      6    1
  SPATA5L1 WILD-TYPE  251   17
   clus
vv  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  0                6                251
  1                1                 17
[1] 2 2
[1] FALSE
D474V7, binary
                    cls
clus                   0   1
  SPATA5L1 MUTATED     4   3
  SPATA5L1 WILD-TYPE 106 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SPATA5L1 MUTATED      4    3
  SPATA5L1 WILD-TYPE  106  176
        clus
vv       SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  FEMALE                4                106
  MALE                  3                176
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SPATA5L1 MUTATED                                       2
  SPATA5L1 WILD-TYPE                                    48
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SPATA5L1 MUTATED                                                        2
  SPATA5L1 WILD-TYPE                                                    133
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SPATA5L1 MUTATED                                                                   1
  SPATA5L1 WILD-TYPE                                                                39
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SPATA5L1 MUTATED                                                  2
  SPATA5L1 WILD-TYPE                                               36
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SPATA5L1 MUTATED                                                          0
  SPATA5L1 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SPATA5L1 MUTATED                                                           0
  SPATA5L1 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SPATA5L1 MUTATED                                          0
  SPATA5L1 WILD-TYPE                                        3
D474V8, multiclass
                                                                   clus
vv                                                                  SPATA5L1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  SPATA5L1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D474V9, binary
                    cls
clus                   0   1
  SPATA5L1 MUTATED     0   7
  SPATA5L1 WILD-TYPE   5 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SPATA5L1 MUTATED      0    7
  SPATA5L1 WILD-TYPE    5  277
     clus
vv    SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  NO                 0                  5
  YES                7                277
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  SPATA5L1 MUTATED     7   0   0   0
  SPATA5L1 WILD-TYPE 220  10  10  24
D474V10, multiclass
    clus
vv   SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  R0                7                220
  R1                0                 10
  R2                0                 10
  RX                0                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D474V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SPATA5L1 MUTATED       3                         0     3
  SPATA5L1 WILD-TYPE    73                         4   165
D474V12, multiclass
                           clus
vv                          SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  ASIAN                                    3                 73
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    3                165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(475) Variable = TACC2 MUTATION ANALYSIS
D475V1, survival
                 sevent
clus2               0   1
  TACC2 MUTATED    16  10
  TACC2 WILD-TYPE 165  70
  TACC2 MUTATED TACC2 WILD-TYPE 
             26             235 
  TACC2 MUTATED TACC2 WILD-TYPE 
             10              70 
$`TACC2 MUTATED`
TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6706 
        6.97         7.43        30.90         6.61        34.68        18.05 
TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4QL 
       14.43        20.55         0.26         1.12        15.81        11.57 
TCGA-CG-4305 TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-6520 
       15.95         9.01         6.02       105.07        21.07        18.84 
TCGA-D7-6526 TCGA-FP-7829 TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GH 
       17.19        19.53        11.08        11.41        11.84        11.77 
TCGA-HU-A4GQ TCGA-HU-A4H5 
        0.10        12.30 

$`TACC2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4267 
       26.70        11.70         6.61         4.64        18.35         6.18 
TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        9.57        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 
       39.12        26.10         9.17        32.78        25.61        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       18.71        17.49         0.69        12.26         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        19.50        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
        0.10        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       47.05        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       20.55        18.54        18.61        17.85        13.35        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23        21.27         3.48        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 
       59.54         5.03        13.58         0.56         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       25.81        29.98         8.98         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        23.84         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  TACC2 MUTATED TACC2 WILD-TYPE 
            0.1             0.0 
  TACC2 MUTATED TACC2 WILD-TYPE 
         105.07           79.07 
  TACC2 MUTATED TACC2 WILD-TYPE 
          12.07           12.66 
[1] "0.1 - 105.1 (12.1)" "0.0 - 79.1 (12.7)" 
[1] "hr=" "1.1"
D475V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TACC2 MUTATED         0        1        3        3         3         4
  TACC2 WILD-TYPE       1        8       24       23        28        40
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TACC2 MUTATED           2          5          1          1        3
  TACC2 WILD-TYPE         1         44         35         23       21
D475V3, multiclass
            clus
vv           TACC2 MUTATED TACC2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               3              24
  STAGE II               3              23
  STAGE IIA              3              28
  STAGE IIB              4              40
  STAGE III              2               1
  STAGE IIIA             5              44
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               3              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TACC2 MUTATED     1  10   9   7
  TACC2 WILD-TYPE  10  62 113  68
D475V4, multiclass
    clus
vv   TACC2 MUTATED TACC2 WILD-TYPE
  T1             1              10
  T2            10              62
  T3             9             113
  T4             7              68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  TACC2 MUTATED    9 11  5  2
  TACC2 WILD-TYPE 84 70 45 51
D475V5, multiclass
    clus
vv   TACC2 MUTATED TACC2 WILD-TYPE
  N0             9              84
  N1            11              70
  N2             5              45
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D475V6, binary
                 cls
clus                0   1
  TACC2 MUTATED    27   2
  TACC2 WILD-TYPE 230  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TACC2 MUTATED     27    2
  TACC2 WILD-TYPE  230   16
   clus
vv  TACC2 MUTATED TACC2 WILD-TYPE
  0            27             230
  1             2              16
[1] 2 2
[1] FALSE
D475V7, binary
                 cls
clus                0   1
  TACC2 MUTATED    14  16
  TACC2 WILD-TYPE  96 163
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TACC2 MUTATED     14   16
  TACC2 WILD-TYPE   96  163
        clus
vv       TACC2 MUTATED TACC2 WILD-TYPE
  FEMALE            14              96
  MALE              16             163
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TACC2 MUTATED                                       3
  TACC2 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TACC2 MUTATED                                                       15
  TACC2 WILD-TYPE                                                    120
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TACC2 MUTATED                                                                   4
  TACC2 WILD-TYPE                                                                36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TACC2 MUTATED                                                  5
  TACC2 WILD-TYPE                                               33
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TACC2 MUTATED                                                          2
  TACC2 WILD-TYPE                                                       14
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TACC2 MUTATED                                                           1
  TACC2 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TACC2 MUTATED                                          0
  TACC2 WILD-TYPE                                        3
D475V8, multiclass
                                                                   clus
vv                                                                  TACC2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       15
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  TACC2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        120
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D475V9, binary
                 cls
clus                0   1
  TACC2 MUTATED     1  29
  TACC2 WILD-TYPE   4 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TACC2 MUTATED      1   29
  TACC2 WILD-TYPE    4  255
     clus
vv    TACC2 MUTATED TACC2 WILD-TYPE
  NO              1               4
  YES            29             255
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TACC2 MUTATED    22   0   1   6
  TACC2 WILD-TYPE 205  10   9  18
D475V10, multiclass
    clus
vv   TACC2 MUTATED TACC2 WILD-TYPE
  R0            22             205
  R1             0              10
  R2             1               9
  RX             6              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D475V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TACC2 MUTATED       6                         1    16
  TACC2 WILD-TYPE    70                         3   152
D475V12, multiclass
                           clus
vv                          TACC2 MUTATED TACC2 WILD-TYPE
  ASIAN                                 6              70
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                16             152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(476) Variable = CD58 MUTATION ANALYSIS
D476V1, survival
                sevent
clus2              0   1
  CD58 MUTATED     4   1
  CD58 WILD-TYPE 177  79
  CD58 MUTATED CD58 WILD-TYPE 
             5            256 
  CD58 MUTATED CD58 WILD-TYPE 
             1             79 
$`CD58 MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-CD-A4MG TCGA-CG-5721 TCGA-HU-A4G8 
       34.68        12.26         6.58         6.02        11.84 

$`CD58 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  CD58 MUTATED CD58 WILD-TYPE 
          6.02           0.00 
  CD58 MUTATED CD58 WILD-TYPE 
         34.68         105.07 
  CD58 MUTATED CD58 WILD-TYPE 
         11.84          12.71 
[1] "6.0 - 34.7 (11.8)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.5"
D476V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CD58 MUTATED         0        0        0        0         2         2
  CD58 WILD-TYPE       1        9       27       26        29        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CD58 MUTATED           0          1          0          0        1
  CD58 WILD-TYPE         3         48         36         24       23
D476V3, multiclass
            clus
vv           CD58 MUTATED CD58 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              0             26
  STAGE IIA             2             29
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CD58 MUTATED     0   0   4   2
  CD58 WILD-TYPE  11  72 118  73
D476V4, multiclass
    clus
vv   CD58 MUTATED CD58 WILD-TYPE
  T1            0             11
  T2            0             72
  T3            4            118
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  CD58 MUTATED    3  3  0  0
  CD58 WILD-TYPE 90 78 50 53
D476V5, multiclass
    clus
vv   CD58 MUTATED CD58 WILD-TYPE
  N0            3             90
  N1            3             78
  N2            0             50
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D476V6, binary
                cls
clus               0   1
  CD58 MUTATED     6   0
  CD58 WILD-TYPE 251  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD58 MUTATED      6    0
  CD58 WILD-TYPE  251   18
   clus
vv  CD58 MUTATED CD58 WILD-TYPE
  0            6            251
  1            0             18
[1] 2 2
[1] FALSE
D476V7, binary
                cls
clus               0   1
  CD58 MUTATED     4   2
  CD58 WILD-TYPE 106 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD58 MUTATED      4    2
  CD58 WILD-TYPE  106  177
        clus
vv       CD58 MUTATED CD58 WILD-TYPE
  FEMALE            4            106
  MALE              2            177
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CD58 MUTATED                                       2
  CD58 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CD58 MUTATED                                                        3
  CD58 WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CD58 MUTATED                                                                   1
  CD58 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CD58 MUTATED                                                  0
  CD58 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CD58 MUTATED                                                          0
  CD58 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CD58 MUTATED                                                           0
  CD58 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CD58 MUTATED                                          0
  CD58 WILD-TYPE                                        3
D476V8, multiclass
                                                                   clus
vv                                                                  CD58 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  CD58 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D476V9, binary
                cls
clus               0   1
  CD58 MUTATED     0   6
  CD58 WILD-TYPE   5 278
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD58 MUTATED      0    6
  CD58 WILD-TYPE    5  278
     clus
vv    CD58 MUTATED CD58 WILD-TYPE
  NO             0              5
  YES            6            278
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CD58 MUTATED     3   0   0   1
  CD58 WILD-TYPE 224  10  10  23
D476V10, multiclass
    clus
vv   CD58 MUTATED CD58 WILD-TYPE
  R0            3            224
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D476V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD58 MUTATED       2                         0     3
  CD58 WILD-TYPE    74                         4   165
D476V12, multiclass
                           clus
vv                          CD58 MUTATED CD58 WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                3            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(477) Variable = KCTD9 MUTATION ANALYSIS
D477V1, survival
                 sevent
clus2               0   1
  KCTD9 MUTATED     7   0
  KCTD9 WILD-TYPE 174  80
  KCTD9 MUTATED KCTD9 WILD-TYPE 
              7             254 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
              0              80 
$`KCTD9 MUTATED`
TCGA-BR-8370 TCGA-CD-8536 TCGA-CG-4305 TCGA-CG-5721 TCGA-D7-A4YU TCGA-HU-A4G8 
        3.32         0.10        15.95         6.02        16.44        11.84 
TCGA-HU-A4GX 
       10.19 

$`KCTD9 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 
       17.52         0.95        26.33         4.31        14.04        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.13         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  KCTD9 MUTATED KCTD9 WILD-TYPE 
            0.1             0.0 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
          16.44          105.07 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
          10.19           12.71 
[1] "0.1 - 16.4 (10.2)"  "0.0 - 105.1 (12.7)"
[1] "hr="     "9200000"
D477V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCTD9 MUTATED         0        0        0        2         0         1
  KCTD9 WILD-TYPE       1        9       27       24        31        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCTD9 MUTATED           0          0          2          1        2
  KCTD9 WILD-TYPE         3         49         34         23       22
D477V3, multiclass
            clus
vv           KCTD9 MUTATED KCTD9 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               2              24
  STAGE IIA              0              31
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             2              34
  STAGE IIIC             1              23
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCTD9 MUTATED     0   1   5   3
  KCTD9 WILD-TYPE  11  71 117  72
D477V4, multiclass
    clus
vv   KCTD9 MUTATED KCTD9 WILD-TYPE
  T1             0              11
  T2             1              71
  T3             5             117
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  KCTD9 MUTATED    1  3  2  2
  KCTD9 WILD-TYPE 92 78 48 51
D477V5, multiclass
    clus
vv   KCTD9 MUTATED KCTD9 WILD-TYPE
  N0             1              92
  N1             3              78
  N2             2              48
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D477V6, binary
                 cls
clus                0   1
  KCTD9 MUTATED     9   0
  KCTD9 WILD-TYPE 248  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD9 MUTATED      9    0
  KCTD9 WILD-TYPE  248   18
   clus
vv  KCTD9 MUTATED KCTD9 WILD-TYPE
  0             9             248
  1             0              18
[1] 2 2
[1] FALSE
D477V7, binary
                 cls
clus                0   1
  KCTD9 MUTATED     5   5
  KCTD9 WILD-TYPE 105 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD9 MUTATED      5    5
  KCTD9 WILD-TYPE  105  174
        clus
vv       KCTD9 MUTATED KCTD9 WILD-TYPE
  FEMALE             5             105
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KCTD9 MUTATED                                       3
  KCTD9 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KCTD9 MUTATED                                                        5
  KCTD9 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KCTD9 MUTATED                                                                   1
  KCTD9 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KCTD9 MUTATED                                                  1
  KCTD9 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KCTD9 MUTATED                                                          0
  KCTD9 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KCTD9 MUTATED                                                           0
  KCTD9 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KCTD9 MUTATED                                          0
  KCTD9 WILD-TYPE                                        3
D477V8, multiclass
                                                                   clus
vv                                                                  KCTD9 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  KCTD9 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D477V9, binary
                 cls
clus                0   1
  KCTD9 MUTATED     0  10
  KCTD9 WILD-TYPE   5 274
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD9 MUTATED      0   10
  KCTD9 WILD-TYPE    5  274
     clus
vv    KCTD9 MUTATED KCTD9 WILD-TYPE
  NO              0               5
  YES            10             274
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KCTD9 MUTATED     6   0   0   3
  KCTD9 WILD-TYPE 221  10  10  21
D477V10, multiclass
    clus
vv   KCTD9 MUTATED KCTD9 WILD-TYPE
  R0             6             221
  R1             0              10
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D477V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KCTD9 MUTATED       3                         0     5
  KCTD9 WILD-TYPE    73                         4   163
D477V12, multiclass
                           clus
vv                          KCTD9 MUTATED KCTD9 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(478) Variable = KIAA1539 MUTATION ANALYSIS
D478V1, survival
                    sevent
clus2                  0   1
  KIAA1539 MUTATED     6   0
  KIAA1539 WILD-TYPE 175  80
  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
                 6                255 
  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
                 0                 80 
$`KIAA1539 MUTATED`
TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-A4QL TCGA-HU-8602 
       11.70        34.68         1.12        13.45        11.57        11.41 

$`KIAA1539 WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
        9.21        20.22        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        13.64         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
              1.12               0.00 
  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
             34.68             105.07 
  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
            11.635             12.660 
[1] "1.1 - 34.7 (11.6)"  "0.0 - 105.1 (12.7)"
[1] "hr="     "9300000"
D478V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1539 MUTATED         0        0        1        0         2         1
  KIAA1539 WILD-TYPE       1        9       26       26        29        43
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1539 MUTATED           0          0          1          1        0
  KIAA1539 WILD-TYPE         3         49         35         23       24
D478V3, multiclass
            clus
vv           KIAA1539 MUTATED KIAA1539 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  1                 26
  STAGE II                  0                 26
  STAGE IIA                 2                 29
  STAGE IIB                 1                 43
  STAGE III                 0                  3
  STAGE IIIA                0                 49
  STAGE IIIB                1                 35
  STAGE IIIC                1                 23
  STAGE IV                  0                 24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1539 MUTATED     0   1   3   2
  KIAA1539 WILD-TYPE  11  71 119  73
D478V4, multiclass
    clus
vv   KIAA1539 MUTATED KIAA1539 WILD-TYPE
  T1                0                 11
  T2                1                 71
  T3                3                119
  T4                2                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  KIAA1539 MUTATED    4  0  0  2
  KIAA1539 WILD-TYPE 89 81 50 51
D478V5, multiclass
    clus
vv   KIAA1539 MUTATED KIAA1539 WILD-TYPE
  N0                4                 89
  N1                0                 81
  N2                0                 50
  N3                2                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D478V6, binary
                    cls
clus                   0   1
  KIAA1539 MUTATED     6   0
  KIAA1539 WILD-TYPE 251  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1539 MUTATED      6    0
  KIAA1539 WILD-TYPE  251   18
   clus
vv  KIAA1539 MUTATED KIAA1539 WILD-TYPE
  0                6                251
  1                0                 18
[1] 2 2
[1] FALSE
D478V7, binary
                    cls
clus                   0   1
  KIAA1539 MUTATED     4   2
  KIAA1539 WILD-TYPE 106 177
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1539 MUTATED      4    2
  KIAA1539 WILD-TYPE  106  177
        clus
vv       KIAA1539 MUTATED KIAA1539 WILD-TYPE
  FEMALE                4                106
  MALE                  2                177
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KIAA1539 MUTATED                                       2
  KIAA1539 WILD-TYPE                                    48
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA1539 MUTATED                                                        4
  KIAA1539 WILD-TYPE                                                    131
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA1539 MUTATED                                                                   0
  KIAA1539 WILD-TYPE                                                                40
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KIAA1539 MUTATED                                                  0
  KIAA1539 WILD-TYPE                                               38
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KIAA1539 MUTATED                                                          0
  KIAA1539 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KIAA1539 MUTATED                                                           0
  KIAA1539 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KIAA1539 MUTATED                                          0
  KIAA1539 WILD-TYPE                                        3
D478V8, multiclass
                                                                   clus
vv                                                                  KIAA1539 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  KIAA1539 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D478V9, binary
                    cls
clus                   0   1
  KIAA1539 MUTATED     0   6
  KIAA1539 WILD-TYPE   5 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1539 MUTATED      0    6
  KIAA1539 WILD-TYPE    5  278
     clus
vv    KIAA1539 MUTATED KIAA1539 WILD-TYPE
  NO                 0                  5
  YES                6                278
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA1539 MUTATED     6   0   0   0
  KIAA1539 WILD-TYPE 221  10  10  24
D478V10, multiclass
    clus
vv   KIAA1539 MUTATED KIAA1539 WILD-TYPE
  R0                6                221
  R1                0                 10
  R2                0                 10
  RX                0                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D478V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA1539 MUTATED       1                         0     5
  KIAA1539 WILD-TYPE    75                         4   163
D478V12, multiclass
                           clus
vv                          KIAA1539 MUTATED KIAA1539 WILD-TYPE
  ASIAN                                    1                 75
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    5                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(479) Variable = ZFP36L2 MUTATION ANALYSIS
D479V1, survival
                   sevent
clus2                 0   1
  ZFP36L2 MUTATED     6   2
  ZFP36L2 WILD-TYPE 175  78
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
                8               253 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
                2                78 
$`ZFP36L2 MUTATED`
TCGA-BR-8361 TCGA-BR-8367 TCGA-BR-8487 TCGA-CD-A4MG TCGA-HU-A4G9 TCGA-HU-A4GT 
       19.50        26.33         1.12         6.58        24.20         6.51 
TCGA-HU-A4H8 TCGA-IP-7968 
        8.88         2.53 

$`ZFP36L2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        11.84         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         0.10         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       12.30         9.67        27.42        21.21         3.45        18.81 
TCGA-IN-8663 
        3.39 

  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
             1.12              0.00 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
            26.33            105.07 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
             7.73             12.66 
[1] "1.1 - 26.3 (7.7)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1"  
D479V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZFP36L2 MUTATED         0        1        1        0         3         0
  ZFP36L2 WILD-TYPE       1        8       26       26        28        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFP36L2 MUTATED           0          0          2          1        0
  ZFP36L2 WILD-TYPE         3         49         34         23       24
D479V3, multiclass
            clus
vv           ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 1                 8
  STAGE IB                 1                26
  STAGE II                 0                26
  STAGE IIA                3                28
  STAGE IIB                0                44
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               2                34
  STAGE IIIC               1                23
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZFP36L2 MUTATED     2   0   5   1
  ZFP36L2 WILD-TYPE   9  72 117  74
D479V4, multiclass
    clus
vv   ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  T1               2                 9
  T2               0                72
  T3               5               117
  T4               1                74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  ZFP36L2 MUTATED    4  1  2  1
  ZFP36L2 WILD-TYPE 89 80 48 52
D479V5, multiclass
    clus
vv   ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  N0               4                89
  N1               1                80
  N2               2                48
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D479V6, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED     7   0
  ZFP36L2 WILD-TYPE 250  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED      7    0
  ZFP36L2 WILD-TYPE  250   18
   clus
vv  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  0               7               250
  1               0                18
[1] 2 2
[1] FALSE
D479V7, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED     4   4
  ZFP36L2 WILD-TYPE 106 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED      4    4
  ZFP36L2 WILD-TYPE  106  175
        clus
vv       ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  FEMALE               4               106
  MALE                 4               175
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZFP36L2 MUTATED                                       1
  ZFP36L2 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZFP36L2 MUTATED                                                        4
  ZFP36L2 WILD-TYPE                                                    131
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZFP36L2 MUTATED                                                                   0
  ZFP36L2 WILD-TYPE                                                                40
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZFP36L2 MUTATED                                                  3
  ZFP36L2 WILD-TYPE                                               35
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZFP36L2 MUTATED                                                          0
  ZFP36L2 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZFP36L2 MUTATED                                                           0
  ZFP36L2 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZFP36L2 MUTATED                                          0
  ZFP36L2 WILD-TYPE                                        3
D479V8, multiclass
                                                                   clus
vv                                                                  ZFP36L2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  ZFP36L2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D479V9, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED     0   8
  ZFP36L2 WILD-TYPE   5 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED      0    8
  ZFP36L2 WILD-TYPE    5  276
     clus
vv    ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  NO                0                 5
  YES               8               276
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZFP36L2 MUTATED     7   0   0   0
  ZFP36L2 WILD-TYPE 220  10  10  24
D479V10, multiclass
    clus
vv   ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  R0               7               220
  R1               0                10
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D479V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZFP36L2 MUTATED       4                         0     4
  ZFP36L2 WILD-TYPE    72                         4   164
D479V12, multiclass
                           clus
vv                          ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  ASIAN                                   4                72
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   4               164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(480) Variable = TNS4 MUTATION ANALYSIS
D480V1, survival
                sevent
clus2              0   1
  TNS4 MUTATED     8   1
  TNS4 WILD-TYPE 173  79
  TNS4 MUTATED TNS4 WILD-TYPE 
             9            252 
  TNS4 MUTATED TNS4 WILD-TYPE 
             1             79 
$`TNS4 MUTATED`
TCGA-BR-6452 TCGA-BR-7851 TCGA-BR-8363 TCGA-BR-8372 TCGA-CD-A4MH TCGA-CD-A4MI 
       34.68        12.43         0.26        19.17        12.20         0.10 
TCGA-CG-5723 TCGA-F1-6874 TCGA-HU-A4H5 
      105.07        14.47        12.30 

$`TNS4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        19.50        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        6.58        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         6.02         0.99        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
       13.78        14.76         0.62         7.99        16.24        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        19.36        23.84         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  TNS4 MUTATED TNS4 WILD-TYPE 
           0.1            0.0 
  TNS4 MUTATED TNS4 WILD-TYPE 
        105.07          79.07 
  TNS4 MUTATED TNS4 WILD-TYPE 
         12.43          12.64 
[1] "0.1 - 105.1 (12.4)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "4.4"
D480V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TNS4 MUTATED         0        0        3        1         2         1
  TNS4 WILD-TYPE       1        9       24       25        29        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNS4 MUTATED           0          1          1          1        1
  TNS4 WILD-TYPE         3         48         35         23       23
D480V3, multiclass
            clus
vv           TNS4 MUTATED TNS4 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              3             24
  STAGE II              1             25
  STAGE IIA             2             29
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            1             23
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TNS4 MUTATED     0   4   3   4
  TNS4 WILD-TYPE  11  68 119  71
D480V4, multiclass
    clus
vv   TNS4 MUTATED TNS4 WILD-TYPE
  T1            0             11
  T2            4             68
  T3            3            119
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  TNS4 MUTATED    7  3  1  1
  TNS4 WILD-TYPE 86 78 49 52
D480V5, multiclass
    clus
vv   TNS4 MUTATED TNS4 WILD-TYPE
  N0            7             86
  N1            3             78
  N2            1             49
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D480V6, binary
                cls
clus               0   1
  TNS4 MUTATED    11   1
  TNS4 WILD-TYPE 246  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNS4 MUTATED     11    1
  TNS4 WILD-TYPE  246   17
   clus
vv  TNS4 MUTATED TNS4 WILD-TYPE
  0           11            246
  1            1             17
[1] 2 2
[1] FALSE
D480V7, binary
                cls
clus               0   1
  TNS4 MUTATED     6   6
  TNS4 WILD-TYPE 104 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNS4 MUTATED      6    6
  TNS4 WILD-TYPE  104  173
        clus
vv       TNS4 MUTATED TNS4 WILD-TYPE
  FEMALE            6            104
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TNS4 MUTATED                                       1
  TNS4 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TNS4 MUTATED                                                        8
  TNS4 WILD-TYPE                                                    127
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TNS4 MUTATED                                                                   2
  TNS4 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TNS4 MUTATED                                                  0
  TNS4 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TNS4 MUTATED                                                          0
  TNS4 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TNS4 MUTATED                                                           1
  TNS4 WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TNS4 MUTATED                                          0
  TNS4 WILD-TYPE                                        3
D480V8, multiclass
                                                                   clus
vv                                                                  TNS4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  TNS4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D480V9, binary
                cls
clus               0   1
  TNS4 MUTATED     0  12
  TNS4 WILD-TYPE   5 272
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNS4 MUTATED      0   12
  TNS4 WILD-TYPE    5  272
     clus
vv    TNS4 MUTATED TNS4 WILD-TYPE
  NO             0              5
  YES           12            272
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TNS4 MUTATED     7   0   1   2
  TNS4 WILD-TYPE 220  10   9  22
D480V10, multiclass
    clus
vv   TNS4 MUTATED TNS4 WILD-TYPE
  R0            7            220
  R1            0             10
  R2            1              9
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D480V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TNS4 MUTATED       3                         0     7
  TNS4 WILD-TYPE    73                         4   161
D480V12, multiclass
                           clus
vv                          TNS4 MUTATED TNS4 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                7            161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(481) Variable = ZBTB49 MUTATION ANALYSIS
D481V1, survival
                  sevent
clus2                0   1
  ZBTB49 MUTATED     6   1
  ZBTB49 WILD-TYPE 175  79
  ZBTB49 MUTATED ZBTB49 WILD-TYPE 
               7              254 
  ZBTB49 MUTATED ZBTB49 WILD-TYPE 
               1               79 
$`ZBTB49 MUTATED`
TCGA-BR-6802 TCGA-BR-7901 TCGA-BR-8368 TCGA-CD-8530 TCGA-F1-6874 TCGA-HU-8602 
       30.90         3.45         4.31         0.16        14.47        11.41 
TCGA-HU-A4GN 
       29.98 

$`ZBTB49 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73        12.43         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.07         0.10         0.13         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.99        16.24        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  ZBTB49 MUTATED ZBTB49 WILD-TYPE 
            0.16             0.00 
  ZBTB49 MUTATED ZBTB49 WILD-TYPE 
           30.90           105.07 
  ZBTB49 MUTATED ZBTB49 WILD-TYPE 
           11.41            12.64 
[1] "0.2 - 30.9 (11.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.3"
D481V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZBTB49 MUTATED         0        0        2        1         1         2
  ZBTB49 WILD-TYPE       1        9       25       25        30        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB49 MUTATED           0          1          0          0        0
  ZBTB49 WILD-TYPE         3         48         36         24       24
D481V3, multiclass
            clus
vv           ZBTB49 MUTATED ZBTB49 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                2               25
  STAGE II                1               25
  STAGE IIA               1               30
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZBTB49 MUTATED     0   3   3   1
  ZBTB49 WILD-TYPE  11  69 119  74
D481V4, multiclass
    clus
vv   ZBTB49 MUTATED ZBTB49 WILD-TYPE
  T1              0               11
  T2              3               69
  T3              3              119
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZBTB49 MUTATED    4  2  1  0
  ZBTB49 WILD-TYPE 89 79 49 53
D481V5, multiclass
    clus
vv   ZBTB49 MUTATED ZBTB49 WILD-TYPE
  N0              4               89
  N1              2               79
  N2              1               49
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D481V6, binary
                  cls
clus                 0   1
  ZBTB49 MUTATED     7   0
  ZBTB49 WILD-TYPE 250  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB49 MUTATED      7    0
  ZBTB49 WILD-TYPE  250   18
   clus
vv  ZBTB49 MUTATED ZBTB49 WILD-TYPE
  0              7              250
  1              0               18
[1] 2 2
[1] FALSE
D481V7, binary
                  cls
clus                 0   1
  ZBTB49 MUTATED     2   5
  ZBTB49 WILD-TYPE 108 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB49 MUTATED      2    5
  ZBTB49 WILD-TYPE  108  174
        clus
vv       ZBTB49 MUTATED ZBTB49 WILD-TYPE
  FEMALE              2              108
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZBTB49 MUTATED                                       2
  ZBTB49 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZBTB49 MUTATED                                                        3
  ZBTB49 WILD-TYPE                                                    132
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZBTB49 MUTATED                                                                   1
  ZBTB49 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZBTB49 MUTATED                                                  1
  ZBTB49 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZBTB49 MUTATED                                                          0
  ZBTB49 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZBTB49 MUTATED                                                           0
  ZBTB49 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZBTB49 MUTATED                                          0
  ZBTB49 WILD-TYPE                                        3
D481V8, multiclass
                                                                   clus
vv                                                                  ZBTB49 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ZBTB49 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D481V9, binary
                  cls
clus                 0   1
  ZBTB49 MUTATED     0   7
  ZBTB49 WILD-TYPE   5 277
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB49 MUTATED      0    7
  ZBTB49 WILD-TYPE    5  277
     clus
vv    ZBTB49 MUTATED ZBTB49 WILD-TYPE
  NO               0                5
  YES              7              277
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZBTB49 MUTATED     7   0   0   0
  ZBTB49 WILD-TYPE 220  10  10  24
D481V10, multiclass
    clus
vv   ZBTB49 MUTATED ZBTB49 WILD-TYPE
  R0              7              220
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D481V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZBTB49 MUTATED       3                         0     4
  ZBTB49 WILD-TYPE    73                         4   164
D481V12, multiclass
                           clus
vv                          ZBTB49 MUTATED ZBTB49 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(482) Variable = CAMTA2 MUTATION ANALYSIS
D482V1, survival
                  sevent
clus2                0   1
  CAMTA2 MUTATED    12   2
  CAMTA2 WILD-TYPE 169  78
  CAMTA2 MUTATED CAMTA2 WILD-TYPE 
              14              247 
  CAMTA2 MUTATED CAMTA2 WILD-TYPE 
               2               78 
$`CAMTA2 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-8591 TCGA-BR-A4QL 
       26.70        34.68        32.78        32.94        13.45        11.57 
TCGA-CG-5722 TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-8570 TCGA-D7-A4YV TCGA-HU-A4G8 
        0.99        28.96        65.10        24.72         5.92        11.84 
TCGA-HU-A4GX TCGA-HU-A4H8 
       10.19         8.88 

$`CAMTA2 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       31.20        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        15.81         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 
        1.02         0.99         6.02       105.07        12.03        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 
       12.79        10.55        11.31        12.33        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       16.44        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        9.67        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  CAMTA2 MUTATED CAMTA2 WILD-TYPE 
            0.99             0.00 
  CAMTA2 MUTATED CAMTA2 WILD-TYPE 
           65.10           105.07 
  CAMTA2 MUTATED CAMTA2 WILD-TYPE 
          19.085           12.590 
[1] "1.0 - 65.1 (19.1)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "3.7"
D482V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CAMTA2 MUTATED         1        1        2        0         3         3
  CAMTA2 WILD-TYPE       0        8       25       26        28        41
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CAMTA2 MUTATED           0          1          2          2        1
  CAMTA2 WILD-TYPE         3         48         34         22       23
D482V3, multiclass
            clus
vv           CAMTA2 MUTATED CAMTA2 WILD-TYPE
  STAGE I                 1                0
  STAGE IA                1                8
  STAGE IB                2               25
  STAGE II                0               26
  STAGE IIA               3               28
  STAGE IIB               3               41
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              2               34
  STAGE IIIC              2               22
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CAMTA2 MUTATED     3   1   8   4
  CAMTA2 WILD-TYPE   8  71 114  71
D482V4, multiclass
    clus
vv   CAMTA2 MUTATED CAMTA2 WILD-TYPE
  T1              3                8
  T2              1               71
  T3              8              114
  T4              4               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CAMTA2 MUTATED    7  4  2  3
  CAMTA2 WILD-TYPE 86 77 48 50
D482V5, multiclass
    clus
vv   CAMTA2 MUTATED CAMTA2 WILD-TYPE
  N0              7               86
  N1              4               77
  N2              2               48
  N3              3               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D482V6, binary
                  cls
clus                 0   1
  CAMTA2 MUTATED    14   1
  CAMTA2 WILD-TYPE 243  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAMTA2 MUTATED     14    1
  CAMTA2 WILD-TYPE  243   17
   clus
vv  CAMTA2 MUTATED CAMTA2 WILD-TYPE
  0             14              243
  1              1               17
[1] 2 2
[1] FALSE
D482V7, binary
                  cls
clus                 0   1
  CAMTA2 MUTATED    11   5
  CAMTA2 WILD-TYPE  99 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAMTA2 MUTATED     11    5
  CAMTA2 WILD-TYPE   99  174
        clus
vv       CAMTA2 MUTATED CAMTA2 WILD-TYPE
  FEMALE             11               99
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CAMTA2 MUTATED                                       3
  CAMTA2 WILD-TYPE                                    47
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CAMTA2 MUTATED                                                        7
  CAMTA2 WILD-TYPE                                                    128
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CAMTA2 MUTATED                                                                   3
  CAMTA2 WILD-TYPE                                                                37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CAMTA2 MUTATED                                                  3
  CAMTA2 WILD-TYPE                                               35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CAMTA2 MUTATED                                                          0
  CAMTA2 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CAMTA2 MUTATED                                                           0
  CAMTA2 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CAMTA2 MUTATED                                          0
  CAMTA2 WILD-TYPE                                        3
D482V8, multiclass
                                                                   clus
vv                                                                  CAMTA2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  CAMTA2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D482V9, binary
                  cls
clus                 0   1
  CAMTA2 MUTATED     0  16
  CAMTA2 WILD-TYPE   5 268
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAMTA2 MUTATED      0   16
  CAMTA2 WILD-TYPE    5  268
     clus
vv    CAMTA2 MUTATED CAMTA2 WILD-TYPE
  NO               0                5
  YES             16              268
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CAMTA2 MUTATED    13   0   1   1
  CAMTA2 WILD-TYPE 214  10   9  23
D482V10, multiclass
    clus
vv   CAMTA2 MUTATED CAMTA2 WILD-TYPE
  R0             13              214
  R1              0               10
  R2              1                9
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D482V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CAMTA2 MUTATED       3                         1     9
  CAMTA2 WILD-TYPE    73                         3   159
D482V12, multiclass
                           clus
vv                          CAMTA2 MUTATED CAMTA2 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  9              159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(483) Variable = KRT24 MUTATION ANALYSIS
D483V1, survival
                 sevent
clus2               0   1
  KRT24 MUTATED     4   1
  KRT24 WILD-TYPE 177  79
  KRT24 MUTATED KRT24 WILD-TYPE 
              5             256 
  KRT24 MUTATED KRT24 WILD-TYPE 
              1              79 
$`KRT24 MUTATED`
TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8690 TCGA-D7-8575 TCGA-HU-A4GU 
       32.94        12.26        10.68        18.21         6.25 

$`KRT24 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        30.90        31.20        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         9.86        15.68         8.22        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  KRT24 MUTATED KRT24 WILD-TYPE 
           6.25            0.00 
  KRT24 MUTATED KRT24 WILD-TYPE 
          32.94          105.07 
  KRT24 MUTATED KRT24 WILD-TYPE 
          12.26           12.64 
[1] "6.2 - 32.9 (12.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.8"
D483V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KRT24 MUTATED         0        0        0        0         1         2
  KRT24 WILD-TYPE       1        9       27       26        30        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KRT24 MUTATED           0          1          1          0        0
  KRT24 WILD-TYPE         3         48         35         24       24
D483V3, multiclass
            clus
vv           KRT24 MUTATED KRT24 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KRT24 MUTATED     0   0   4   1
  KRT24 WILD-TYPE  11  72 118  74
D483V4, multiclass
    clus
vv   KRT24 MUTATED KRT24 WILD-TYPE
  T1             0              11
  T2             0              72
  T3             4             118
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  KRT24 MUTATED    2  1  1  1
  KRT24 WILD-TYPE 91 80 49 52
D483V5, multiclass
    clus
vv   KRT24 MUTATED KRT24 WILD-TYPE
  N0             2              91
  N1             1              80
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D483V6, binary
                 cls
clus                0   1
  KRT24 MUTATED     5   0
  KRT24 WILD-TYPE 252  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT24 MUTATED      5    0
  KRT24 WILD-TYPE  252   18
   clus
vv  KRT24 MUTATED KRT24 WILD-TYPE
  0             5             252
  1             0              18
[1] 2 2
[1] FALSE
D483V7, binary
                 cls
clus                0   1
  KRT24 MUTATED     3   2
  KRT24 WILD-TYPE 107 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT24 MUTATED      3    2
  KRT24 WILD-TYPE  107  177
        clus
vv       KRT24 MUTATED KRT24 WILD-TYPE
  FEMALE             3             107
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KRT24 MUTATED                                       1
  KRT24 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KRT24 MUTATED                                                        3
  KRT24 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KRT24 MUTATED                                                                   0
  KRT24 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KRT24 MUTATED                                                  1
  KRT24 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KRT24 MUTATED                                                          0
  KRT24 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KRT24 MUTATED                                                           0
  KRT24 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KRT24 MUTATED                                          0
  KRT24 WILD-TYPE                                        3
D483V8, multiclass
                                                                   clus
vv                                                                  KRT24 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  KRT24 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D483V9, binary
                 cls
clus                0   1
  KRT24 MUTATED     0   5
  KRT24 WILD-TYPE   5 279
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT24 MUTATED      0    5
  KRT24 WILD-TYPE    5  279
     clus
vv    KRT24 MUTATED KRT24 WILD-TYPE
  NO              0               5
  YES             5             279
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KRT24 MUTATED     5   0   0   0
  KRT24 WILD-TYPE 222  10  10  24
D483V10, multiclass
    clus
vv   KRT24 MUTATED KRT24 WILD-TYPE
  R0             5             222
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D483V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRT24 MUTATED       1                         0     4
  KRT24 WILD-TYPE    75                         4   164
D483V12, multiclass
                           clus
vv                          KRT24 MUTATED KRT24 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(484) Variable = EEF2K MUTATION ANALYSIS
D484V1, survival
                 sevent
clus2               0   1
  EEF2K MUTATED     4   2
  EEF2K WILD-TYPE 177  78
  EEF2K MUTATED EEF2K WILD-TYPE 
              6             255 
  EEF2K MUTATED EEF2K WILD-TYPE 
              2              78 
$`EEF2K MUTATED`
TCGA-BR-4184 TCGA-CG-4305 TCGA-CG-5721 TCGA-FP-7735 TCGA-FP-A4BE TCGA-HU-8602 
        6.97        15.95         6.02         3.48        11.08        11.41 

$`EEF2K WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  EEF2K MUTATED EEF2K WILD-TYPE 
           3.48            0.00 
  EEF2K MUTATED EEF2K WILD-TYPE 
          15.95          105.07 
  EEF2K MUTATED EEF2K WILD-TYPE 
          9.025          12.760 
[1] "3.5 - 15.9 (9.0)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.9"
D484V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EEF2K MUTATED         0        0        1        1         1         1
  EEF2K WILD-TYPE       1        9       26       25        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EEF2K MUTATED           0          3          0          0        2
  EEF2K WILD-TYPE         3         46         36         24       22
D484V3, multiclass
            clus
vv           EEF2K MUTATED EEF2K WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             3              46
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EEF2K MUTATED     0   2   3   4
  EEF2K WILD-TYPE  11  70 119  71
D484V4, multiclass
    clus
vv   EEF2K MUTATED EEF2K WILD-TYPE
  T1             0              11
  T2             2              70
  T3             3             119
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  EEF2K MUTATED    4  4  1  0
  EEF2K WILD-TYPE 89 77 49 53
D484V5, multiclass
    clus
vv   EEF2K MUTATED EEF2K WILD-TYPE
  N0             4              89
  N1             4              77
  N2             1              49
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D484V6, binary
                 cls
clus                0   1
  EEF2K MUTATED     7   0
  EEF2K WILD-TYPE 250  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EEF2K MUTATED      7    0
  EEF2K WILD-TYPE  250   18
   clus
vv  EEF2K MUTATED EEF2K WILD-TYPE
  0             7             250
  1             0              18
[1] 2 2
[1] FALSE
D484V7, binary
                 cls
clus                0   1
  EEF2K MUTATED     3   6
  EEF2K WILD-TYPE 107 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EEF2K MUTATED      3    6
  EEF2K WILD-TYPE  107  173
        clus
vv       EEF2K MUTATED EEF2K WILD-TYPE
  FEMALE             3             107
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  EEF2K MUTATED                                       1
  EEF2K WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EEF2K MUTATED                                                        7
  EEF2K WILD-TYPE                                                    128
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EEF2K MUTATED                                                                   1
  EEF2K WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  EEF2K MUTATED                                                  0
  EEF2K WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  EEF2K MUTATED                                                          0
  EEF2K WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  EEF2K MUTATED                                                           0
  EEF2K WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  EEF2K MUTATED                                          0
  EEF2K WILD-TYPE                                        3
D484V8, multiclass
                                                                   clus
vv                                                                  EEF2K MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  EEF2K WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D484V9, binary
                 cls
clus                0   1
  EEF2K MUTATED     1   8
  EEF2K WILD-TYPE   4 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EEF2K MUTATED      1    8
  EEF2K WILD-TYPE    4  276
     clus
vv    EEF2K MUTATED EEF2K WILD-TYPE
  NO              1               4
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EEF2K MUTATED     5   1   0   3
  EEF2K WILD-TYPE 222   9  10  21
D484V10, multiclass
    clus
vv   EEF2K MUTATED EEF2K WILD-TYPE
  R0             5             222
  R1             1               9
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D484V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EEF2K MUTATED       1                         2     3
  EEF2K WILD-TYPE    75                         2   165
D484V12, multiclass
                           clus
vv                          EEF2K MUTATED EEF2K WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             2               2
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(485) Variable = RERE MUTATION ANALYSIS
D485V1, survival
                sevent
clus2              0   1
  RERE MUTATED    11   4
  RERE WILD-TYPE 170  76
  RERE MUTATED RERE WILD-TYPE 
            15            246 
  RERE MUTATED RERE WILD-TYPE 
             4             76 
$`RERE MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8591 
       26.70        34.68        23.93         4.31         1.12        13.45 
TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-5723 TCGA-CG-5726 TCGA-F1-6874 
        6.58         1.02         9.01       105.07        28.96        14.47 
TCGA-HU-8602 TCGA-HU-A4H3 TCGA-HU-A4H4 
       11.41        19.36        23.84 

$`RERE WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        15.81         9.34         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       19.07        12.03         0.00        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
        0.99        12.03        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       16.24        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        0.26         2.10        12.95        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  RERE MUTATED RERE WILD-TYPE 
          1.02           0.00 
  RERE MUTATED RERE WILD-TYPE 
        105.07          79.07 
  RERE MUTATED RERE WILD-TYPE 
        14.470         12.575 
[1] "1.0 - 105.1 (14.5)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.7"
D485V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RERE MUTATED         1        1        4        1         3         3
  RERE WILD-TYPE       0        8       23       25        28        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RERE MUTATED           0          0          0          2        2
  RERE WILD-TYPE         3         49         36         22       22
D485V3, multiclass
            clus
vv           RERE MUTATED RERE WILD-TYPE
  STAGE I               1              0
  STAGE IA              1              8
  STAGE IB              4             23
  STAGE II              1             25
  STAGE IIA             3             28
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            2             22
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RERE MUTATED     3   6   5   5
  RERE WILD-TYPE   8  66 117  70
D485V4, multiclass
    clus
vv   RERE MUTATED RERE WILD-TYPE
  T1            3              8
  T2            6             66
  T3            5            117
  T4            5             70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  RERE MUTATED   10  3  2  3
  RERE WILD-TYPE 83 78 48 50
D485V5, multiclass
    clus
vv   RERE MUTATED RERE WILD-TYPE
  N0           10             83
  N1            3             78
  N2            2             48
  N3            3             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D485V6, binary
                cls
clus               0   1
  RERE MUTATED    17   2
  RERE WILD-TYPE 240  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  RERE MUTATED     17    2
  RERE WILD-TYPE  240   16
   clus
vv  RERE MUTATED RERE WILD-TYPE
  0           17            240
  1            2             16
[1] 2 2
[1] FALSE
D485V7, binary
                cls
clus               0   1
  RERE MUTATED    13   8
  RERE WILD-TYPE  97 171
[1] "tbl2"
                cls
clus             [,1] [,2]
  RERE MUTATED     13    8
  RERE WILD-TYPE   97  171
        clus
vv       RERE MUTATED RERE WILD-TYPE
  FEMALE           13             97
  MALE              8            171
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RERE MUTATED                                       5
  RERE WILD-TYPE                                    45
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RERE MUTATED                                                       12
  RERE WILD-TYPE                                                    123
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RERE MUTATED                                                                   3
  RERE WILD-TYPE                                                                37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RERE MUTATED                                                  1
  RERE WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RERE MUTATED                                                          0
  RERE WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RERE MUTATED                                                           0
  RERE WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RERE MUTATED                                          0
  RERE WILD-TYPE                                        3
D485V8, multiclass
                                                                   clus
vv                                                                  RERE MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      12
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  RERE WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       123
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D485V9, binary
                cls
clus               0   1
  RERE MUTATED     0  21
  RERE WILD-TYPE   5 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  RERE MUTATED      0   21
  RERE WILD-TYPE    5  263
     clus
vv    RERE MUTATED RERE WILD-TYPE
  NO             0              5
  YES           21            263
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RERE MUTATED    14   0   2   4
  RERE WILD-TYPE 213  10   8  20
D485V10, multiclass
    clus
vv   RERE MUTATED RERE WILD-TYPE
  R0           14            213
  R1            0             10
  R2            2              8
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D485V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RERE MUTATED       4                         1    11
  RERE WILD-TYPE    72                         3   157
D485V12, multiclass
                           clus
vv                          RERE MUTATED RERE WILD-TYPE
  ASIAN                                4             72
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                               11            157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(486) Variable = TRAM1L1 MUTATION ANALYSIS
D486V1, survival
                   sevent
clus2                 0   1
  TRAM1L1 MUTATED     4   3
  TRAM1L1 WILD-TYPE 177  77
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
                7               254 
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
                3                77 
$`TRAM1L1 MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8284 TCGA-CD-A4MG TCGA-CG-4437 TCGA-D7-6822 
       34.68        12.26         8.05         6.58         8.05        12.33 
TCGA-HU-A4GQ 
        0.10 

$`TRAM1L1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8286 
       17.49        14.43         0.69         9.60        20.55        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         7.99        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
              0.1               0.0 
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
            34.68            105.07 
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
            8.050            12.775 
[1] "0.1 - 34.7 (8.1)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.7"
D486V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRAM1L1 MUTATED         1        0        3        2         2         1
  TRAM1L1 WILD-TYPE       0        9       24       24        29        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRAM1L1 MUTATED           0          0          0          2        1
  TRAM1L1 WILD-TYPE         3         49         36         22       23
D486V3, multiclass
            clus
vv           TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                 0                 9
  STAGE IB                 3                24
  STAGE II                 2                24
  STAGE IIA                2                29
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               0                36
  STAGE IIIC               2                22
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TRAM1L1 MUTATED     1   5   2   4
  TRAM1L1 WILD-TYPE  10  67 120  71
D486V4, multiclass
    clus
vv   TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  T1               1                10
  T2               5                67
  T3               2               120
  T4               4                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  TRAM1L1 MUTATED    6  4  2  1
  TRAM1L1 WILD-TYPE 87 77 48 52
D486V5, multiclass
    clus
vv   TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  N0               6                87
  N1               4                77
  N2               2                48
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D486V6, binary
                   cls
clus                  0   1
  TRAM1L1 MUTATED    12   0
  TRAM1L1 WILD-TYPE 245  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TRAM1L1 MUTATED     12    0
  TRAM1L1 WILD-TYPE  245   18
   clus
vv  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  0              12               245
  1               0                18
[1] 2 2
[1] FALSE
D486V7, binary
                   cls
clus                  0   1
  TRAM1L1 MUTATED     5   8
  TRAM1L1 WILD-TYPE 105 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TRAM1L1 MUTATED      5    8
  TRAM1L1 WILD-TYPE  105  171
        clus
vv       TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  FEMALE               5               105
  MALE                 8               171
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TRAM1L1 MUTATED                                       1
  TRAM1L1 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TRAM1L1 MUTATED                                                        6
  TRAM1L1 WILD-TYPE                                                    129
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TRAM1L1 MUTATED                                                                   3
  TRAM1L1 WILD-TYPE                                                                37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TRAM1L1 MUTATED                                                  2
  TRAM1L1 WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TRAM1L1 MUTATED                                                          1
  TRAM1L1 WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TRAM1L1 MUTATED                                                           0
  TRAM1L1 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TRAM1L1 MUTATED                                          0
  TRAM1L1 WILD-TYPE                                        3
D486V8, multiclass
                                                                   clus
vv                                                                  TRAM1L1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  TRAM1L1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D486V9, binary
                   cls
clus                  0   1
  TRAM1L1 MUTATED     1  12
  TRAM1L1 WILD-TYPE   4 272
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TRAM1L1 MUTATED      1   12
  TRAM1L1 WILD-TYPE    4  272
     clus
vv    TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  NO                1                 4
  YES              12               272
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TRAM1L1 MUTATED    10   0   0   2
  TRAM1L1 WILD-TYPE 217  10  10  22
D486V10, multiclass
    clus
vv   TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  R0              10               217
  R1               0                10
  R2               0                10
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D486V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TRAM1L1 MUTATED       2                         1     7
  TRAM1L1 WILD-TYPE    74                         3   161
D486V12, multiclass
                           clus
vv                          TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  ASIAN                                   2                74
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   7               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(487) Variable = EXOSC8 MUTATION ANALYSIS
D487V1, survival
                  sevent
clus2                0   1
  EXOSC8 MUTATED     3   1
  EXOSC8 WILD-TYPE 178  79
  EXOSC8 MUTATED EXOSC8 WILD-TYPE 
               4              257 
  EXOSC8 MUTATED EXOSC8 WILD-TYPE 
               1               79 
$`EXOSC8 MUTATED`
TCGA-BR-4201 TCGA-BR-8078 TCGA-BR-8372 TCGA-HU-A4H4 
       30.90        12.26        19.17        23.84 

$`EXOSC8 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       12.95        19.36        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  EXOSC8 MUTATED EXOSC8 WILD-TYPE 
           12.26             0.00 
  EXOSC8 MUTATED EXOSC8 WILD-TYPE 
           30.90           105.07 
  EXOSC8 MUTATED EXOSC8 WILD-TYPE 
          21.505           12.590 
[1] "12.3 - 30.9 (21.5)" "0.0 - 105.1 (12.6)"
[1] "hr=" "2"  
D487V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EXOSC8 MUTATED         0        0        0        0         0         2
  EXOSC8 WILD-TYPE       1        9       27       26        31        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EXOSC8 MUTATED           0          1          0          1        0
  EXOSC8 WILD-TYPE         3         48         36         23       24
D487V3, multiclass
            clus
vv           EXOSC8 MUTATED EXOSC8 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               0               31
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EXOSC8 MUTATED     0   2   0   3
  EXOSC8 WILD-TYPE  11  70 122  72
D487V4, multiclass
    clus
vv   EXOSC8 MUTATED EXOSC8 WILD-TYPE
  T1              0               11
  T2              2               70
  T3              0              122
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  EXOSC8 MUTATED    2  0  1  1
  EXOSC8 WILD-TYPE 91 81 49 52
D487V5, multiclass
    clus
vv   EXOSC8 MUTATED EXOSC8 WILD-TYPE
  N0              2               91
  N1              0               81
  N2              1               49
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D487V6, binary
                  cls
clus                 0   1
  EXOSC8 MUTATED     5   0
  EXOSC8 WILD-TYPE 252  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EXOSC8 MUTATED      5    0
  EXOSC8 WILD-TYPE  252   18
   clus
vv  EXOSC8 MUTATED EXOSC8 WILD-TYPE
  0              5              252
  1              0               18
[1] 2 2
[1] FALSE
D487V7, binary
                  cls
clus                 0   1
  EXOSC8 MUTATED     4   1
  EXOSC8 WILD-TYPE 106 178
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EXOSC8 MUTATED      4    1
  EXOSC8 WILD-TYPE  106  178
        clus
vv       EXOSC8 MUTATED EXOSC8 WILD-TYPE
  FEMALE              4              106
  MALE                1              178
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  EXOSC8 MUTATED                                       0
  EXOSC8 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EXOSC8 MUTATED                                                        4
  EXOSC8 WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EXOSC8 MUTATED                                                                   0
  EXOSC8 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  EXOSC8 MUTATED                                                  1
  EXOSC8 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  EXOSC8 MUTATED                                                          0
  EXOSC8 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  EXOSC8 MUTATED                                                           0
  EXOSC8 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  EXOSC8 MUTATED                                          0
  EXOSC8 WILD-TYPE                                        3
D487V8, multiclass
                                                                   clus
vv                                                                  EXOSC8 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  EXOSC8 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D487V9, binary
                  cls
clus                 0   1
  EXOSC8 MUTATED     0   5
  EXOSC8 WILD-TYPE   5 279
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EXOSC8 MUTATED      0    5
  EXOSC8 WILD-TYPE    5  279
     clus
vv    EXOSC8 MUTATED EXOSC8 WILD-TYPE
  NO               0                5
  YES              5              279
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  EXOSC8 MUTATED     3   0   0   2
  EXOSC8 WILD-TYPE 224  10  10  22
D487V10, multiclass
    clus
vv   EXOSC8 MUTATED EXOSC8 WILD-TYPE
  R0              3              224
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D487V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EXOSC8 MUTATED       1                         0     4
  EXOSC8 WILD-TYPE    75                         4   164
D487V12, multiclass
                           clus
vv                          EXOSC8 MUTATED EXOSC8 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(488) Variable = SUCLG2 MUTATION ANALYSIS
D488V1, survival
                  sevent
clus2                0   1
  SUCLG2 MUTATED     3   0
  SUCLG2 WILD-TYPE 178  80
  SUCLG2 MUTATED SUCLG2 WILD-TYPE 
               3              258 
  SUCLG2 MUTATED SUCLG2 WILD-TYPE 
               0               80 
$`SUCLG2 MUTATED`
TCGA-BR-A4QL TCGA-CG-5723 TCGA-HU-A4H8 
       11.57       105.07         8.88 

$`SUCLG2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         6.02         0.99        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  SUCLG2 MUTATED SUCLG2 WILD-TYPE 
            8.88             0.00 
  SUCLG2 MUTATED SUCLG2 WILD-TYPE 
          105.07            79.07 
  SUCLG2 MUTATED SUCLG2 WILD-TYPE 
           11.57            12.64 
[1] "8.9 - 105.1 (11.6)" "0.0 - 79.1 (12.6)" 
[1] "hr="   "3e+07"
D488V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SUCLG2 MUTATED         1        0        1        1         0         0
  SUCLG2 WILD-TYPE       0        9       26       25        31        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SUCLG2 MUTATED           0          1          1          0        0
  SUCLG2 WILD-TYPE         3         48         35         24       24
D488V3, multiclass
            clus
vv           SUCLG2 MUTATED SUCLG2 WILD-TYPE
  STAGE I                 1                0
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                1               25
  STAGE IIA               0               31
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SUCLG2 MUTATED     2   1   1   1
  SUCLG2 WILD-TYPE   9  71 121  74
D488V4, multiclass
    clus
vv   SUCLG2 MUTATED SUCLG2 WILD-TYPE
  T1              2                9
  T2              1               71
  T3              1              121
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  SUCLG2 MUTATED    1  3  0  1
  SUCLG2 WILD-TYPE 92 78 50 52
D488V5, multiclass
    clus
vv   SUCLG2 MUTATED SUCLG2 WILD-TYPE
  N0              1               92
  N1              3               78
  N2              0               50
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D488V6, binary
                  cls
clus                 0   1
  SUCLG2 MUTATED     4   0
  SUCLG2 WILD-TYPE 253  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUCLG2 MUTATED      4    0
  SUCLG2 WILD-TYPE  253   18
   clus
vv  SUCLG2 MUTATED SUCLG2 WILD-TYPE
  0              4              253
  1              0               18
[1] 2 2
[1] FALSE
D488V7, binary
                  cls
clus                 0   1
  SUCLG2 MUTATED     2   3
  SUCLG2 WILD-TYPE 108 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUCLG2 MUTATED      2    3
  SUCLG2 WILD-TYPE  108  176
        clus
vv       SUCLG2 MUTATED SUCLG2 WILD-TYPE
  FEMALE              2              108
  MALE                3              176
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SUCLG2 MUTATED                                       0
  SUCLG2 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SUCLG2 MUTATED                                                        4
  SUCLG2 WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SUCLG2 MUTATED                                                                   0
  SUCLG2 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SUCLG2 MUTATED                                                  1
  SUCLG2 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SUCLG2 MUTATED                                                          0
  SUCLG2 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SUCLG2 MUTATED                                                           0
  SUCLG2 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SUCLG2 MUTATED                                          0
  SUCLG2 WILD-TYPE                                        3
D488V8, multiclass
                                                                   clus
vv                                                                  SUCLG2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  SUCLG2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D488V9, binary
                  cls
clus                 0   1
  SUCLG2 MUTATED     0   5
  SUCLG2 WILD-TYPE   5 279
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUCLG2 MUTATED      0    5
  SUCLG2 WILD-TYPE    5  279
     clus
vv    SUCLG2 MUTATED SUCLG2 WILD-TYPE
  NO               0                5
  YES              5              279
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SUCLG2 MUTATED     4   0   0   1
  SUCLG2 WILD-TYPE 223  10  10  23
D488V10, multiclass
    clus
vv   SUCLG2 MUTATED SUCLG2 WILD-TYPE
  R0              4              223
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D488V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SUCLG2 MUTATED       1                         1     2
  SUCLG2 WILD-TYPE    75                         3   166
D488V12, multiclass
                           clus
vv                          SUCLG2 MUTATED SUCLG2 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  2              166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(489) Variable = CNOT6 MUTATION ANALYSIS
D489V1, survival
                 sevent
clus2               0   1
  CNOT6 MUTATED     3   2
  CNOT6 WILD-TYPE 178  78
  CNOT6 MUTATED CNOT6 WILD-TYPE 
              5             256 
  CNOT6 MUTATED CNOT6 WILD-TYPE 
              2              78 
$`CNOT6 MUTATED`
TCGA-B7-5816 TCGA-CG-5721 TCGA-CG-5728 TCGA-HJ-7597 TCGA-HU-A4GQ 
       26.70         6.02        65.10        26.47         0.10 

$`CNOT6 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 
        5.03        13.58         0.56        11.08         5.52         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        11.77        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  CNOT6 MUTATED CNOT6 WILD-TYPE 
            0.1             0.0 
  CNOT6 MUTATED CNOT6 WILD-TYPE 
          65.10          105.07 
  CNOT6 MUTATED CNOT6 WILD-TYPE 
         26.470          12.605 
[1] "0.1 - 65.1 (26.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D489V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CNOT6 MUTATED         0        0        3        0         0         1
  CNOT6 WILD-TYPE       1        9       24       26        31        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNOT6 MUTATED           0          0          0          1        1
  CNOT6 WILD-TYPE         3         49         36         23       23
D489V3, multiclass
            clus
vv           CNOT6 MUTATED CNOT6 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               3              24
  STAGE II               0              26
  STAGE IIA              0              31
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CNOT6 MUTATED     1   3   0   3
  CNOT6 WILD-TYPE  10  69 122  72
D489V4, multiclass
    clus
vv   CNOT6 MUTATED CNOT6 WILD-TYPE
  T1             1              10
  T2             3              69
  T3             0             122
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CNOT6 MUTATED    4  1  1  0
  CNOT6 WILD-TYPE 89 80 49 53
D489V5, multiclass
    clus
vv   CNOT6 MUTATED CNOT6 WILD-TYPE
  N0             4              89
  N1             1              80
  N2             1              49
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D489V6, binary
                 cls
clus                0   1
  CNOT6 MUTATED     6   0
  CNOT6 WILD-TYPE 251  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT6 MUTATED      6    0
  CNOT6 WILD-TYPE  251   18
   clus
vv  CNOT6 MUTATED CNOT6 WILD-TYPE
  0             6             251
  1             0              18
[1] 2 2
[1] FALSE
D489V7, binary
                 cls
clus                0   1
  CNOT6 MUTATED     4   3
  CNOT6 WILD-TYPE 106 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT6 MUTATED      4    3
  CNOT6 WILD-TYPE  106  176
        clus
vv       CNOT6 MUTATED CNOT6 WILD-TYPE
  FEMALE             4             106
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CNOT6 MUTATED                                       1
  CNOT6 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CNOT6 MUTATED                                                        1
  CNOT6 WILD-TYPE                                                    134
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CNOT6 MUTATED                                                                   3
  CNOT6 WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CNOT6 MUTATED                                                  1
  CNOT6 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CNOT6 MUTATED                                                          0
  CNOT6 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CNOT6 MUTATED                                                           0
  CNOT6 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CNOT6 MUTATED                                          1
  CNOT6 WILD-TYPE                                        2
D489V8, multiclass
                                                                   clus
vv                                                                  CNOT6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        1
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  CNOT6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D489V9, binary
                 cls
clus                0   1
  CNOT6 MUTATED     0   7
  CNOT6 WILD-TYPE   5 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT6 MUTATED      0    7
  CNOT6 WILD-TYPE    5  277
     clus
vv    CNOT6 MUTATED CNOT6 WILD-TYPE
  NO              0               5
  YES             7             277
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CNOT6 MUTATED     6   0   0   1
  CNOT6 WILD-TYPE 221  10  10  23
D489V10, multiclass
    clus
vv   CNOT6 MUTATED CNOT6 WILD-TYPE
  R0             6             221
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D489V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CNOT6 MUTATED       1                         0     3
  CNOT6 WILD-TYPE    75                         4   165
D489V12, multiclass
                           clus
vv                          CNOT6 MUTATED CNOT6 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(490) Variable = TIGD7 MUTATION ANALYSIS
D490V1, survival
                 sevent
clus2               0   1
  TIGD7 MUTATED     7   1
  TIGD7 WILD-TYPE 174  79
  TIGD7 MUTATED TIGD7 WILD-TYPE 
              8             253 
  TIGD7 MUTATED TIGD7 WILD-TYPE 
              1              79 
$`TIGD7 MUTATED`
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-8487 
       34.68        32.78        32.94        23.93        12.43         1.12 
TCGA-BR-8680 TCGA-CD-A4MG 
       15.81         6.58 

$`TIGD7 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 
       30.90        31.20        12.82         9.21        24.76        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       28.01        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        20.55         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  TIGD7 MUTATED TIGD7 WILD-TYPE 
           1.12            0.00 
  TIGD7 MUTATED TIGD7 WILD-TYPE 
          34.68          105.07 
  TIGD7 MUTATED TIGD7 WILD-TYPE 
          19.87           12.59 
[1] "1.1 - 34.7 (19.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "3.9"
D490V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TIGD7 MUTATED         0        0        1        0         5         1
  TIGD7 WILD-TYPE       1        9       26       26        26        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TIGD7 MUTATED           0          0          0          0        1
  TIGD7 WILD-TYPE         3         49         36         24       23
D490V3, multiclass
            clus
vv           TIGD7 MUTATED TIGD7 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              5              26
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TIGD7 MUTATED     0   1   5   2
  TIGD7 WILD-TYPE  11  71 117  73
D490V4, multiclass
    clus
vv   TIGD7 MUTATED TIGD7 WILD-TYPE
  T1             0              11
  T2             1              71
  T3             5             117
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  TIGD7 MUTATED    7  0  1  0
  TIGD7 WILD-TYPE 86 81 49 53
D490V5, multiclass
    clus
vv   TIGD7 MUTATED TIGD7 WILD-TYPE
  N0             7              86
  N1             0              81
  N2             1              49
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D490V6, binary
                 cls
clus                0   1
  TIGD7 MUTATED     7   1
  TIGD7 WILD-TYPE 250  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD7 MUTATED      7    1
  TIGD7 WILD-TYPE  250   17
   clus
vv  TIGD7 MUTATED TIGD7 WILD-TYPE
  0             7             250
  1             1              17
[1] 2 2
[1] FALSE
D490V7, binary
                 cls
clus                0   1
  TIGD7 MUTATED     5   3
  TIGD7 WILD-TYPE 105 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD7 MUTATED      5    3
  TIGD7 WILD-TYPE  105  176
        clus
vv       TIGD7 MUTATED TIGD7 WILD-TYPE
  FEMALE             5             105
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TIGD7 MUTATED                                       1
  TIGD7 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TIGD7 MUTATED                                                        5
  TIGD7 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TIGD7 MUTATED                                                                   1
  TIGD7 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TIGD7 MUTATED                                                  1
  TIGD7 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TIGD7 MUTATED                                                          0
  TIGD7 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TIGD7 MUTATED                                                           0
  TIGD7 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TIGD7 MUTATED                                          0
  TIGD7 WILD-TYPE                                        3
D490V8, multiclass
                                                                   clus
vv                                                                  TIGD7 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  TIGD7 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D490V9, binary
                 cls
clus                0   1
  TIGD7 MUTATED     0   8
  TIGD7 WILD-TYPE   5 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD7 MUTATED      0    8
  TIGD7 WILD-TYPE    5  276
     clus
vv    TIGD7 MUTATED TIGD7 WILD-TYPE
  NO              0               5
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TIGD7 MUTATED     7   0   0   0
  TIGD7 WILD-TYPE 220  10  10  24
D490V10, multiclass
    clus
vv   TIGD7 MUTATED TIGD7 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D490V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TIGD7 MUTATED       2                         0     6
  TIGD7 WILD-TYPE    74                         4   162
D490V12, multiclass
                           clus
vv                          TIGD7 MUTATED TIGD7 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(491) Variable = ITSN2 MUTATION ANALYSIS
D491V1, survival
                 sevent
clus2               0   1
  ITSN2 MUTATED     7   4
  ITSN2 WILD-TYPE 174  76
  ITSN2 MUTATED ITSN2 WILD-TYPE 
             11             250 
  ITSN2 MUTATED ITSN2 WILD-TYPE 
              4              76 
$`ITSN2 MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-8081 TCGA-BR-8487 
        6.97         6.61        34.68        19.33        20.55         1.12 
TCGA-BR-8591 TCGA-BR-A4QI TCGA-CD-5801 TCGA-CG-5721 TCGA-D7-A4YY 
       13.45        13.64        13.18         6.02        13.78 

$`ITSN2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       30.90         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       12.26         9.60         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       15.81         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       16.44         5.92        15.16        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  ITSN2 MUTATED ITSN2 WILD-TYPE 
           1.12            0.00 
  ITSN2 MUTATED ITSN2 WILD-TYPE 
          34.68          105.07 
  ITSN2 MUTATED ITSN2 WILD-TYPE 
         13.450          12.575 
[1] "1.1 - 34.7 (13.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D491V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ITSN2 MUTATED         1        0        0        1         3         2
  ITSN2 WILD-TYPE       0        9       27       25        28        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ITSN2 MUTATED           1          2          1          1        2
  ITSN2 WILD-TYPE         2         47         35         23       22
D491V3, multiclass
            clus
vv           ITSN2 MUTATED ITSN2 WILD-TYPE
  STAGE I                1               0
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              3              28
  STAGE IIB              2              42
  STAGE III              1               2
  STAGE IIIA             2              47
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITSN2 MUTATED     1   2   7   4
  ITSN2 WILD-TYPE  10  70 115  71
D491V4, multiclass
    clus
vv   ITSN2 MUTATED ITSN2 WILD-TYPE
  T1             1              10
  T2             2              70
  T3             7             115
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ITSN2 MUTATED    4  7  1  2
  ITSN2 WILD-TYPE 89 74 49 51
D491V5, multiclass
    clus
vv   ITSN2 MUTATED ITSN2 WILD-TYPE
  N0             4              89
  N1             7              74
  N2             1              49
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D491V6, binary
                 cls
clus                0   1
  ITSN2 MUTATED    14   0
  ITSN2 WILD-TYPE 243  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITSN2 MUTATED     14    0
  ITSN2 WILD-TYPE  243   18
   clus
vv  ITSN2 MUTATED ITSN2 WILD-TYPE
  0            14             243
  1             0              18
[1] 2 2
[1] FALSE
D491V7, binary
                 cls
clus                0   1
  ITSN2 MUTATED     9   7
  ITSN2 WILD-TYPE 101 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITSN2 MUTATED      9    7
  ITSN2 WILD-TYPE  101  172
        clus
vv       ITSN2 MUTATED ITSN2 WILD-TYPE
  FEMALE             9             101
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ITSN2 MUTATED                                       0
  ITSN2 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ITSN2 MUTATED                                                       14
  ITSN2 WILD-TYPE                                                    121
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ITSN2 MUTATED                                                                   1
  ITSN2 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ITSN2 MUTATED                                                  0
  ITSN2 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ITSN2 MUTATED                                                          1
  ITSN2 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ITSN2 MUTATED                                                           0
  ITSN2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ITSN2 MUTATED                                          0
  ITSN2 WILD-TYPE                                        3
D491V8, multiclass
                                                                   clus
vv                                                                  ITSN2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       14
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ITSN2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        121
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D491V9, binary
                 cls
clus                0   1
  ITSN2 MUTATED     1  15
  ITSN2 WILD-TYPE   4 269
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITSN2 MUTATED      1   15
  ITSN2 WILD-TYPE    4  269
     clus
vv    ITSN2 MUTATED ITSN2 WILD-TYPE
  NO              1               4
  YES            15             269
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ITSN2 MUTATED    11   0   0   5
  ITSN2 WILD-TYPE 216  10  10  19
D491V10, multiclass
    clus
vv   ITSN2 MUTATED ITSN2 WILD-TYPE
  R0            11             216
  R1             0              10
  R2             0              10
  RX             5              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D491V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ITSN2 MUTATED       1                         1    12
  ITSN2 WILD-TYPE    75                         3   156
D491V12, multiclass
                           clus
vv                          ITSN2 MUTATED ITSN2 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                12             156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(492) Variable = OGFRL1 MUTATION ANALYSIS
D492V1, survival
                  sevent
clus2                0   1
  OGFRL1 MUTATED     6   2
  OGFRL1 WILD-TYPE 175  78
  OGFRL1 MUTATED OGFRL1 WILD-TYPE 
               8              253 
  OGFRL1 MUTATED OGFRL1 WILD-TYPE 
               2               78 
$`OGFRL1 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8382 TCGA-CG-4469 TCGA-D7-6822 
       30.90        34.68        23.93        15.85         7.07        12.33 
TCGA-F1-6874 TCGA-HU-A4GX 
       14.47        10.19 

$`OGFRL1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       18.35         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        0.26         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51         6.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  OGFRL1 MUTATED OGFRL1 WILD-TYPE 
            7.07             0.00 
  OGFRL1 MUTATED OGFRL1 WILD-TYPE 
           34.68           105.07 
  OGFRL1 MUTATED OGFRL1 WILD-TYPE 
           15.16            12.59 
[1] "7.1 - 34.7 (15.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.8"
D492V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OGFRL1 MUTATED         0        0        4        0         1         0
  OGFRL1 WILD-TYPE       1        9       23       26        30        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OGFRL1 MUTATED           0          0          0          2        1
  OGFRL1 WILD-TYPE         3         49         36         22       23
D492V3, multiclass
            clus
vv           OGFRL1 MUTATED OGFRL1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                4               23
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              2               22
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OGFRL1 MUTATED     0   5   2   2
  OGFRL1 WILD-TYPE  11  67 120  73
D492V4, multiclass
    clus
vv   OGFRL1 MUTATED OGFRL1 WILD-TYPE
  T1              0               11
  T2              5               67
  T3              2              120
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  OGFRL1 MUTATED    5  0  1  2
  OGFRL1 WILD-TYPE 88 81 49 51
D492V5, multiclass
    clus
vv   OGFRL1 MUTATED OGFRL1 WILD-TYPE
  N0              5               88
  N1              0               81
  N2              1               49
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D492V6, binary
                  cls
clus                 0   1
  OGFRL1 MUTATED    10   0
  OGFRL1 WILD-TYPE 247  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OGFRL1 MUTATED     10    0
  OGFRL1 WILD-TYPE  247   18
   clus
vv  OGFRL1 MUTATED OGFRL1 WILD-TYPE
  0             10              247
  1              0               18
[1] 2 2
[1] FALSE
D492V7, binary
                  cls
clus                 0   1
  OGFRL1 MUTATED     6   4
  OGFRL1 WILD-TYPE 104 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OGFRL1 MUTATED      6    4
  OGFRL1 WILD-TYPE  104  175
        clus
vv       OGFRL1 MUTATED OGFRL1 WILD-TYPE
  FEMALE              6              104
  MALE                4              175
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  OGFRL1 MUTATED                                       1
  OGFRL1 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OGFRL1 MUTATED                                                        5
  OGFRL1 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OGFRL1 MUTATED                                                                   3
  OGFRL1 WILD-TYPE                                                                37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  OGFRL1 MUTATED                                                  1
  OGFRL1 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  OGFRL1 MUTATED                                                          0
  OGFRL1 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  OGFRL1 MUTATED                                                           0
  OGFRL1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  OGFRL1 MUTATED                                          0
  OGFRL1 WILD-TYPE                                        3
D492V8, multiclass
                                                                   clus
vv                                                                  OGFRL1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  OGFRL1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D492V9, binary
                  cls
clus                 0   1
  OGFRL1 MUTATED     0  10
  OGFRL1 WILD-TYPE   5 274
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OGFRL1 MUTATED      0   10
  OGFRL1 WILD-TYPE    5  274
     clus
vv    OGFRL1 MUTATED OGFRL1 WILD-TYPE
  NO               0                5
  YES             10              274
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OGFRL1 MUTATED     7   1   0   2
  OGFRL1 WILD-TYPE 220   9  10  22
D492V10, multiclass
    clus
vv   OGFRL1 MUTATED OGFRL1 WILD-TYPE
  R0              7              220
  R1              1                9
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D492V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OGFRL1 MUTATED       1                         0     7
  OGFRL1 WILD-TYPE    75                         4   161
D492V12, multiclass
                           clus
vv                          OGFRL1 MUTATED OGFRL1 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  7              161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(493) Variable = KIAA1462 MUTATION ANALYSIS
D493V1, survival
                    sevent
clus2                  0   1
  KIAA1462 MUTATED    11   6
  KIAA1462 WILD-TYPE 170  74
  KIAA1462 MUTATED KIAA1462 WILD-TYPE 
                17                244 
  KIAA1462 MUTATED KIAA1462 WILD-TYPE 
                 6                 74 
$`KIAA1462 MUTATED`
TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-A4J1 TCGA-BR-A4QL TCGA-CD-8527 
       34.68         6.18        19.50         0.72        11.57         0.07 
TCGA-CD-A489 TCGA-CG-4436 TCGA-CG-5721 TCGA-CG-5733 TCGA-EQ-8122 TCGA-HJ-7597 
       11.31         7.99         6.02        21.07         7.99        26.47 
TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GF TCGA-HU-A4H8 TCGA-IN-8663 
       11.41        11.84        25.81         8.88         3.39 

$`KIAA1462 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        7.40         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
       12.89         8.98        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        13.64         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 
        0.39         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56        11.08         5.52         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        22.75        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
       12.95        19.36        23.84        12.30         9.67        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IP-7968 
       21.21         3.45        18.81         2.53 

  KIAA1462 MUTATED KIAA1462 WILD-TYPE 
              0.07               0.00 
  KIAA1462 MUTATED KIAA1462 WILD-TYPE 
             34.68             105.07 
  KIAA1462 MUTATED KIAA1462 WILD-TYPE 
             11.31              12.79 
[1] "0.1 - 34.7 (11.3)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.3"
D493V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1462 MUTATED         0        0        3        2         4         4
  KIAA1462 WILD-TYPE       1        9       24       24        27        40
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1462 MUTATED           0          3          1          1        1
  KIAA1462 WILD-TYPE         3         46         35         23       23
D493V3, multiclass
            clus
vv           KIAA1462 MUTATED KIAA1462 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  3                 24
  STAGE II                  2                 24
  STAGE IIA                 4                 27
  STAGE IIB                 4                 40
  STAGE III                 0                  3
  STAGE IIIA                3                 46
  STAGE IIIB                1                 35
  STAGE IIIC                1                 23
  STAGE IV                  1                 23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1462 MUTATED     1   6   7   5
  KIAA1462 WILD-TYPE  10  66 115  70
D493V4, multiclass
    clus
vv   KIAA1462 MUTATED KIAA1462 WILD-TYPE
  T1                1                 10
  T2                6                 66
  T3                7                115
  T4                5                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  KIAA1462 MUTATED    8  9  3  1
  KIAA1462 WILD-TYPE 85 72 47 52
D493V5, multiclass
    clus
vv   KIAA1462 MUTATED KIAA1462 WILD-TYPE
  N0                8                 85
  N1                9                 72
  N2                3                 47
  N3                1                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D493V6, binary
                    cls
clus                   0   1
  KIAA1462 MUTATED    20   0
  KIAA1462 WILD-TYPE 237  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1462 MUTATED     20    0
  KIAA1462 WILD-TYPE  237   18
   clus
vv  KIAA1462 MUTATED KIAA1462 WILD-TYPE
  0               20                237
  1                0                 18
[1] 2 2
[1] FALSE
D493V7, binary
                    cls
clus                   0   1
  KIAA1462 MUTATED    12  10
  KIAA1462 WILD-TYPE  98 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1462 MUTATED     12   10
  KIAA1462 WILD-TYPE   98  169
        clus
vv       KIAA1462 MUTATED KIAA1462 WILD-TYPE
  FEMALE               12                 98
  MALE                 10                169
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KIAA1462 MUTATED                                       3
  KIAA1462 WILD-TYPE                                    47
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA1462 MUTATED                                                        9
  KIAA1462 WILD-TYPE                                                    126
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA1462 MUTATED                                                                   6
  KIAA1462 WILD-TYPE                                                                34
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KIAA1462 MUTATED                                                  2
  KIAA1462 WILD-TYPE                                               36
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KIAA1462 MUTATED                                                          1
  KIAA1462 WILD-TYPE                                                       15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KIAA1462 MUTATED                                                           0
  KIAA1462 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KIAA1462 MUTATED                                          1
  KIAA1462 WILD-TYPE                                        2
D493V8, multiclass
                                                                   clus
vv                                                                  KIAA1462 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  KIAA1462 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D493V9, binary
                    cls
clus                   0   1
  KIAA1462 MUTATED     1  21
  KIAA1462 WILD-TYPE   4 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1462 MUTATED      1   21
  KIAA1462 WILD-TYPE    4  263
     clus
vv    KIAA1462 MUTATED KIAA1462 WILD-TYPE
  NO                 1                  4
  YES               21                263
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA1462 MUTATED    15   0   0   4
  KIAA1462 WILD-TYPE 212  10  10  20
D493V10, multiclass
    clus
vv   KIAA1462 MUTATED KIAA1462 WILD-TYPE
  R0               15                212
  R1                0                 10
  R2                0                 10
  RX                4                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D493V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA1462 MUTATED       7                         0    11
  KIAA1462 WILD-TYPE    69                         4   157
D493V12, multiclass
                           clus
vv                          KIAA1462 MUTATED KIAA1462 WILD-TYPE
  ASIAN                                    7                 69
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                   11                157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(494) Variable = MAP1A MUTATION ANALYSIS
D494V1, survival
                 sevent
clus2               0   1
  MAP1A MUTATED     9   5
  MAP1A WILD-TYPE 172  75
  MAP1A MUTATED MAP1A WILD-TYPE 
             14             247 
  MAP1A MUTATED MAP1A WILD-TYPE 
              5              75 
$`MAP1A MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7901 TCGA-BR-8361 
        6.97        34.68        32.78        32.94         3.45        19.50 
TCGA-BR-8372 TCGA-BR-8487 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-4466 
       19.17         1.12         0.10         6.58         1.02        18.97 
TCGA-CG-5721 TCGA-CG-5726 
        6.02        28.96 

$`MAP1A WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       31.20        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 
       28.01        18.15        15.32        28.73        12.43         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        20.55         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
        2.20        15.58         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 
        1.02         0.99         0.99       105.07        12.03        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  MAP1A MUTATED MAP1A WILD-TYPE 
            0.1             0.0 
  MAP1A MUTATED MAP1A WILD-TYPE 
          34.68          105.07 
  MAP1A MUTATED MAP1A WILD-TYPE 
          12.97           12.62 
[1] "0.1 - 34.7 (13.0)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1"  
D494V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAP1A MUTATED         0        1        1        1         5         1
  MAP1A WILD-TYPE       1        8       26       25        26        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP1A MUTATED           0          1          0          2        2
  MAP1A WILD-TYPE         3         48         36         22       22
D494V3, multiclass
            clus
vv           MAP1A MUTATED MAP1A WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              5              26
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             2              22
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MAP1A MUTATED     1   1  10   3
  MAP1A WILD-TYPE  10  71 112  72
D494V4, multiclass
    clus
vv   MAP1A MUTATED MAP1A WILD-TYPE
  T1             1              10
  T2             1              71
  T3            10             112
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  MAP1A MUTATED    8  3  2  1
  MAP1A WILD-TYPE 85 78 48 52
D494V5, multiclass
    clus
vv   MAP1A MUTATED MAP1A WILD-TYPE
  N0             8              85
  N1             3              78
  N2             2              48
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D494V6, binary
                 cls
clus                0   1
  MAP1A MUTATED    12   1
  MAP1A WILD-TYPE 245  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAP1A MUTATED     12    1
  MAP1A WILD-TYPE  245   17
   clus
vv  MAP1A MUTATED MAP1A WILD-TYPE
  0            12             245
  1             1              17
[1] 2 2
[1] FALSE
D494V7, binary
                 cls
clus                0   1
  MAP1A MUTATED     7   8
  MAP1A WILD-TYPE 103 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAP1A MUTATED      7    8
  MAP1A WILD-TYPE  103  171
        clus
vv       MAP1A MUTATED MAP1A WILD-TYPE
  FEMALE             7             103
  MALE               8             171
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MAP1A MUTATED                                       1
  MAP1A WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MAP1A MUTATED                                                       11
  MAP1A WILD-TYPE                                                    124
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MAP1A MUTATED                                                                   3
  MAP1A WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MAP1A MUTATED                                                  0
  MAP1A WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MAP1A MUTATED                                                          0
  MAP1A WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MAP1A MUTATED                                                           0
  MAP1A WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MAP1A MUTATED                                          0
  MAP1A WILD-TYPE                                        3
D494V8, multiclass
                                                                   clus
vv                                                                  MAP1A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  MAP1A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D494V9, binary
                 cls
clus                0   1
  MAP1A MUTATED     0  15
  MAP1A WILD-TYPE   5 269
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAP1A MUTATED      0   15
  MAP1A WILD-TYPE    5  269
     clus
vv    MAP1A MUTATED MAP1A WILD-TYPE
  NO              0               5
  YES            15             269
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MAP1A MUTATED    11   0   1   2
  MAP1A WILD-TYPE 216  10   9  22
D494V10, multiclass
    clus
vv   MAP1A MUTATED MAP1A WILD-TYPE
  R0            11             216
  R1             0              10
  R2             1               9
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D494V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAP1A MUTATED       2                         0     9
  MAP1A WILD-TYPE    74                         4   159
D494V12, multiclass
                           clus
vv                          MAP1A MUTATED MAP1A WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 9             159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(495) Variable = NOB1 MUTATION ANALYSIS
D495V1, survival
                sevent
clus2              0   1
  NOB1 MUTATED     5   1
  NOB1 WILD-TYPE 176  79
  NOB1 MUTATED NOB1 WILD-TYPE 
             6            255 
  NOB1 MUTATED NOB1 WILD-TYPE 
             1             79 
$`NOB1 MUTATED`
TCGA-BR-7707 TCGA-BR-8487 TCGA-CG-4305 TCGA-CG-4306 TCGA-HU-8608 TCGA-HU-A4H6 
       23.93         1.12        15.95         1.02        10.62         9.67 

$`NOB1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       20.02         3.02        27.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        11.41        12.10         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        12.30         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  NOB1 MUTATED NOB1 WILD-TYPE 
          1.02           0.00 
  NOB1 MUTATED NOB1 WILD-TYPE 
         23.93         105.07 
  NOB1 MUTATED NOB1 WILD-TYPE 
        10.145         12.660 
[1] "1.0 - 23.9 (10.1)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.3"
D495V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NOB1 MUTATED         0        0        1        1         1         0
  NOB1 WILD-TYPE       1        9       26       25        30        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NOB1 MUTATED           0          1          1          0        1
  NOB1 WILD-TYPE         3         48         35         24       23
D495V3, multiclass
            clus
vv           NOB1 MUTATED NOB1 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              1             25
  STAGE IIA             1             30
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NOB1 MUTATED     0   2   3   1
  NOB1 WILD-TYPE  11  70 119  74
D495V4, multiclass
    clus
vv   NOB1 MUTATED NOB1 WILD-TYPE
  T1            0             11
  T2            2             70
  T3            3            119
  T4            1             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  NOB1 MUTATED    2  1  3  0
  NOB1 WILD-TYPE 91 80 47 53
D495V5, multiclass
    clus
vv   NOB1 MUTATED NOB1 WILD-TYPE
  N0            2             91
  N1            1             80
  N2            3             47
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D495V6, binary
                cls
clus               0   1
  NOB1 MUTATED     6   1
  NOB1 WILD-TYPE 251  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOB1 MUTATED      6    1
  NOB1 WILD-TYPE  251   17
   clus
vv  NOB1 MUTATED NOB1 WILD-TYPE
  0            6            251
  1            1             17
[1] 2 2
[1] FALSE
D495V7, binary
                cls
clus               0   1
  NOB1 MUTATED     4   3
  NOB1 WILD-TYPE 106 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOB1 MUTATED      4    3
  NOB1 WILD-TYPE  106  176
        clus
vv       NOB1 MUTATED NOB1 WILD-TYPE
  FEMALE            4            106
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NOB1 MUTATED                                       1
  NOB1 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NOB1 MUTATED                                                        5
  NOB1 WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NOB1 MUTATED                                                                   0
  NOB1 WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NOB1 MUTATED                                                  1
  NOB1 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NOB1 MUTATED                                                          0
  NOB1 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NOB1 MUTATED                                                           0
  NOB1 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NOB1 MUTATED                                          0
  NOB1 WILD-TYPE                                        3
D495V8, multiclass
                                                                   clus
vv                                                                  NOB1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  NOB1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D495V9, binary
                cls
clus               0   1
  NOB1 MUTATED     0   7
  NOB1 WILD-TYPE   5 277
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOB1 MUTATED      0    7
  NOB1 WILD-TYPE    5  277
     clus
vv    NOB1 MUTATED NOB1 WILD-TYPE
  NO             0              5
  YES            7            277
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NOB1 MUTATED     5   0   1   1
  NOB1 WILD-TYPE 222  10   9  23
D495V10, multiclass
    clus
vv   NOB1 MUTATED NOB1 WILD-TYPE
  R0            5            222
  R1            0             10
  R2            1              9
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D495V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NOB1 MUTATED       2                         0     3
  NOB1 WILD-TYPE    74                         4   165
D495V12, multiclass
                           clus
vv                          NOB1 MUTATED NOB1 WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                3            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(496) Variable = TNK2 MUTATION ANALYSIS
D496V1, survival
                sevent
clus2              0   1
  TNK2 MUTATED     8   2
  TNK2 WILD-TYPE 173  78
  TNK2 MUTATED TNK2 WILD-TYPE 
            10            251 
  TNK2 MUTATED TNK2 WILD-TYPE 
             2             78 
$`TNK2 MUTATED`
TCGA-BR-8078 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8680 TCGA-BR-A4PE TCGA-D7-A4YT 
       12.26        19.17        15.85        15.81        20.42        14.27 
TCGA-D7-A4YV TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4G8 
        5.92        26.47        11.41        11.84 

$`TNK2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51        20.65         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YX 
       18.21        14.66        21.14        20.91        16.44        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        5.52         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  TNK2 MUTATED TNK2 WILD-TYPE 
          5.92           0.00 
  TNK2 MUTATED TNK2 WILD-TYPE 
         26.47         105.07 
  TNK2 MUTATED TNK2 WILD-TYPE 
         15.04          12.59 
[1] "5.9 - 26.5 (15.0)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.7"
D496V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TNK2 MUTATED         0        0        2        0         0         4
  TNK2 WILD-TYPE       1        9       25       26        31        40
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNK2 MUTATED           0          1          0          2        1
  TNK2 WILD-TYPE         3         48         36         22       23
D496V3, multiclass
            clus
vv           TNK2 MUTATED TNK2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              0             26
  STAGE IIA             0             31
  STAGE IIB             4             40
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            2             22
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TNK2 MUTATED     1   3   2   5
  TNK2 WILD-TYPE  10  69 120  70
D496V4, multiclass
    clus
vv   TNK2 MUTATED TNK2 WILD-TYPE
  T1            1             10
  T2            3             69
  T3            2            120
  T4            5             70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  TNK2 MUTATED    4  2  1  3
  TNK2 WILD-TYPE 89 79 49 50
D496V5, multiclass
    clus
vv   TNK2 MUTATED TNK2 WILD-TYPE
  N0            4             89
  N1            2             79
  N2            1             49
  N3            3             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D496V6, binary
                cls
clus               0   1
  TNK2 MUTATED     9   1
  TNK2 WILD-TYPE 248  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNK2 MUTATED      9    1
  TNK2 WILD-TYPE  248   17
   clus
vv  TNK2 MUTATED TNK2 WILD-TYPE
  0            9            248
  1            1             17
[1] 2 2
[1] FALSE
D496V7, binary
                cls
clus               0   1
  TNK2 MUTATED     8   3
  TNK2 WILD-TYPE 102 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNK2 MUTATED      8    3
  TNK2 WILD-TYPE  102  176
        clus
vv       TNK2 MUTATED TNK2 WILD-TYPE
  FEMALE            8            102
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TNK2 MUTATED                                       2
  TNK2 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TNK2 MUTATED                                                        5
  TNK2 WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TNK2 MUTATED                                                                   0
  TNK2 WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TNK2 MUTATED                                                  3
  TNK2 WILD-TYPE                                               35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TNK2 MUTATED                                                          0
  TNK2 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TNK2 MUTATED                                                           0
  TNK2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TNK2 MUTATED                                          1
  TNK2 WILD-TYPE                                        2
D496V8, multiclass
                                                                   clus
vv                                                                  TNK2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  TNK2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D496V9, binary
                cls
clus               0   1
  TNK2 MUTATED     0  11
  TNK2 WILD-TYPE   5 273
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNK2 MUTATED      0   11
  TNK2 WILD-TYPE    5  273
     clus
vv    TNK2 MUTATED TNK2 WILD-TYPE
  NO             0              5
  YES           11            273
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TNK2 MUTATED     9   0   0   1
  TNK2 WILD-TYPE 218  10  10  23
D496V10, multiclass
    clus
vv   TNK2 MUTATED TNK2 WILD-TYPE
  R0            9            218
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D496V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TNK2 MUTATED       3                         0     8
  TNK2 WILD-TYPE    73                         4   160
D496V12, multiclass
                           clus
vv                          TNK2 MUTATED TNK2 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                8            160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(497) Variable = CYP7B1 MUTATION ANALYSIS
D497V1, survival
                  sevent
clus2                0   1
  CYP7B1 MUTATED    12   3
  CYP7B1 WILD-TYPE 169  77
  CYP7B1 MUTATED CYP7B1 WILD-TYPE 
              15              246 
  CYP7B1 MUTATED CYP7B1 WILD-TYPE 
               3               77 
$`CYP7B1 MUTATED`
TCGA-BR-4201 TCGA-BR-7703 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8483 TCGA-BR-8591 
       30.90        24.76        14.43        12.26         5.39        13.45 
TCGA-CD-5798 TCGA-CD-8535 TCGA-CD-A487 TCGA-CG-4465 TCGA-CG-5723 TCGA-CG-5728 
        2.83         0.13         9.34         9.01       105.07        65.10 
TCGA-D7-5579 TCGA-D7-6818 TCGA-D7-A4YU 
       11.93        10.55        16.44 

$`CYP7B1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
       15.85         3.72        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        15.81         9.34         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 
       20.42         1.15        13.64        11.57         5.13         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.10         0.10         3.42        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
       12.03         0.00        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        79.07         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        7.99        12.36        12.66        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        15.98        12.79        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  CYP7B1 MUTATED CYP7B1 WILD-TYPE 
            0.13             0.00 
  CYP7B1 MUTATED CYP7B1 WILD-TYPE 
          105.07            79.07 
  CYP7B1 MUTATED CYP7B1 WILD-TYPE 
           12.26            12.64 
[1] "0.1 - 105.1 (12.3)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "2.2"
D497V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CYP7B1 MUTATED         0        1        1        2         0         2
  CYP7B1 WILD-TYPE       1        8       26       24        31        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP7B1 MUTATED           1          4          1          1        1
  CYP7B1 WILD-TYPE         2         45         35         23       23
D497V3, multiclass
            clus
vv           CYP7B1 MUTATED CYP7B1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                1               26
  STAGE II                2               24
  STAGE IIA               0               31
  STAGE IIB               2               42
  STAGE III               1                2
  STAGE IIIA              4               45
  STAGE IIIB              1               35
  STAGE IIIC              1               23
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CYP7B1 MUTATED     1   4   6   4
  CYP7B1 WILD-TYPE  10  68 116  71
D497V4, multiclass
    clus
vv   CYP7B1 MUTATED CYP7B1 WILD-TYPE
  T1              1               10
  T2              4               68
  T3              6              116
  T4              4               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CYP7B1 MUTATED    4  4  2  4
  CYP7B1 WILD-TYPE 89 77 48 49
D497V5, multiclass
    clus
vv   CYP7B1 MUTATED CYP7B1 WILD-TYPE
  N0              4               89
  N1              4               77
  N2              2               48
  N3              4               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D497V6, binary
                  cls
clus                 0   1
  CYP7B1 MUTATED    15   1
  CYP7B1 WILD-TYPE 242  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP7B1 MUTATED     15    1
  CYP7B1 WILD-TYPE  242   17
   clus
vv  CYP7B1 MUTATED CYP7B1 WILD-TYPE
  0             15              242
  1              1               17
[1] 2 2
[1] FALSE
D497V7, binary
                  cls
clus                 0   1
  CYP7B1 MUTATED     4  12
  CYP7B1 WILD-TYPE 106 167
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP7B1 MUTATED      4   12
  CYP7B1 WILD-TYPE  106  167
        clus
vv       CYP7B1 MUTATED CYP7B1 WILD-TYPE
  FEMALE              4              106
  MALE               12              167
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CYP7B1 MUTATED                                       3
  CYP7B1 WILD-TYPE                                    47
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CYP7B1 MUTATED                                                        6
  CYP7B1 WILD-TYPE                                                    129
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CYP7B1 MUTATED                                                                   3
  CYP7B1 WILD-TYPE                                                                37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CYP7B1 MUTATED                                                  1
  CYP7B1 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CYP7B1 MUTATED                                                          2
  CYP7B1 WILD-TYPE                                                       14
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CYP7B1 MUTATED                                                           1
  CYP7B1 WILD-TYPE                                                         5
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CYP7B1 MUTATED                                          0
  CYP7B1 WILD-TYPE                                        3
D497V8, multiclass
                                                                   clus
vv                                                                  CYP7B1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  CYP7B1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D497V9, binary
                  cls
clus                 0   1
  CYP7B1 MUTATED     1  15
  CYP7B1 WILD-TYPE   4 269
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP7B1 MUTATED      1   15
  CYP7B1 WILD-TYPE    4  269
     clus
vv    CYP7B1 MUTATED CYP7B1 WILD-TYPE
  NO               1                4
  YES             15              269
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CYP7B1 MUTATED    11   1   1   2
  CYP7B1 WILD-TYPE 216   9   9  22
D497V10, multiclass
    clus
vv   CYP7B1 MUTATED CYP7B1 WILD-TYPE
  R0             11              216
  R1              1                9
  R2              1                9
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D497V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CYP7B1 MUTATED       3                         0    10
  CYP7B1 WILD-TYPE    73                         4   158
D497V12, multiclass
                           clus
vv                          CYP7B1 MUTATED CYP7B1 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                 10              158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(498) Variable = EDNRB MUTATION ANALYSIS
D498V1, survival
                 sevent
clus2               0   1
  EDNRB MUTATED    14   7
  EDNRB WILD-TYPE 167  73
  EDNRB MUTATED EDNRB WILD-TYPE 
             21             240 
  EDNRB MUTATED EDNRB WILD-TYPE 
              7              73 
$`EDNRB MUTATED`
TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8372 
        6.97        18.35         6.61        34.68        32.78        19.17 
TCGA-BR-A4QL TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4455 
       11.57        13.15         0.07         0.10         6.58        12.03 
TCGA-CG-4466 TCGA-CG-5721 TCGA-CG-5724 TCGA-D7-6527 TCGA-D7-A4Z0 TCGA-HU-A4GQ 
       18.97         6.02        12.03        10.26        14.76         0.10 
TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4H8 
        6.25        23.84         8.88 

$`EDNRB WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
       26.70        11.70         6.61         4.64         7.43        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10         9.17        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       12.82         9.21        24.76        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        20.55         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8525 TCGA-CD-8526 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        47.05        19.07         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99         0.99       105.07        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-EQ-5647 TCGA-EQ-8122 
       16.44         5.92        15.16        13.78         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GX 
       25.81        11.77        29.98         8.98         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  EDNRB MUTATED EDNRB WILD-TYPE 
           0.07            0.00 
  EDNRB MUTATED EDNRB WILD-TYPE 
          34.68          105.07 
  EDNRB MUTATED EDNRB WILD-TYPE 
         11.570          12.775 
[1] "0.1 - 34.7 (11.6)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.2"
D498V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EDNRB MUTATED         0        0        3        5         3         3
  EDNRB WILD-TYPE       1        9       24       21        28        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EDNRB MUTATED           1          3          1          2        2
  EDNRB WILD-TYPE         2         46         35         22       22
D498V3, multiclass
            clus
vv           EDNRB MUTATED EDNRB WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               3              24
  STAGE II               5              21
  STAGE IIA              3              28
  STAGE IIB              3              41
  STAGE III              1               2
  STAGE IIIA             3              46
  STAGE IIIB             1              35
  STAGE IIIC             2              22
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EDNRB MUTATED     2   7  11   4
  EDNRB WILD-TYPE   9  65 111  71
D498V4, multiclass
    clus
vv   EDNRB MUTATED EDNRB WILD-TYPE
  T1             2               9
  T2             7              65
  T3            11             111
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  EDNRB MUTATED    9  9  3  3
  EDNRB WILD-TYPE 84 72 47 50
D498V5, multiclass
    clus
vv   EDNRB MUTATED EDNRB WILD-TYPE
  N0             9              84
  N1             9              72
  N2             3              47
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D498V6, binary
                 cls
clus                0   1
  EDNRB MUTATED    23   1
  EDNRB WILD-TYPE 234  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EDNRB MUTATED     23    1
  EDNRB WILD-TYPE  234   17
   clus
vv  EDNRB MUTATED EDNRB WILD-TYPE
  0            23             234
  1             1              17
[1] 2 2
[1] FALSE
D498V7, binary
                 cls
clus                0   1
  EDNRB MUTATED    12  13
  EDNRB WILD-TYPE  98 166
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EDNRB MUTATED     12   13
  EDNRB WILD-TYPE   98  166
        clus
vv       EDNRB MUTATED EDNRB WILD-TYPE
  FEMALE            12              98
  MALE              13             166
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  EDNRB MUTATED                                       3
  EDNRB WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EDNRB MUTATED                                                       11
  EDNRB WILD-TYPE                                                    124
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EDNRB MUTATED                                                                   4
  EDNRB WILD-TYPE                                                                36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  EDNRB MUTATED                                                  3
  EDNRB WILD-TYPE                                               35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  EDNRB MUTATED                                                          2
  EDNRB WILD-TYPE                                                       14
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  EDNRB MUTATED                                                           2
  EDNRB WILD-TYPE                                                         4
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  EDNRB MUTATED                                          0
  EDNRB WILD-TYPE                                        3
D498V8, multiclass
                                                                   clus
vv                                                                  EDNRB MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  EDNRB WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D498V9, binary
                 cls
clus                0   1
  EDNRB MUTATED     0  25
  EDNRB WILD-TYPE   5 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EDNRB MUTATED      0   25
  EDNRB WILD-TYPE    5  259
     clus
vv    EDNRB MUTATED EDNRB WILD-TYPE
  NO              0               5
  YES            25             259
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EDNRB MUTATED    17   0   1   6
  EDNRB WILD-TYPE 210  10   9  18
D498V10, multiclass
    clus
vv   EDNRB MUTATED EDNRB WILD-TYPE
  R0            17             210
  R1             0              10
  R2             1               9
  RX             6              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D498V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EDNRB MUTATED       8                         0    12
  EDNRB WILD-TYPE    68                         4   156
D498V12, multiclass
                           clus
vv                          EDNRB MUTATED EDNRB WILD-TYPE
  ASIAN                                 8              68
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                12             156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(499) Variable = STAU2 MUTATION ANALYSIS
D499V1, survival
                 sevent
clus2               0   1
  STAU2 MUTATED     2   2
  STAU2 WILD-TYPE 179  78
  STAU2 MUTATED STAU2 WILD-TYPE 
              4             257 
  STAU2 MUTATED STAU2 WILD-TYPE 
              2              78 
$`STAU2 MUTATED`
TCGA-BR-4184 TCGA-BR-7703 TCGA-D7-8572 TCGA-HU-A4GQ 
        6.97        24.76        16.80         0.10 

$`STAU2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  STAU2 MUTATED STAU2 WILD-TYPE 
            0.1             0.0 
  STAU2 MUTATED STAU2 WILD-TYPE 
          24.76          105.07 
  STAU2 MUTATED STAU2 WILD-TYPE 
         11.885          12.620 
[1] "0.1 - 24.8 (11.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.1"
D499V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  STAU2 MUTATED         0        1        0        0         0         1
  STAU2 WILD-TYPE       1        8       27       26        31        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STAU2 MUTATED           0          1          0          1        0
  STAU2 WILD-TYPE         3         48         36         23       24
D499V3, multiclass
            clus
vv           STAU2 MUTATED STAU2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              0              31
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STAU2 MUTATED     2   1   2   1
  STAU2 WILD-TYPE   9  71 120  74
D499V4, multiclass
    clus
vv   STAU2 MUTATED STAU2 WILD-TYPE
  T1             2               9
  T2             1              71
  T3             2             120
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  STAU2 MUTATED    1  2  2  0
  STAU2 WILD-TYPE 92 79 48 53
D499V5, multiclass
    clus
vv   STAU2 MUTATED STAU2 WILD-TYPE
  N0             1              92
  N1             2              79
  N2             2              48
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D499V6, binary
                 cls
clus                0   1
  STAU2 MUTATED     6   0
  STAU2 WILD-TYPE 251  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU2 MUTATED      6    0
  STAU2 WILD-TYPE  251   18
   clus
vv  STAU2 MUTATED STAU2 WILD-TYPE
  0             6             251
  1             0              18
[1] 2 2
[1] FALSE
D499V7, binary
                 cls
clus                0   1
  STAU2 MUTATED     3   5
  STAU2 WILD-TYPE 107 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU2 MUTATED      3    5
  STAU2 WILD-TYPE  107  174
        clus
vv       STAU2 MUTATED STAU2 WILD-TYPE
  FEMALE             3             107
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  STAU2 MUTATED                                       0
  STAU2 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  STAU2 MUTATED                                                        6
  STAU2 WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  STAU2 MUTATED                                                                   0
  STAU2 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  STAU2 MUTATED                                                  1
  STAU2 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  STAU2 MUTATED                                                          0
  STAU2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  STAU2 MUTATED                                                           1
  STAU2 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  STAU2 MUTATED                                          0
  STAU2 WILD-TYPE                                        3
D499V8, multiclass
                                                                   clus
vv                                                                  STAU2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  STAU2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D499V9, binary
                 cls
clus                0   1
  STAU2 MUTATED     0   8
  STAU2 WILD-TYPE   5 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU2 MUTATED      0    8
  STAU2 WILD-TYPE    5  276
     clus
vv    STAU2 MUTATED STAU2 WILD-TYPE
  NO              0               5
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  STAU2 MUTATED     3   0   0   5
  STAU2 WILD-TYPE 224  10  10  19
D499V10, multiclass
    clus
vv   STAU2 MUTATED STAU2 WILD-TYPE
  R0             3             224
  R1             0              10
  R2             0              10
  RX             5              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D499V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STAU2 MUTATED       1                         0     7
  STAU2 WILD-TYPE    75                         4   161
D499V12, multiclass
                           clus
vv                          STAU2 MUTATED STAU2 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 7             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(500) Variable = ARHGEF17 MUTATION ANALYSIS
D500V1, survival
                    sevent
clus2                  0   1
  ARHGEF17 MUTATED    13   2
  ARHGEF17 WILD-TYPE 168  78
  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE 
                15                246 
  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE 
                 2                 78 
$`ARHGEF17 MUTATED`
TCGA-BR-4184 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8368 TCGA-BR-8381 
        6.97        23.93        12.26         6.18         4.31         0.26 
TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-A4IY TCGA-CD-A4MI TCGA-CG-5721 TCGA-D7-8579 
        1.12        13.45        12.89         0.10         6.02        20.91 
TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-A4GH 
       11.08        26.47        11.77 

$`ARHGEF17 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        2.66        16.31         2.20        15.58         7.40        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        19.17        14.79        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       13.51         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        14.66        21.14        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.52         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        22.75        25.81        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE 
               0.1                0.0 
  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE 
             26.47             105.07 
  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE 
            11.080             12.775 
[1] "0.1 - 26.5 (11.1)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.7"
D500V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARHGEF17 MUTATED         0        1        4        1         3         4
  ARHGEF17 WILD-TYPE       1        8       23       25        28        40
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGEF17 MUTATED           0          1          1          1        1
  ARHGEF17 WILD-TYPE         3         48         35         23       23
D500V3, multiclass
            clus
vv           ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  1                  8
  STAGE IB                  4                 23
  STAGE II                  1                 25
  STAGE IIA                 3                 28
  STAGE IIB                 4                 40
  STAGE III                 0                  3
  STAGE IIIA                1                 48
  STAGE IIIB                1                 35
  STAGE IIIC                1                 23
  STAGE IV                  1                 23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ARHGEF17 MUTATED     1   6   6   4
  ARHGEF17 WILD-TYPE  10  66 116  71
D500V4, multiclass
    clus
vv   ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  T1                1                 10
  T2                6                 66
  T3                6                116
  T4                4                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  ARHGEF17 MUTATED   10  5  1  1
  ARHGEF17 WILD-TYPE 83 76 49 52
D500V5, multiclass
    clus
vv   ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  N0               10                 83
  N1                5                 76
  N2                1                 49
  N3                1                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D500V6, binary
                    cls
clus                   0   1
  ARHGEF17 MUTATED    15   0
  ARHGEF17 WILD-TYPE 242  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF17 MUTATED     15    0
  ARHGEF17 WILD-TYPE  242   18
   clus
vv  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  0               15                242
  1                0                 18
[1] 2 2
[1] FALSE
D500V7, binary
                    cls
clus                   0   1
  ARHGEF17 MUTATED     6  11
  ARHGEF17 WILD-TYPE 104 168
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF17 MUTATED      6   11
  ARHGEF17 WILD-TYPE  104  168
        clus
vv       ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  FEMALE                6                104
  MALE                 11                168
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ARHGEF17 MUTATED                                       0
  ARHGEF17 WILD-TYPE                                    50
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ARHGEF17 MUTATED                                                       10
  ARHGEF17 WILD-TYPE                                                    125
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ARHGEF17 MUTATED                                                                   4
  ARHGEF17 WILD-TYPE                                                                36
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ARHGEF17 MUTATED                                                  1
  ARHGEF17 WILD-TYPE                                               37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ARHGEF17 MUTATED                                                          1
  ARHGEF17 WILD-TYPE                                                       15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ARHGEF17 MUTATED                                                           0
  ARHGEF17 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ARHGEF17 MUTATED                                          1
  ARHGEF17 WILD-TYPE                                        2
D500V8, multiclass
                                                                   clus
vv                                                                  ARHGEF17 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  ARHGEF17 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D500V9, binary
                    cls
clus                   0   1
  ARHGEF17 MUTATED     1  16
  ARHGEF17 WILD-TYPE   4 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF17 MUTATED      1   16
  ARHGEF17 WILD-TYPE    4  268
     clus
vv    ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  NO                 1                  4
  YES               16                268
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  ARHGEF17 MUTATED    15   0   0   1
  ARHGEF17 WILD-TYPE 212  10  10  23
D500V10, multiclass
    clus
vv   ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  R0               15                212
  R1                0                 10
  R2                0                 10
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D500V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARHGEF17 MUTATED       3                         1    10
  ARHGEF17 WILD-TYPE    73                         3   158
D500V12, multiclass
                           clus
vv                          ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  ASIAN                                    3                 73
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                   10                158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(501) Variable = C10ORF120 MUTATION ANALYSIS
D501V1, survival
                     sevent
clus2                   0   1
  C10ORF120 MUTATED     1   3
  C10ORF120 WILD-TYPE 180  77
  C10ORF120 MUTATED C10ORF120 WILD-TYPE 
                  4                 257 
  C10ORF120 MUTATED C10ORF120 WILD-TYPE 
                  3                  77 
$`C10ORF120 MUTATED`
TCGA-BR-4184 TCGA-CG-5733 TCGA-HU-8243 TCGA-HU-A4GU 
        6.97        21.07         5.92         6.25 

$`C10ORF120 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10         4.01        69.04         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       26.47        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  C10ORF120 MUTATED C10ORF120 WILD-TYPE 
               5.92                0.00 
  C10ORF120 MUTATED C10ORF120 WILD-TYPE 
              21.07              105.07 
  C10ORF120 MUTATED C10ORF120 WILD-TYPE 
               6.61               12.66 
[1] "5.9 - 21.1 (6.6)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "3.8"
D501V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C10ORF120 MUTATED         0        0        1        0         0         1
  C10ORF120 WILD-TYPE       1        9       26       26        31        43
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C10ORF120 MUTATED           0          2          0          1        0
  C10ORF120 WILD-TYPE         3         47         36         23       24
D501V3, multiclass
            clus
vv           C10ORF120 MUTATED C10ORF120 WILD-TYPE
  STAGE I                    0                   1
  STAGE IA                   0                   9
  STAGE IB                   1                  26
  STAGE II                   0                  26
  STAGE IIA                  0                  31
  STAGE IIB                  1                  43
  STAGE III                  0                   3
  STAGE IIIA                 2                  47
  STAGE IIIB                 0                  36
  STAGE IIIC                 1                  23
  STAGE IV                   0                  24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  C10ORF120 MUTATED     0   2   2   1
  C10ORF120 WILD-TYPE  11  70 120  74
D501V4, multiclass
    clus
vv   C10ORF120 MUTATED C10ORF120 WILD-TYPE
  T1                 0                  11
  T2                 2                  70
  T3                 2                 120
  T4                 1                  74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  N0 N1 N2 N3
  C10ORF120 MUTATED    1  2  1  1
  C10ORF120 WILD-TYPE 92 79 49 52
D501V5, multiclass
    clus
vv   C10ORF120 MUTATED C10ORF120 WILD-TYPE
  N0                 1                  92
  N1                 2                  79
  N2                 1                  49
  N3                 1                  52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D501V6, binary
                     cls
clus                    0   1
  C10ORF120 MUTATED     4   0
  C10ORF120 WILD-TYPE 253  18
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C10ORF120 MUTATED      4    0
  C10ORF120 WILD-TYPE  253   18
   clus
vv  C10ORF120 MUTATED C10ORF120 WILD-TYPE
  0                 4                 253
  1                 0                  18
[1] 2 2
[1] FALSE
D501V7, binary
                     cls
clus                    0   1
  C10ORF120 MUTATED     1   4
  C10ORF120 WILD-TYPE 109 175
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C10ORF120 MUTATED      1    4
  C10ORF120 WILD-TYPE  109  175
        clus
vv       C10ORF120 MUTATED C10ORF120 WILD-TYPE
  FEMALE                 1                 109
  MALE                   4                 175
[1] 2 2
[1] FALSE
                     vv
clus                  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C10ORF120 MUTATED                                       1
  C10ORF120 WILD-TYPE                                    49
                     vv
clus                  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C10ORF120 MUTATED                                                        1
  C10ORF120 WILD-TYPE                                                    134
                     vv
clus                  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C10ORF120 MUTATED                                                                   2
  C10ORF120 WILD-TYPE                                                                38
                     vv
clus                  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C10ORF120 MUTATED                                                  1
  C10ORF120 WILD-TYPE                                               37
                     vv
clus                  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C10ORF120 MUTATED                                                          0
  C10ORF120 WILD-TYPE                                                       16
                     vv
clus                  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C10ORF120 MUTATED                                                           0
  C10ORF120 WILD-TYPE                                                         6
                     vv
clus                  STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C10ORF120 MUTATED                                          0
  C10ORF120 WILD-TYPE                                        3
D501V8, multiclass
                                                                   clus
vv                                                                  C10ORF120 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            1
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          0
                                                                   clus
vv                                                                  C10ORF120 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                              49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                   37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                           16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                           6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                            3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D501V9, binary
                     cls
clus                    0   1
  C10ORF120 MUTATED     0   5
  C10ORF120 WILD-TYPE   5 279
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C10ORF120 MUTATED      0    5
  C10ORF120 WILD-TYPE    5  279
     clus
vv    C10ORF120 MUTATED C10ORF120 WILD-TYPE
  NO                  0                   5
  YES                 5                 279
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  C10ORF120 MUTATED     4   0   0   1
  C10ORF120 WILD-TYPE 223  10  10  23
D501V10, multiclass
    clus
vv   C10ORF120 MUTATED C10ORF120 WILD-TYPE
  R0                 4                 223
  R1                 0                  10
  R2                 0                  10
  RX                 1                  23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D501V11, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C10ORF120 MUTATED       2                         0     1
  C10ORF120 WILD-TYPE    74                         4   167
D501V12, multiclass
                           clus
vv                          C10ORF120 MUTATED C10ORF120 WILD-TYPE
  ASIAN                                     2                  74
  BLACK OR AFRICAN AMERICAN                 0                   4
  WHITE                                     1                 167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(502) Variable = SLC45A4 MUTATION ANALYSIS
D502V1, survival
                   sevent
clus2                 0   1
  SLC45A4 MUTATED    14   1
  SLC45A4 WILD-TYPE 167  79
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
               15               246 
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
                1                79 
$`SLC45A4 MUTATED`
TCGA-BR-6452 TCGA-BR-8284 TCGA-BR-8372 TCGA-BR-8382 TCGA-CD-8536 TCGA-CD-A4MJ 
       34.68         8.05        19.17        15.85         0.10        12.62 
TCGA-CG-4449 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-F1-A448 TCGA-FP-A4BE 
       19.07         6.02       105.07        65.10        21.27        11.08 
TCGA-HU-8602 TCGA-HU-A4G9 TCGA-HU-A4GU 
       11.41        24.20         6.25 

$`SLC45A4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        0.26         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        47.05        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        0.99         0.99        12.03        28.96        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        7.99        16.24        14.47        72.23         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       11.84         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
              0.1               0.0 
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
           105.07             79.07 
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
           15.850            12.575 
[1] "0.1 - 105.1 (15.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "7.7"
D502V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC45A4 MUTATED         1        1        2        3         2         2
  SLC45A4 WILD-TYPE       0        8       25       23        29        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC45A4 MUTATED           0          1          1          3        1
  SLC45A4 WILD-TYPE         3         48         35         21       23
D502V3, multiclass
            clus
vv           SLC45A4 MUTATED SLC45A4 WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                 1                 8
  STAGE IB                 2                25
  STAGE II                 3                23
  STAGE IIA                2                29
  STAGE IIB                2                42
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               1                35
  STAGE IIIC               3                21
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC45A4 MUTATED     2   4   5   6
  SLC45A4 WILD-TYPE   9  68 117  69
D502V4, multiclass
    clus
vv   SLC45A4 MUTATED SLC45A4 WILD-TYPE
  T1               2                 9
  T2               4                68
  T3               5               117
  T4               6                69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  SLC45A4 MUTATED    8  5  0  4
  SLC45A4 WILD-TYPE 85 76 50 49
D502V5, multiclass
    clus
vv   SLC45A4 MUTATED SLC45A4 WILD-TYPE
  N0               8                85
  N1               5                76
  N2               0                50
  N3               4                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D502V6, binary
                   cls
clus                  0   1
  SLC45A4 MUTATED    17   0
  SLC45A4 WILD-TYPE 240  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A4 MUTATED     17    0
  SLC45A4 WILD-TYPE  240   18
   clus
vv  SLC45A4 MUTATED SLC45A4 WILD-TYPE
  0              17               240
  1               0                18
[1] 2 2
[1] FALSE
D502V7, binary
                   cls
clus                  0   1
  SLC45A4 MUTATED     8  10
  SLC45A4 WILD-TYPE 102 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A4 MUTATED      8   10
  SLC45A4 WILD-TYPE  102  169
        clus
vv       SLC45A4 MUTATED SLC45A4 WILD-TYPE
  FEMALE               8               102
  MALE                10               169
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SLC45A4 MUTATED                                       2
  SLC45A4 WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC45A4 MUTATED                                                       10
  SLC45A4 WILD-TYPE                                                    125
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC45A4 MUTATED                                                                   3
  SLC45A4 WILD-TYPE                                                                37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SLC45A4 MUTATED                                                  1
  SLC45A4 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SLC45A4 MUTATED                                                          2
  SLC45A4 WILD-TYPE                                                       14
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SLC45A4 MUTATED                                                           0
  SLC45A4 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SLC45A4 MUTATED                                          0
  SLC45A4 WILD-TYPE                                        3
D502V8, multiclass
                                                                   clus
vv                                                                  SLC45A4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  SLC45A4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D502V9, binary
                   cls
clus                  0   1
  SLC45A4 MUTATED     0  18
  SLC45A4 WILD-TYPE   5 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A4 MUTATED      0   18
  SLC45A4 WILD-TYPE    5  266
     clus
vv    SLC45A4 MUTATED SLC45A4 WILD-TYPE
  NO                0                 5
  YES              18               266
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC45A4 MUTATED    15   0   0   2
  SLC45A4 WILD-TYPE 212  10  10  22
D502V10, multiclass
    clus
vv   SLC45A4 MUTATED SLC45A4 WILD-TYPE
  R0              15               212
  R1               0                10
  R2               0                10
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D502V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC45A4 MUTATED       5                         2     7
  SLC45A4 WILD-TYPE    71                         2   161
D502V12, multiclass
                           clus
vv                          SLC45A4 MUTATED SLC45A4 WILD-TYPE
  ASIAN                                   5                71
  BLACK OR AFRICAN AMERICAN               2                 2
  WHITE                                   7               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(503) Variable = CSNK1G3 MUTATION ANALYSIS
D503V1, survival
                   sevent
clus2                 0   1
  CSNK1G3 MUTATED     4   2
  CSNK1G3 WILD-TYPE 177  78
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
                6               255 
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
                2                78 
$`CSNK1G3 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8487 TCGA-CG-5721 TCGA-HU-8602 TCGA-HU-A4GQ 
        6.97        34.68         1.12         6.02        11.41         0.10 

$`CSNK1G3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
              0.1               0.0 
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
            34.68            105.07 
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
            6.495            12.760 
[1] "0.1 - 34.7 (6.5)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.5"
D503V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CSNK1G3 MUTATED         1        0        0        0         2         1
  CSNK1G3 WILD-TYPE       0        9       27       26        29        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSNK1G3 MUTATED           0          1          0          1        1
  CSNK1G3 WILD-TYPE         3         48         36         23       23
D503V3, multiclass
            clus
vv           CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                 0                 9
  STAGE IB                 0                27
  STAGE II                 0                26
  STAGE IIA                2                29
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               0                36
  STAGE IIIC               1                23
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CSNK1G3 MUTATED     1   0   3   3
  CSNK1G3 WILD-TYPE  10  72 119  72
D503V4, multiclass
    clus
vv   CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  T1               1                10
  T2               0                72
  T3               3               119
  T4               3                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  CSNK1G3 MUTATED    3  3  1  0
  CSNK1G3 WILD-TYPE 90 78 49 53
D503V5, multiclass
    clus
vv   CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  N0               3                90
  N1               3                78
  N2               1                49
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D503V6, binary
                   cls
clus                  0   1
  CSNK1G3 MUTATED     5   0
  CSNK1G3 WILD-TYPE 252  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G3 MUTATED      5    0
  CSNK1G3 WILD-TYPE  252   18
   clus
vv  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  0               5               252
  1               0                18
[1] 2 2
[1] FALSE
D503V7, binary
                   cls
clus                  0   1
  CSNK1G3 MUTATED     3   4
  CSNK1G3 WILD-TYPE 107 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G3 MUTATED      3    4
  CSNK1G3 WILD-TYPE  107  175
        clus
vv       CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  FEMALE               3               107
  MALE                 4               175
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CSNK1G3 MUTATED                                       1
  CSNK1G3 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CSNK1G3 MUTATED                                                        4
  CSNK1G3 WILD-TYPE                                                    131
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CSNK1G3 MUTATED                                                                   1
  CSNK1G3 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CSNK1G3 MUTATED                                                  1
  CSNK1G3 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CSNK1G3 MUTATED                                                          0
  CSNK1G3 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CSNK1G3 MUTATED                                                           0
  CSNK1G3 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CSNK1G3 MUTATED                                          0
  CSNK1G3 WILD-TYPE                                        3
D503V8, multiclass
                                                                   clus
vv                                                                  CSNK1G3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  CSNK1G3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D503V9, binary
                   cls
clus                  0   1
  CSNK1G3 MUTATED     0   7
  CSNK1G3 WILD-TYPE   5 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G3 MUTATED      0    7
  CSNK1G3 WILD-TYPE    5  277
     clus
vv    CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  NO                0                 5
  YES               7               277
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CSNK1G3 MUTATED     6   0   0   1
  CSNK1G3 WILD-TYPE 221  10  10  23
D503V10, multiclass
    clus
vv   CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  R0               6               221
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D503V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CSNK1G3 MUTATED       2                         1     3
  CSNK1G3 WILD-TYPE    74                         3   165
D503V12, multiclass
                           clus
vv                          CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  ASIAN                                   2                74
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   3               165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(504) Variable = SLFN12 MUTATION ANALYSIS
D504V1, survival
                  sevent
clus2                0   1
  SLFN12 MUTATED     7   0
  SLFN12 WILD-TYPE 174  80
  SLFN12 MUTATED SLFN12 WILD-TYPE 
               7              254 
  SLFN12 MUTATED SLFN12 WILD-TYPE 
               0               80 
$`SLFN12 MUTATED`
TCGA-B7-5816 TCGA-BR-8487 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-5721 
       26.70         1.12        11.57         0.10         0.10         6.02 
TCGA-CG-5730 
        4.01 

$`SLFN12 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        65.10        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  SLFN12 MUTATED SLFN12 WILD-TYPE 
             0.1              0.0 
  SLFN12 MUTATED SLFN12 WILD-TYPE 
           26.70           105.07 
  SLFN12 MUTATED SLFN12 WILD-TYPE 
           4.010           12.775 
[1] "0.1 - 26.7 (4.0)"   "0.0 - 105.1 (12.8)"
[1] "hr="     "9200000"
D504V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLFN12 MUTATED         0        0        0        1         1         1
  SLFN12 WILD-TYPE       1        9       27       25        30        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLFN12 MUTATED           0          0          2          0        2
  SLFN12 WILD-TYPE         3         49         34         24       22
D504V3, multiclass
            clus
vv           SLFN12 MUTATED SLFN12 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                1               25
  STAGE IIA               1               30
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              2               34
  STAGE IIIC              0               24
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SLFN12 MUTATED     0   1   4   2
  SLFN12 WILD-TYPE  11  71 118  73
D504V4, multiclass
    clus
vv   SLFN12 MUTATED SLFN12 WILD-TYPE
  T1              0               11
  T2              1               71
  T3              4              118
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  SLFN12 MUTATED    3  3  0  1
  SLFN12 WILD-TYPE 90 78 50 52
D504V5, multiclass
    clus
vv   SLFN12 MUTATED SLFN12 WILD-TYPE
  N0              3               90
  N1              3               78
  N2              0               50
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D504V6, binary
                  cls
clus                 0   1
  SLFN12 MUTATED     6   1
  SLFN12 WILD-TYPE 251  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLFN12 MUTATED      6    1
  SLFN12 WILD-TYPE  251   17
   clus
vv  SLFN12 MUTATED SLFN12 WILD-TYPE
  0              6              251
  1              1               17
[1] 2 2
[1] FALSE
D504V7, binary
                  cls
clus                 0   1
  SLFN12 MUTATED     4   3
  SLFN12 WILD-TYPE 106 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLFN12 MUTATED      4    3
  SLFN12 WILD-TYPE  106  176
        clus
vv       SLFN12 MUTATED SLFN12 WILD-TYPE
  FEMALE              4              106
  MALE                3              176
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SLFN12 MUTATED                                       1
  SLFN12 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLFN12 MUTATED                                                        4
  SLFN12 WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLFN12 MUTATED                                                                   2
  SLFN12 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SLFN12 MUTATED                                                  0
  SLFN12 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SLFN12 MUTATED                                                          0
  SLFN12 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SLFN12 MUTATED                                                           0
  SLFN12 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SLFN12 MUTATED                                          0
  SLFN12 WILD-TYPE                                        3
D504V8, multiclass
                                                                   clus
vv                                                                  SLFN12 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  SLFN12 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D504V9, binary
                  cls
clus                 0   1
  SLFN12 MUTATED     0   7
  SLFN12 WILD-TYPE   5 277
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLFN12 MUTATED      0    7
  SLFN12 WILD-TYPE    5  277
     clus
vv    SLFN12 MUTATED SLFN12 WILD-TYPE
  NO               0                5
  YES              7              277
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SLFN12 MUTATED     5   0   1   0
  SLFN12 WILD-TYPE 222  10   9  24
D504V10, multiclass
    clus
vv   SLFN12 MUTATED SLFN12 WILD-TYPE
  R0              5              222
  R1              0               10
  R2              1                9
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D504V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLFN12 MUTATED       2                         0     3
  SLFN12 WILD-TYPE    74                         4   165
D504V12, multiclass
                           clus
vv                          SLFN12 MUTATED SLFN12 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  3              165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(505) Variable = ARFGEF1 MUTATION ANALYSIS
D505V1, survival
                   sevent
clus2                 0   1
  ARFGEF1 MUTATED    15   5
  ARFGEF1 WILD-TYPE 166  75
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
               20               241 
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
                5                75 
$`ARFGEF1 MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8081 TCGA-BR-8363 
        6.97         6.61        34.68        23.93        20.55         0.26 
TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8680 TCGA-CD-A4MG 
        4.31        19.17         1.12        15.81        15.81         6.58 
TCGA-CG-5721 TCGA-CG-5724 TCGA-F1-6874 TCGA-F1-A448 TCGA-HU-8602 TCGA-HU-A4G8 
        6.02        12.03        14.47        21.27        11.41        11.84 
TCGA-HU-A4GF TCGA-HU-A4GT 
       25.81         6.51 

$`ARFGEF1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       30.90         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 
       31.20        32.94        12.82         9.21        24.76        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       12.26         9.60         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
        2.20        15.58         7.40         6.18        19.50        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        9.21        20.22        12.79         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 
        1.02         0.99         0.99       105.07        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7735 
       14.76         0.62         7.99        16.24        72.23         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH 
        5.59        12.30        24.20         3.25        22.75        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
             0.26              0.00 
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
            34.68            105.07 
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
           11.935            12.660 
[1] "0.3 - 34.7 (11.9)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.2"
D505V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARFGEF1 MUTATED         0        0        4        0         5         3
  ARFGEF1 WILD-TYPE       1        9       23       26        26        41
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARFGEF1 MUTATED           1          2          2          1        3
  ARFGEF1 WILD-TYPE         2         47         34         23       21
D505V3, multiclass
            clus
vv           ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 4                23
  STAGE II                 0                26
  STAGE IIA                5                26
  STAGE IIB                3                41
  STAGE III                1                 2
  STAGE IIIA               2                47
  STAGE IIIB               2                34
  STAGE IIIC               1                23
  STAGE IV                 3                21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ARFGEF1 MUTATED     0   5   9   7
  ARFGEF1 WILD-TYPE  11  67 113  68
D505V4, multiclass
    clus
vv   ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  T1               0                11
  T2               5                67
  T3               9               113
  T4               7                68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  ARFGEF1 MUTATED   12  6  1  3
  ARFGEF1 WILD-TYPE 81 75 49 50
D505V5, multiclass
    clus
vv   ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  N0              12                81
  N1               6                75
  N2               1                49
  N3               3                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D505V6, binary
                   cls
clus                  0   1
  ARFGEF1 MUTATED    21   2
  ARFGEF1 WILD-TYPE 236  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGEF1 MUTATED     21    2
  ARFGEF1 WILD-TYPE  236   16
   clus
vv  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  0              21               236
  1               2                16
[1] 2 2
[1] FALSE
D505V7, binary
                   cls
clus                  0   1
  ARFGEF1 MUTATED    14  10
  ARFGEF1 WILD-TYPE  96 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGEF1 MUTATED     14   10
  ARFGEF1 WILD-TYPE   96  169
        clus
vv       ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  FEMALE              14                96
  MALE                10               169
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ARFGEF1 MUTATED                                       4
  ARFGEF1 WILD-TYPE                                    46
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ARFGEF1 MUTATED                                                       14
  ARFGEF1 WILD-TYPE                                                    121
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ARFGEF1 MUTATED                                                                   2
  ARFGEF1 WILD-TYPE                                                                38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ARFGEF1 MUTATED                                                  3
  ARFGEF1 WILD-TYPE                                               35
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ARFGEF1 MUTATED                                                          1
  ARFGEF1 WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ARFGEF1 MUTATED                                                           0
  ARFGEF1 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ARFGEF1 MUTATED                                          0
  ARFGEF1 WILD-TYPE                                        3
D505V8, multiclass
                                                                   clus
vv                                                                  ARFGEF1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         14
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  ARFGEF1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          121
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D505V9, binary
                   cls
clus                  0   1
  ARFGEF1 MUTATED     0  24
  ARFGEF1 WILD-TYPE   5 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGEF1 MUTATED      0   24
  ARFGEF1 WILD-TYPE    5  260
     clus
vv    ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  NO                0                 5
  YES              24               260
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ARFGEF1 MUTATED    15   0   1   6
  ARFGEF1 WILD-TYPE 212  10   9  18
D505V10, multiclass
    clus
vv   ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  R0              15               212
  R1               0                10
  R2               1                 9
  RX               6                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D505V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARFGEF1 MUTATED       6                         0    16
  ARFGEF1 WILD-TYPE    70                         4   152
D505V12, multiclass
                           clus
vv                          ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  ASIAN                                   6                70
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                  16               152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(506) Variable = HDLBP MUTATION ANALYSIS
D506V1, survival
                 sevent
clus2               0   1
  HDLBP MUTATED    19   1
  HDLBP WILD-TYPE 162  79
  HDLBP MUTATED HDLBP WILD-TYPE 
             20             241 
  HDLBP MUTATED HDLBP WILD-TYPE 
              1              79 
$`HDLBP MUTATED`
TCGA-B7-5816 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8382 
       26.70        32.94        12.26         0.26         4.31        15.85 
TCGA-BR-A4QL TCGA-CD-8530 TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-6518 
       11.57         0.16        15.95         6.02       105.07        19.13 
TCGA-D7-6817 TCGA-D7-A4YT TCGA-FP-A4BE TCGA-HU-8604 TCGA-HU-A4GN TCGA-HU-A4GT 
       12.79        14.27        11.08        12.10        29.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4H4 
        6.25        23.84 

$`HDLBP WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
       19.50        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
        3.32        11.80        19.17        14.79         0.26         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
        0.07         0.07         0.07         0.10         0.13         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 
       21.07         7.99        12.36        12.66        11.93        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.22        15.98        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 
       59.54         5.03        13.58         0.56         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        11.41        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX 
       22.75        25.81        11.77         8.98         0.10        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  HDLBP MUTATED HDLBP WILD-TYPE 
           0.16            0.00 
  HDLBP MUTATED HDLBP WILD-TYPE 
         105.07           79.07 
  HDLBP MUTATED HDLBP WILD-TYPE 
         12.525          12.620 
[1] "0.2 - 105.1 (12.5)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "8.3"
D506V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HDLBP MUTATED         0        0        3        3         5         4
  HDLBP WILD-TYPE       1        9       24       23        26        40
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HDLBP MUTATED           0          4          1          1        1
  HDLBP WILD-TYPE         3         45         35         23       23
D506V3, multiclass
            clus
vv           HDLBP MUTATED HDLBP WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               3              24
  STAGE II               3              23
  STAGE IIA              5              26
  STAGE IIB              4              40
  STAGE III              0               3
  STAGE IIIA             4              45
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HDLBP MUTATED     0  10   7   5
  HDLBP WILD-TYPE  11  62 115  70
D506V4, multiclass
    clus
vv   HDLBP MUTATED HDLBP WILD-TYPE
  T1             0              11
  T2            10              62
  T3             7             115
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  HDLBP MUTATED   11  6  1  5
  HDLBP WILD-TYPE 82 75 49 48
D506V5, multiclass
    clus
vv   HDLBP MUTATED HDLBP WILD-TYPE
  N0            11              82
  N1             6              75
  N2             1              49
  N3             5              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D506V6, binary
                 cls
clus                0   1
  HDLBP MUTATED    24   0
  HDLBP WILD-TYPE 233  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDLBP MUTATED     24    0
  HDLBP WILD-TYPE  233   18
   clus
vv  HDLBP MUTATED HDLBP WILD-TYPE
  0            24             233
  1             0              18
[1] 2 2
[1] FALSE
D506V7, binary
                 cls
clus                0   1
  HDLBP MUTATED    12  12
  HDLBP WILD-TYPE  98 167
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDLBP MUTATED     12   12
  HDLBP WILD-TYPE   98  167
        clus
vv       HDLBP MUTATED HDLBP WILD-TYPE
  FEMALE            12              98
  MALE              12             167
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  HDLBP MUTATED                                       4
  HDLBP WILD-TYPE                                    46
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HDLBP MUTATED                                                       12
  HDLBP WILD-TYPE                                                    123
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HDLBP MUTATED                                                                   2
  HDLBP WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  HDLBP MUTATED                                                  6
  HDLBP WILD-TYPE                                               32
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  HDLBP MUTATED                                                          0
  HDLBP WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  HDLBP MUTATED                                                           0
  HDLBP WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  HDLBP MUTATED                                          0
  HDLBP WILD-TYPE                                        3
D506V8, multiclass
                                                                   clus
vv                                                                  HDLBP MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       12
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  HDLBP WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        123
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D506V9, binary
                 cls
clus                0   1
  HDLBP MUTATED     1  23
  HDLBP WILD-TYPE   4 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDLBP MUTATED      1   23
  HDLBP WILD-TYPE    4  261
     clus
vv    HDLBP MUTATED HDLBP WILD-TYPE
  NO              1               4
  YES            23             261
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HDLBP MUTATED    20   1   0   3
  HDLBP WILD-TYPE 207   9  10  21
D506V10, multiclass
    clus
vv   HDLBP MUTATED HDLBP WILD-TYPE
  R0            20             207
  R1             1               9
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D506V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HDLBP MUTATED       6                         1    13
  HDLBP WILD-TYPE    70                         3   155
D506V12, multiclass
                           clus
vv                          HDLBP MUTATED HDLBP WILD-TYPE
  ASIAN                                 6              70
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                13             155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(507) Variable = SYCP2 MUTATION ANALYSIS
D507V1, survival
                 sevent
clus2               0   1
  SYCP2 MUTATED    12   2
  SYCP2 WILD-TYPE 169  78
  SYCP2 MUTATED SYCP2 WILD-TYPE 
             14             247 
  SYCP2 MUTATED SYCP2 WILD-TYPE 
              2              78 
$`SYCP2 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-8360 TCGA-BR-8487 TCGA-BR-8591 
        6.97        34.68        30.90         6.18         1.12        13.45 
TCGA-BR-8680 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-5721 TCGA-D7-6528 
       15.81        15.95         1.02         7.99         6.02        15.22 
TCGA-HU-A4GH TCGA-HU-A4GN 
       11.77        29.98 

$`SYCP2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        2.66        16.31         2.20        15.58         7.40        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        15.81         9.34         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4437 TCGA-CG-4438 
       12.62        20.02         3.02        27.02         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  SYCP2 MUTATED SYCP2 WILD-TYPE 
           1.02            0.00 
  SYCP2 MUTATED SYCP2 WILD-TYPE 
          34.68          105.07 
  SYCP2 MUTATED SYCP2 WILD-TYPE 
          12.61           12.62 
[1] "1.0 - 34.7 (12.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.3"
D507V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SYCP2 MUTATED         0        1        3        1         4         0
  SYCP2 WILD-TYPE       1        8       24       25        27        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SYCP2 MUTATED           0          3          0          1        3
  SYCP2 WILD-TYPE         3         46         36         23       21
D507V3, multiclass
            clus
vv           SYCP2 MUTATED SYCP2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               3              24
  STAGE II               1              25
  STAGE IIA              4              27
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             3              46
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               3              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SYCP2 MUTATED     1   5   6   4
  SYCP2 WILD-TYPE  10  67 116  71
D507V4, multiclass
    clus
vv   SYCP2 MUTATED SYCP2 WILD-TYPE
  T1             1              10
  T2             5              67
  T3             6             116
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  SYCP2 MUTATED    8  4  3  1
  SYCP2 WILD-TYPE 85 77 47 52
D507V5, multiclass
    clus
vv   SYCP2 MUTATED SYCP2 WILD-TYPE
  N0             8              85
  N1             4              77
  N2             3              47
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D507V6, binary
                 cls
clus                0   1
  SYCP2 MUTATED    14   2
  SYCP2 WILD-TYPE 243  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP2 MUTATED     14    2
  SYCP2 WILD-TYPE  243   16
   clus
vv  SYCP2 MUTATED SYCP2 WILD-TYPE
  0            14             243
  1             2              16
[1] 2 2
[1] FALSE
D507V7, binary
                 cls
clus                0   1
  SYCP2 MUTATED     5  12
  SYCP2 WILD-TYPE 105 167
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP2 MUTATED      5   12
  SYCP2 WILD-TYPE  105  167
        clus
vv       SYCP2 MUTATED SYCP2 WILD-TYPE
  FEMALE             5             105
  MALE              12             167
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SYCP2 MUTATED                                       0
  SYCP2 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SYCP2 MUTATED                                                        9
  SYCP2 WILD-TYPE                                                    126
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SYCP2 MUTATED                                                                   4
  SYCP2 WILD-TYPE                                                                36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SYCP2 MUTATED                                                  4
  SYCP2 WILD-TYPE                                               34
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SYCP2 MUTATED                                                          0
  SYCP2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SYCP2 MUTATED                                                           0
  SYCP2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SYCP2 MUTATED                                          0
  SYCP2 WILD-TYPE                                        3
D507V8, multiclass
                                                                   clus
vv                                                                  SYCP2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  SYCP2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D507V9, binary
                 cls
clus                0   1
  SYCP2 MUTATED     0  17
  SYCP2 WILD-TYPE   5 267
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP2 MUTATED      0   17
  SYCP2 WILD-TYPE    5  267
     clus
vv    SYCP2 MUTATED SYCP2 WILD-TYPE
  NO              0               5
  YES            17             267
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SYCP2 MUTATED    13   0   1   3
  SYCP2 WILD-TYPE 214  10   9  21
D507V10, multiclass
    clus
vv   SYCP2 MUTATED SYCP2 WILD-TYPE
  R0            13             214
  R1             0              10
  R2             1               9
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D507V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SYCP2 MUTATED       3                         0     9
  SYCP2 WILD-TYPE    73                         4   159
D507V12, multiclass
                           clus
vv                          SYCP2 MUTATED SYCP2 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 9             159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(508) Variable = TUBE1 MUTATION ANALYSIS
D508V1, survival
                 sevent
clus2               0   1
  TUBE1 MUTATED     5   2
  TUBE1 WILD-TYPE 176  78
  TUBE1 MUTATED TUBE1 WILD-TYPE 
              7             254 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
              2              78 
$`TUBE1 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8361 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL 
        6.97        30.90        19.50        13.45        15.81        11.57 
TCGA-D7-8572 
       16.80 

$`TUBE1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.33        24.72        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  TUBE1 MUTATED TUBE1 WILD-TYPE 
           6.97            0.00 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
          30.90          105.07 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
         15.810          12.575 
[1] "7.0 - 30.9 (15.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D508V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TUBE1 MUTATED         0        0        0        0         0         1
  TUBE1 WILD-TYPE       1        9       27       26        31        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TUBE1 MUTATED           0          1          1          2        1
  TUBE1 WILD-TYPE         3         48         35         22       23
D508V3, multiclass
            clus
vv           TUBE1 MUTATED TUBE1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              0              31
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             2              22
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TUBE1 MUTATED     0   2   2   3
  TUBE1 WILD-TYPE  11  70 120  72
D508V4, multiclass
    clus
vv   TUBE1 MUTATED TUBE1 WILD-TYPE
  T1             0              11
  T2             2              70
  T3             2             120
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  TUBE1 MUTATED    0  1  3  2
  TUBE1 WILD-TYPE 93 80 47 51
D508V5, multiclass
    clus
vv   TUBE1 MUTATED TUBE1 WILD-TYPE
  N0             0              93
  N1             1              80
  N2             3              47
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D508V6, binary
                 cls
clus                0   1
  TUBE1 MUTATED     5   1
  TUBE1 WILD-TYPE 252  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBE1 MUTATED      5    1
  TUBE1 WILD-TYPE  252   17
   clus
vv  TUBE1 MUTATED TUBE1 WILD-TYPE
  0             5             252
  1             1              17
[1] 2 2
[1] FALSE
D508V7, binary
                 cls
clus                0   1
  TUBE1 MUTATED     3   4
  TUBE1 WILD-TYPE 107 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBE1 MUTATED      3    4
  TUBE1 WILD-TYPE  107  175
        clus
vv       TUBE1 MUTATED TUBE1 WILD-TYPE
  FEMALE             3             107
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TUBE1 MUTATED                                       0
  TUBE1 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TUBE1 MUTATED                                                        6
  TUBE1 WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TUBE1 MUTATED                                                                   0
  TUBE1 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TUBE1 MUTATED                                                  1
  TUBE1 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TUBE1 MUTATED                                                          0
  TUBE1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TUBE1 MUTATED                                                           0
  TUBE1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TUBE1 MUTATED                                          0
  TUBE1 WILD-TYPE                                        3
D508V8, multiclass
                                                                   clus
vv                                                                  TUBE1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  TUBE1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D508V9, binary
                 cls
clus                0   1
  TUBE1 MUTATED     0   7
  TUBE1 WILD-TYPE   5 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBE1 MUTATED      0    7
  TUBE1 WILD-TYPE    5  277
     clus
vv    TUBE1 MUTATED TUBE1 WILD-TYPE
  NO              0               5
  YES             7             277
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TUBE1 MUTATED     5   0   0   2
  TUBE1 WILD-TYPE 222  10  10  22
D508V10, multiclass
    clus
vv   TUBE1 MUTATED TUBE1 WILD-TYPE
  R0             5             222
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D508V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TUBE1 MUTATED       1                         0     6
  TUBE1 WILD-TYPE    75                         4   162
D508V12, multiclass
                           clus
vv                          TUBE1 MUTATED TUBE1 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(509) Variable = PTPRJ MUTATION ANALYSIS
D509V1, survival
                 sevent
clus2               0   1
  PTPRJ MUTATED    15   4
  PTPRJ WILD-TYPE 166  76
  PTPRJ MUTATED PTPRJ WILD-TYPE 
             19             242 
  PTPRJ MUTATED PTPRJ WILD-TYPE 
              4              76 
$`PTPRJ MUTATED`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6802 
       26.70        11.70         6.97        30.90        34.68        30.90 
TCGA-BR-7851 TCGA-BR-8372 TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5727 
       12.43        19.17         6.58         6.02       105.07        79.07 
TCGA-D7-8570 TCGA-F1-A448 TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GU 
       24.72        21.27        24.20        29.98         0.10         6.25 
TCGA-IN-8462 
       18.81 

$`PTPRJ WILD-TYPE`
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 
        6.61         4.64         7.43        18.35         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       19.89         8.98        21.11        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.33        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GT 
        3.25        22.75        25.81        11.77         8.98         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  PTPRJ MUTATED PTPRJ WILD-TYPE 
            0.1             0.0 
  PTPRJ MUTATED PTPRJ WILD-TYPE 
         105.07           72.23 
  PTPRJ MUTATED PTPRJ WILD-TYPE 
         21.270          12.495 
[1] "0.1 - 105.1 (21.3)" "0.0 - 72.2 (12.5)" 
[1] "hr=" "3.1"
D509V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTPRJ MUTATED         1        1        1        3         3         4
  PTPRJ WILD-TYPE       0        8       26       23        28        40
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPRJ MUTATED           0          3          2          2        1
  PTPRJ WILD-TYPE         3         46         34         22       23
D509V3, multiclass
            clus
vv           PTPRJ MUTATED PTPRJ WILD-TYPE
  STAGE I                1               0
  STAGE IA               1               8
  STAGE IB               1              26
  STAGE II               3              23
  STAGE IIA              3              28
  STAGE IIB              4              40
  STAGE III              0               3
  STAGE IIIA             3              46
  STAGE IIIB             2              34
  STAGE IIIC             2              22
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPRJ MUTATED     2   7   8   6
  PTPRJ WILD-TYPE   9  65 114  69
D509V4, multiclass
    clus
vv   PTPRJ MUTATED PTPRJ WILD-TYPE
  T1             2               9
  T2             7              65
  T3             8             114
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PTPRJ MUTATED    8  8  2  3
  PTPRJ WILD-TYPE 85 73 48 50
D509V5, multiclass
    clus
vv   PTPRJ MUTATED PTPRJ WILD-TYPE
  N0             8              85
  N1             8              73
  N2             2              48
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D509V6, binary
                 cls
clus                0   1
  PTPRJ MUTATED    22   0
  PTPRJ WILD-TYPE 235  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRJ MUTATED     22    0
  PTPRJ WILD-TYPE  235   18
   clus
vv  PTPRJ MUTATED PTPRJ WILD-TYPE
  0            22             235
  1             0              18
[1] 2 2
[1] FALSE
D509V7, binary
                 cls
clus                0   1
  PTPRJ MUTATED     7  17
  PTPRJ WILD-TYPE 103 162
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRJ MUTATED      7   17
  PTPRJ WILD-TYPE  103  162
        clus
vv       PTPRJ MUTATED PTPRJ WILD-TYPE
  FEMALE             7             103
  MALE              17             162
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PTPRJ MUTATED                                       4
  PTPRJ WILD-TYPE                                    46
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PTPRJ MUTATED                                                       11
  PTPRJ WILD-TYPE                                                    124
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PTPRJ MUTATED                                                                   3
  PTPRJ WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PTPRJ MUTATED                                                  4
  PTPRJ WILD-TYPE                                               34
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PTPRJ MUTATED                                                          2
  PTPRJ WILD-TYPE                                                       14
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PTPRJ MUTATED                                                           0
  PTPRJ WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PTPRJ MUTATED                                          0
  PTPRJ WILD-TYPE                                        3
D509V8, multiclass
                                                                   clus
vv                                                                  PTPRJ MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  PTPRJ WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D509V9, binary
                 cls
clus                0   1
  PTPRJ MUTATED     1  23
  PTPRJ WILD-TYPE   4 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRJ MUTATED      1   23
  PTPRJ WILD-TYPE    4  261
     clus
vv    PTPRJ MUTATED PTPRJ WILD-TYPE
  NO              1               4
  YES            23             261
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PTPRJ MUTATED    18   0   0   5
  PTPRJ WILD-TYPE 209  10  10  19
D509V10, multiclass
    clus
vv   PTPRJ MUTATED PTPRJ WILD-TYPE
  R0            18             209
  R1             0              10
  R2             0              10
  RX             5              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D509V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTPRJ MUTATED       5                         1    14
  PTPRJ WILD-TYPE    71                         3   154
D509V12, multiclass
                           clus
vv                          PTPRJ MUTATED PTPRJ WILD-TYPE
  ASIAN                                 5              71
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                14             154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(510) Variable = MDM2 MUTATION ANALYSIS
D510V1, survival
                sevent
clus2              0   1
  MDM2 MUTATED     2   3
  MDM2 WILD-TYPE 179  77
  MDM2 MUTATED MDM2 WILD-TYPE 
             5            256 
  MDM2 MUTATED MDM2 WILD-TYPE 
             3             77 
$`MDM2 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8365 TCGA-HJ-7597 TCGA-HU-A4GU 
        6.97        34.68        17.52        26.47         6.25 

$`MDM2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
        6.18        19.50         0.26        22.19         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 
        5.03        13.58         0.56        11.08         5.52         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  MDM2 MUTATED MDM2 WILD-TYPE 
          6.25           0.00 
  MDM2 MUTATED MDM2 WILD-TYPE 
         34.68         105.07 
  MDM2 MUTATED MDM2 WILD-TYPE 
        17.520         12.605 
[1] "6.2 - 34.7 (17.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D510V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MDM2 MUTATED         0        0        1        0         2         1
  MDM2 WILD-TYPE       1        9       26       26        29        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MDM2 MUTATED           0          1          0          0        0
  MDM2 WILD-TYPE         3         48         36         24       24
D510V3, multiclass
            clus
vv           MDM2 MUTATED MDM2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             2             29
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MDM2 MUTATED     0   1   4   0
  MDM2 WILD-TYPE  11  71 118  75
D510V4, multiclass
    clus
vv   MDM2 MUTATED MDM2 WILD-TYPE
  T1            0             11
  T2            1             71
  T3            4            118
  T4            0             75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  MDM2 MUTATED    3  2  0  0
  MDM2 WILD-TYPE 90 79 50 53
D510V5, multiclass
    clus
vv   MDM2 MUTATED MDM2 WILD-TYPE
  N0            3             90
  N1            2             79
  N2            0             50
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D510V6, binary
                cls
clus               0   1
  MDM2 MUTATED     3   0
  MDM2 WILD-TYPE 254  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDM2 MUTATED      3    0
  MDM2 WILD-TYPE  254   18
   clus
vv  MDM2 MUTATED MDM2 WILD-TYPE
  0            3            254
  1            0             18
[1] 2 2
[1] FALSE
D510V7, binary
                cls
clus               0   1
  MDM2 MUTATED     3   2
  MDM2 WILD-TYPE 107 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDM2 MUTATED      3    2
  MDM2 WILD-TYPE  107  177
        clus
vv       MDM2 MUTATED MDM2 WILD-TYPE
  FEMALE            3            107
  MALE              2            177
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MDM2 MUTATED                                       1
  MDM2 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MDM2 MUTATED                                                        3
  MDM2 WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MDM2 MUTATED                                                                   0
  MDM2 WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MDM2 MUTATED                                                  0
  MDM2 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MDM2 MUTATED                                                          0
  MDM2 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MDM2 MUTATED                                                           0
  MDM2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MDM2 MUTATED                                          1
  MDM2 WILD-TYPE                                        2
D510V8, multiclass
                                                                   clus
vv                                                                  MDM2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  MDM2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D510V9, binary
                cls
clus               0   1
  MDM2 MUTATED     0   5
  MDM2 WILD-TYPE   5 279
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDM2 MUTATED      0    5
  MDM2 WILD-TYPE    5  279
     clus
vv    MDM2 MUTATED MDM2 WILD-TYPE
  NO             0              5
  YES            5            279
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MDM2 MUTATED     4   0   0   1
  MDM2 WILD-TYPE 223  10  10  23
D510V10, multiclass
    clus
vv   MDM2 MUTATED MDM2 WILD-TYPE
  R0            4            223
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D510V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MDM2 MUTATED       1                         0     4
  MDM2 WILD-TYPE    75                         4   164
D510V12, multiclass
                           clus
vv                          MDM2 MUTATED MDM2 WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                4            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(511) Variable = MZF1 MUTATION ANALYSIS
D511V1, survival
                sevent
clus2              0   1
  MZF1 MUTATED     6   3
  MZF1 WILD-TYPE 175  77
  MZF1 MUTATED MZF1 WILD-TYPE 
             9            252 
  MZF1 MUTATED MZF1 WILD-TYPE 
             3             77 
$`MZF1 MUTATED`
TCGA-BR-8078 TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-8572 
       12.26         6.02        28.96        65.10        21.07        16.80 
TCGA-D7-A4YV TCGA-D7-A4YY TCGA-HU-A4GX 
        5.92        13.78        10.19 

$`MZF1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5730 
        0.99         0.99       105.07        12.03        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        24.72        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        15.16 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  MZF1 MUTATED MZF1 WILD-TYPE 
          5.92           0.00 
  MZF1 MUTATED MZF1 WILD-TYPE 
         65.10         105.07 
  MZF1 MUTATED MZF1 WILD-TYPE 
        13.780         12.605 
[1] "5.9 - 65.1 (13.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D511V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MZF1 MUTATED         1        1        1        0         0         3
  MZF1 WILD-TYPE       0        8       26       26        31        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MZF1 MUTATED           0          1          1          1        1
  MZF1 WILD-TYPE         3         48         35         23       23
D511V3, multiclass
            clus
vv           MZF1 MUTATED MZF1 WILD-TYPE
  STAGE I               1              0
  STAGE IA              1              8
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             0             31
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            1             23
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MZF1 MUTATED     2   3   2   3
  MZF1 WILD-TYPE   9  69 120  72
D511V4, multiclass
    clus
vv   MZF1 MUTATED MZF1 WILD-TYPE
  T1            2              9
  T2            3             69
  T3            2            120
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  MZF1 MUTATED    3  3  3  1
  MZF1 WILD-TYPE 90 78 47 52
D511V5, multiclass
    clus
vv   MZF1 MUTATED MZF1 WILD-TYPE
  N0            3             90
  N1            3             78
  N2            3             47
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D511V6, binary
                cls
clus               0   1
  MZF1 MUTATED     9   0
  MZF1 WILD-TYPE 248  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  MZF1 MUTATED      9    0
  MZF1 WILD-TYPE  248   18
   clus
vv  MZF1 MUTATED MZF1 WILD-TYPE
  0            9            248
  1            0             18
[1] 2 2
[1] FALSE
D511V7, binary
                cls
clus               0   1
  MZF1 MUTATED     5   5
  MZF1 WILD-TYPE 105 174
[1] "tbl2"
                cls
clus             [,1] [,2]
  MZF1 MUTATED      5    5
  MZF1 WILD-TYPE  105  174
        clus
vv       MZF1 MUTATED MZF1 WILD-TYPE
  FEMALE            5            105
  MALE              5            174
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MZF1 MUTATED                                       1
  MZF1 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MZF1 MUTATED                                                        4
  MZF1 WILD-TYPE                                                    131
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MZF1 MUTATED                                                                   4
  MZF1 WILD-TYPE                                                                36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MZF1 MUTATED                                                  1
  MZF1 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MZF1 MUTATED                                                          0
  MZF1 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MZF1 MUTATED                                                           0
  MZF1 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MZF1 MUTATED                                          0
  MZF1 WILD-TYPE                                        3
D511V8, multiclass
                                                                   clus
vv                                                                  MZF1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  MZF1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D511V9, binary
                cls
clus               0   1
  MZF1 MUTATED     0  10
  MZF1 WILD-TYPE   5 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  MZF1 MUTATED      0   10
  MZF1 WILD-TYPE    5  274
     clus
vv    MZF1 MUTATED MZF1 WILD-TYPE
  NO             0              5
  YES           10            274
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MZF1 MUTATED    10   0   0   0
  MZF1 WILD-TYPE 217  10  10  24
D511V10, multiclass
    clus
vv   MZF1 MUTATED MZF1 WILD-TYPE
  R0           10            217
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D511V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MZF1 MUTATED       1                         1     4
  MZF1 WILD-TYPE    75                         3   164
D511V12, multiclass
                           clus
vv                          MZF1 MUTATED MZF1 WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                                4            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(512) Variable = SIK1 MUTATION ANALYSIS
D512V1, survival
                sevent
clus2              0   1
  SIK1 MUTATED     3   1
  SIK1 WILD-TYPE 178  79
  SIK1 MUTATED SIK1 WILD-TYPE 
             4            257 
  SIK1 MUTATED SIK1 WILD-TYPE 
             1             79 
$`SIK1 MUTATED`
TCGA-BR-6566 TCGA-BR-8363 TCGA-BR-8364 TCGA-HU-A4G8 
       32.78         0.26        22.19        11.84 

$`SIK1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        7.40         6.18        19.50        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  SIK1 MUTATED SIK1 WILD-TYPE 
          0.26           0.00 
  SIK1 MUTATED SIK1 WILD-TYPE 
         32.78         105.07 
  SIK1 MUTATED SIK1 WILD-TYPE 
        17.015         12.620 
[1] "0.3 - 32.8 (17.0)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.6"
D512V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SIK1 MUTATED         0        0        1        1         1         1
  SIK1 WILD-TYPE       1        9       26       25        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SIK1 MUTATED           0          0          0          1        0
  SIK1 WILD-TYPE         3         49         36         23       24
D512V3, multiclass
            clus
vv           SIK1 MUTATED SIK1 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              1             25
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            1             23
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SIK1 MUTATED     0   2   2   1
  SIK1 WILD-TYPE  11  70 120  74
D512V4, multiclass
    clus
vv   SIK1 MUTATED SIK1 WILD-TYPE
  T1            0             11
  T2            2             70
  T3            2            120
  T4            1             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  SIK1 MUTATED    2  2  1  0
  SIK1 WILD-TYPE 91 79 49 53
D512V5, multiclass
    clus
vv   SIK1 MUTATED SIK1 WILD-TYPE
  N0            2             91
  N1            2             79
  N2            1             49
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D512V6, binary
                cls
clus               0   1
  SIK1 MUTATED     5   0
  SIK1 WILD-TYPE 252  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIK1 MUTATED      5    0
  SIK1 WILD-TYPE  252   18
   clus
vv  SIK1 MUTATED SIK1 WILD-TYPE
  0            5            252
  1            0             18
[1] 2 2
[1] FALSE
D512V7, binary
                cls
clus               0   1
  SIK1 MUTATED     4   1
  SIK1 WILD-TYPE 106 178
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIK1 MUTATED      4    1
  SIK1 WILD-TYPE  106  178
        clus
vv       SIK1 MUTATED SIK1 WILD-TYPE
  FEMALE            4            106
  MALE              1            178
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SIK1 MUTATED                                       2
  SIK1 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SIK1 MUTATED                                                        2
  SIK1 WILD-TYPE                                                    133
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SIK1 MUTATED                                                                   0
  SIK1 WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SIK1 MUTATED                                                  0
  SIK1 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SIK1 MUTATED                                                          1
  SIK1 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SIK1 MUTATED                                                           0
  SIK1 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SIK1 MUTATED                                          0
  SIK1 WILD-TYPE                                        3
D512V8, multiclass
                                                                   clus
vv                                                                  SIK1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  SIK1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D512V9, binary
                cls
clus               0   1
  SIK1 MUTATED     1   4
  SIK1 WILD-TYPE   4 280
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIK1 MUTATED      1    4
  SIK1 WILD-TYPE    4  280
     clus
vv    SIK1 MUTATED SIK1 WILD-TYPE
  NO             1              4
  YES            4            280
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SIK1 MUTATED     4   0   0   0
  SIK1 WILD-TYPE 223  10  10  24
D512V10, multiclass
    clus
vv   SIK1 MUTATED SIK1 WILD-TYPE
  R0            4            223
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D512V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SIK1 MUTATED       1                         0     3
  SIK1 WILD-TYPE    75                         4   165
D512V12, multiclass
                           clus
vv                          SIK1 MUTATED SIK1 WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                3            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(513) Variable = PIGT MUTATION ANALYSIS
D513V1, survival
                sevent
clus2              0   1
  PIGT MUTATED     5   3
  PIGT WILD-TYPE 176  77
  PIGT MUTATED PIGT WILD-TYPE 
             8            253 
  PIGT MUTATED PIGT WILD-TYPE 
             3             77 
$`PIGT MUTATED`
TCGA-BR-8059 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 
       14.43         1.12         6.58       105.07        28.96        65.10 
TCGA-F1-6874 TCGA-HU-A4G8 
       14.47        11.84 

$`PIGT WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
        0.99        12.03        79.07         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  PIGT MUTATED PIGT WILD-TYPE 
          1.12           0.00 
  PIGT MUTATED PIGT WILD-TYPE 
        105.07          79.07 
  PIGT MUTATED PIGT WILD-TYPE 
         14.45          12.59 
[1] "1.1 - 105.1 (14.4)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.6"
D513V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIGT MUTATED         0        1        2        1         2         1
  PIGT WILD-TYPE       1        8       25       25        29        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIGT MUTATED           1          0          0          0        0
  PIGT WILD-TYPE         2         49         36         24       24
D513V3, multiclass
            clus
vv           PIGT MUTATED PIGT WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              2             25
  STAGE II              1             25
  STAGE IIA             2             29
  STAGE IIB             1             43
  STAGE III             1              2
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PIGT MUTATED     1   3   3   1
  PIGT WILD-TYPE  10  69 119  74
D513V4, multiclass
    clus
vv   PIGT MUTATED PIGT WILD-TYPE
  T1            1             10
  T2            3             69
  T3            3            119
  T4            1             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  PIGT MUTATED    5  3  0  0
  PIGT WILD-TYPE 88 78 50 53
D513V5, multiclass
    clus
vv   PIGT MUTATED PIGT WILD-TYPE
  N0            5             88
  N1            3             78
  N2            0             50
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D513V6, binary
                cls
clus               0   1
  PIGT MUTATED     8   0
  PIGT WILD-TYPE 249  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGT MUTATED      8    0
  PIGT WILD-TYPE  249   18
   clus
vv  PIGT MUTATED PIGT WILD-TYPE
  0            8            249
  1            0             18
[1] 2 2
[1] FALSE
D513V7, binary
                cls
clus               0   1
  PIGT MUTATED     3   5
  PIGT WILD-TYPE 107 174
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGT MUTATED      3    5
  PIGT WILD-TYPE  107  174
        clus
vv       PIGT MUTATED PIGT WILD-TYPE
  FEMALE            3            107
  MALE              5            174
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PIGT MUTATED                                       2
  PIGT WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIGT MUTATED                                                        2
  PIGT WILD-TYPE                                                    133
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIGT MUTATED                                                                   4
  PIGT WILD-TYPE                                                                36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PIGT MUTATED                                                  0
  PIGT WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PIGT MUTATED                                                          0
  PIGT WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PIGT MUTATED                                                           0
  PIGT WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PIGT MUTATED                                          0
  PIGT WILD-TYPE                                        3
D513V8, multiclass
                                                                   clus
vv                                                                  PIGT MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  PIGT WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D513V9, binary
                cls
clus               0   1
  PIGT MUTATED     0   8
  PIGT WILD-TYPE   5 276
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGT MUTATED      0    8
  PIGT WILD-TYPE    5  276
     clus
vv    PIGT MUTATED PIGT WILD-TYPE
  NO             0              5
  YES            8            276
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PIGT MUTATED     6   0   0   0
  PIGT WILD-TYPE 221  10  10  24
D513V10, multiclass
    clus
vv   PIGT MUTATED PIGT WILD-TYPE
  R0            6            221
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D513V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIGT MUTATED       2                         0     3
  PIGT WILD-TYPE    74                         4   165
D513V12, multiclass
                           clus
vv                          PIGT MUTATED PIGT WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                3            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(514) Variable = NUPL2 MUTATION ANALYSIS
D514V1, survival
                 sevent
clus2               0   1
  NUPL2 MUTATED     3   3
  NUPL2 WILD-TYPE 178  77
  NUPL2 MUTATED NUPL2 WILD-TYPE 
              6             255 
  NUPL2 MUTATED NUPL2 WILD-TYPE 
              3              77 
$`NUPL2 MUTATED`
TCGA-BR-4184 TCGA-BR-8363 TCGA-BR-8591 TCGA-CD-A4MG TCGA-D7-8570 TCGA-FP-8211 
        6.97         0.26        13.45         6.58        24.72        13.58 

$`NUPL2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        19.50        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.55        11.31        12.33        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
       14.07        22.29        17.06        59.54         5.03         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  NUPL2 MUTATED NUPL2 WILD-TYPE 
           0.26            0.00 
  NUPL2 MUTATED NUPL2 WILD-TYPE 
          24.72          105.07 
  NUPL2 MUTATED NUPL2 WILD-TYPE 
          10.21           12.62 
[1] "0.3 - 24.7 (10.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.4"
D514V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NUPL2 MUTATED         0        0        1        0         1         1
  NUPL2 WILD-TYPE       1        9       26       26        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUPL2 MUTATED           0          2          1          1        0
  NUPL2 WILD-TYPE         3         47         35         23       24
D514V3, multiclass
            clus
vv           NUPL2 MUTATED NUPL2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NUPL2 MUTATED     0   1   4   2
  NUPL2 WILD-TYPE  11  71 118  73
D514V4, multiclass
    clus
vv   NUPL2 MUTATED NUPL2 WILD-TYPE
  T1             0              11
  T2             1              71
  T3             4             118
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  NUPL2 MUTATED    3  2  0  2
  NUPL2 WILD-TYPE 90 79 50 51
D514V5, multiclass
    clus
vv   NUPL2 MUTATED NUPL2 WILD-TYPE
  N0             3              90
  N1             2              79
  N2             0              50
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D514V6, binary
                 cls
clus                0   1
  NUPL2 MUTATED     5   0
  NUPL2 WILD-TYPE 252  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUPL2 MUTATED      5    0
  NUPL2 WILD-TYPE  252   18
   clus
vv  NUPL2 MUTATED NUPL2 WILD-TYPE
  0             5             252
  1             0              18
[1] 2 2
[1] FALSE
D514V7, binary
                 cls
clus                0   1
  NUPL2 MUTATED     2   5
  NUPL2 WILD-TYPE 108 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUPL2 MUTATED      2    5
  NUPL2 WILD-TYPE  108  174
        clus
vv       NUPL2 MUTATED NUPL2 WILD-TYPE
  FEMALE             2             108
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NUPL2 MUTATED                                       1
  NUPL2 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NUPL2 MUTATED                                                        5
  NUPL2 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NUPL2 MUTATED                                                                   0
  NUPL2 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NUPL2 MUTATED                                                  1
  NUPL2 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NUPL2 MUTATED                                                          0
  NUPL2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NUPL2 MUTATED                                                           0
  NUPL2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NUPL2 MUTATED                                          0
  NUPL2 WILD-TYPE                                        3
D514V8, multiclass
                                                                   clus
vv                                                                  NUPL2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  NUPL2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D514V9, binary
                 cls
clus                0   1
  NUPL2 MUTATED     0   7
  NUPL2 WILD-TYPE   5 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUPL2 MUTATED      0    7
  NUPL2 WILD-TYPE    5  277
     clus
vv    NUPL2 MUTATED NUPL2 WILD-TYPE
  NO              0               5
  YES             7             277
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NUPL2 MUTATED     3   1   0   2
  NUPL2 WILD-TYPE 224   9  10  22
D514V10, multiclass
    clus
vv   NUPL2 MUTATED NUPL2 WILD-TYPE
  R0             3             224
  R1             1               9
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D514V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NUPL2 MUTATED       1                         0     6
  NUPL2 WILD-TYPE    75                         4   162
D514V12, multiclass
                           clus
vv                          NUPL2 MUTATED NUPL2 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(515) Variable = NOS3 MUTATION ANALYSIS
D515V1, survival
                sevent
clus2              0   1
  NOS3 MUTATED     8   0
  NOS3 WILD-TYPE 173  80
  NOS3 MUTATED NOS3 WILD-TYPE 
             8            253 
  NOS3 MUTATED NOS3 WILD-TYPE 
             0             80 
$`NOS3 MUTATED`
TCGA-BR-8078 TCGA-CD-8526 TCGA-CG-4444 TCGA-CG-5723 TCGA-F1-6874 TCGA-FP-7829 
       12.26         0.07        47.05       105.07        14.47        19.53 
TCGA-HU-A4GT TCGA-HU-A4H3 
        6.51        19.36 

$`NOS3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 
        7.99        16.24        72.23        21.27         3.48        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         0.10         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  NOS3 MUTATED NOS3 WILD-TYPE 
          0.07           0.00 
  NOS3 MUTATED NOS3 WILD-TYPE 
        105.07          79.07 
  NOS3 MUTATED NOS3 WILD-TYPE 
        16.915         12.590 
[1] "0.1 - 105.1 (16.9)" "0.0 - 79.1 (12.6)" 
[1] "hr="     "2.9e+07"
D515V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NOS3 MUTATED         1        0        2        1         1         2
  NOS3 WILD-TYPE       0        9       25       25        30        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NOS3 MUTATED           0          2          0          1        0
  NOS3 WILD-TYPE         3         47         36         23       24
D515V3, multiclass
            clus
vv           NOS3 MUTATED NOS3 WILD-TYPE
  STAGE I               1              0
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              1             25
  STAGE IIA             1             30
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            0             36
  STAGE IIIC            1             23
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NOS3 MUTATED     1   4   3   2
  NOS3 WILD-TYPE  10  68 119  73
D515V4, multiclass
    clus
vv   NOS3 MUTATED NOS3 WILD-TYPE
  T1            1             10
  T2            4             68
  T3            3            119
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  NOS3 MUTATED    4  4  1  1
  NOS3 WILD-TYPE 89 77 49 52
D515V5, multiclass
    clus
vv   NOS3 MUTATED NOS3 WILD-TYPE
  N0            4             89
  N1            4             77
  N2            1             49
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D515V6, binary
                cls
clus               0   1
  NOS3 MUTATED     9   0
  NOS3 WILD-TYPE 248  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED      9    0
  NOS3 WILD-TYPE  248   18
   clus
vv  NOS3 MUTATED NOS3 WILD-TYPE
  0            9            248
  1            0             18
[1] 2 2
[1] FALSE
D515V7, binary
                cls
clus               0   1
  NOS3 MUTATED     4   6
  NOS3 WILD-TYPE 106 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED      4    6
  NOS3 WILD-TYPE  106  173
        clus
vv       NOS3 MUTATED NOS3 WILD-TYPE
  FEMALE            4            106
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NOS3 MUTATED                                       2
  NOS3 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NOS3 MUTATED                                                        3
  NOS3 WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NOS3 MUTATED                                                                   3
  NOS3 WILD-TYPE                                                                37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NOS3 MUTATED                                                  1
  NOS3 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NOS3 MUTATED                                                          1
  NOS3 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NOS3 MUTATED                                                           0
  NOS3 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NOS3 MUTATED                                          0
  NOS3 WILD-TYPE                                        3
D515V8, multiclass
                                                                   clus
vv                                                                  NOS3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  NOS3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D515V9, binary
                cls
clus               0   1
  NOS3 MUTATED     0  10
  NOS3 WILD-TYPE   5 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED      0   10
  NOS3 WILD-TYPE    5  274
     clus
vv    NOS3 MUTATED NOS3 WILD-TYPE
  NO             0              5
  YES           10            274
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NOS3 MUTATED    10   0   0   0
  NOS3 WILD-TYPE 217  10  10  24
D515V10, multiclass
    clus
vv   NOS3 MUTATED NOS3 WILD-TYPE
  R0           10            217
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D515V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NOS3 MUTATED       3                         1     3
  NOS3 WILD-TYPE    73                         3   165
D515V12, multiclass
                           clus
vv                          NOS3 MUTATED NOS3 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                                3            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(516) Variable = LUC7L3 MUTATION ANALYSIS
D516V1, survival
                  sevent
clus2                0   1
  LUC7L3 MUTATED     6   0
  LUC7L3 WILD-TYPE 175  80
  LUC7L3 MUTATED LUC7L3 WILD-TYPE 
               6              255 
  LUC7L3 MUTATED LUC7L3 WILD-TYPE 
               0               80 
$`LUC7L3 MUTATED`
TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-8361 TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4H4 
       23.93        12.43        19.50        25.81         6.51        23.84 

$`LUC7L3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        11.77        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  LUC7L3 MUTATED LUC7L3 WILD-TYPE 
            6.51             0.00 
  LUC7L3 MUTATED LUC7L3 WILD-TYPE 
           25.81           105.07 
  LUC7L3 MUTATED LUC7L3 WILD-TYPE 
           21.67            12.59 
[1] "6.5 - 25.8 (21.7)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "2.6e+07"
D516V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LUC7L3 MUTATED         0        0        1        0         2         2
  LUC7L3 WILD-TYPE       1        9       26       26        29        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LUC7L3 MUTATED           0          0          0          1        0
  LUC7L3 WILD-TYPE         3         49         36         23       24
D516V3, multiclass
            clus
vv           LUC7L3 MUTATED LUC7L3 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               2               29
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LUC7L3 MUTATED     0   2   2   2
  LUC7L3 WILD-TYPE  11  70 120  73
D516V4, multiclass
    clus
vv   LUC7L3 MUTATED LUC7L3 WILD-TYPE
  T1              0               11
  T2              2               70
  T3              2              120
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  LUC7L3 MUTATED    4  0  2  0
  LUC7L3 WILD-TYPE 89 81 48 53
D516V5, multiclass
    clus
vv   LUC7L3 MUTATED LUC7L3 WILD-TYPE
  N0              4               89
  N1              0               81
  N2              2               48
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D516V6, binary
                  cls
clus                 0   1
  LUC7L3 MUTATED     6   0
  LUC7L3 WILD-TYPE 251  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LUC7L3 MUTATED      6    0
  LUC7L3 WILD-TYPE  251   18
   clus
vv  LUC7L3 MUTATED LUC7L3 WILD-TYPE
  0              6              251
  1              0               18
[1] 2 2
[1] FALSE
D516V7, binary
                  cls
clus                 0   1
  LUC7L3 MUTATED     4   2
  LUC7L3 WILD-TYPE 106 177
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LUC7L3 MUTATED      4    2
  LUC7L3 WILD-TYPE  106  177
        clus
vv       LUC7L3 MUTATED LUC7L3 WILD-TYPE
  FEMALE              4              106
  MALE                2              177
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  LUC7L3 MUTATED                                       0
  LUC7L3 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LUC7L3 MUTATED                                                        2
  LUC7L3 WILD-TYPE                                                    133
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LUC7L3 MUTATED                                                                   1
  LUC7L3 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  LUC7L3 MUTATED                                                  3
  LUC7L3 WILD-TYPE                                               35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  LUC7L3 MUTATED                                                          0
  LUC7L3 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  LUC7L3 MUTATED                                                           0
  LUC7L3 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  LUC7L3 MUTATED                                          0
  LUC7L3 WILD-TYPE                                        3
D516V8, multiclass
                                                                   clus
vv                                                                  LUC7L3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  LUC7L3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D516V9, binary
                  cls
clus                 0   1
  LUC7L3 MUTATED     0   6
  LUC7L3 WILD-TYPE   5 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LUC7L3 MUTATED      0    6
  LUC7L3 WILD-TYPE    5  278
     clus
vv    LUC7L3 MUTATED LUC7L3 WILD-TYPE
  NO               0                5
  YES              6              278
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  LUC7L3 MUTATED     6   0   0   0
  LUC7L3 WILD-TYPE 221  10  10  24
D516V10, multiclass
    clus
vv   LUC7L3 MUTATED LUC7L3 WILD-TYPE
  R0              6              221
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D516V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LUC7L3 MUTATED       3                         0     3
  LUC7L3 WILD-TYPE    73                         4   165
D516V12, multiclass
                           clus
vv                          LUC7L3 MUTATED LUC7L3 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  3              165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(517) Variable = LINGO4 MUTATION ANALYSIS
D517V1, survival
                  sevent
clus2                0   1
  LINGO4 MUTATED     5   3
  LINGO4 WILD-TYPE 176  77
  LINGO4 MUTATED LINGO4 WILD-TYPE 
               8              253 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
               3               77 
$`LINGO4 MUTATED`
TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-7707 TCGA-BR-8081 TCGA-CD-A489 TCGA-D7-A4YV 
       34.68        19.33        23.93        20.55        11.31         5.92 
TCGA-FP-A4BE TCGA-HU-A4GT 
       11.08         6.51 

$`LINGO4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69        12.26         9.60         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         3.42         9.34        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  LINGO4 MUTATED LINGO4 WILD-TYPE 
            5.92             0.00 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
           34.68           105.07 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
           15.32            12.62 
[1] "5.9 - 34.7 (15.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1"  
D517V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LINGO4 MUTATED         0        0        1        0         5         3
  LINGO4 WILD-TYPE       1        9       26       26        26        41
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LINGO4 MUTATED           0          0          0          0        1
  LINGO4 WILD-TYPE         3         49         36         24       23
D517V3, multiclass
            clus
vv           LINGO4 MUTATED LINGO4 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               5               26
  STAGE IIB               3               41
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LINGO4 MUTATED     0   1   7   2
  LINGO4 WILD-TYPE  11  71 115  73
D517V4, multiclass
    clus
vv   LINGO4 MUTATED LINGO4 WILD-TYPE
  T1              0               11
  T2              1               71
  T3              7              115
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  LINGO4 MUTATED    7  2  1  0
  LINGO4 WILD-TYPE 86 79 49 53
D517V5, multiclass
    clus
vv   LINGO4 MUTATED LINGO4 WILD-TYPE
  N0              7               86
  N1              2               79
  N2              1               49
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D517V6, binary
                  cls
clus                 0   1
  LINGO4 MUTATED    10   0
  LINGO4 WILD-TYPE 247  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LINGO4 MUTATED     10    0
  LINGO4 WILD-TYPE  247   18
   clus
vv  LINGO4 MUTATED LINGO4 WILD-TYPE
  0             10              247
  1              0               18
[1] 2 2
[1] FALSE
D517V7, binary
                  cls
clus                 0   1
  LINGO4 MUTATED     7   3
  LINGO4 WILD-TYPE 103 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LINGO4 MUTATED      7    3
  LINGO4 WILD-TYPE  103  176
        clus
vv       LINGO4 MUTATED LINGO4 WILD-TYPE
  FEMALE              7              103
  MALE                3              176
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  LINGO4 MUTATED                                       1
  LINGO4 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LINGO4 MUTATED                                                        7
  LINGO4 WILD-TYPE                                                    128
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LINGO4 MUTATED                                                                   0
  LINGO4 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  LINGO4 MUTATED                                                  2
  LINGO4 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  LINGO4 MUTATED                                                          0
  LINGO4 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  LINGO4 MUTATED                                                           0
  LINGO4 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  LINGO4 MUTATED                                          0
  LINGO4 WILD-TYPE                                        3
D517V8, multiclass
                                                                   clus
vv                                                                  LINGO4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  LINGO4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D517V9, binary
                  cls
clus                 0   1
  LINGO4 MUTATED     0  10
  LINGO4 WILD-TYPE   5 274
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LINGO4 MUTATED      0   10
  LINGO4 WILD-TYPE    5  274
     clus
vv    LINGO4 MUTATED LINGO4 WILD-TYPE
  NO               0                5
  YES             10              274
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  LINGO4 MUTATED     8   0   0   1
  LINGO4 WILD-TYPE 219  10  10  23
D517V10, multiclass
    clus
vv   LINGO4 MUTATED LINGO4 WILD-TYPE
  R0              8              219
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D517V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LINGO4 MUTATED       2                         1     7
  LINGO4 WILD-TYPE    74                         3   161
D517V12, multiclass
                           clus
vv                          LINGO4 MUTATED LINGO4 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  7              161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(518) Variable = CHRNB3 MUTATION ANALYSIS
D518V1, survival
                  sevent
clus2                0   1
  CHRNB3 MUTATED     5   3
  CHRNB3 WILD-TYPE 176  77
  CHRNB3 MUTATED CHRNB3 WILD-TYPE 
               8              253 
  CHRNB3 MUTATED CHRNB3 WILD-TYPE 
               3               77 
$`CHRNB3 MUTATED`
TCGA-BR-4184 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8680 TCGA-CD-8530 TCGA-CD-A489 
        6.97         4.31        15.85        15.81         0.16        11.31 
TCGA-CG-4305 TCGA-CG-5726 
       15.95        28.96 

$`CHRNB3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.10         0.13         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        3.42         9.34        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
        0.10        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 
        0.99         6.02         0.99       105.07        12.03        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  CHRNB3 MUTATED CHRNB3 WILD-TYPE 
            0.16             0.00 
  CHRNB3 MUTATED CHRNB3 WILD-TYPE 
           28.96           105.07 
  CHRNB3 MUTATED CHRNB3 WILD-TYPE 
           13.56            12.62 
[1] "0.2 - 29.0 (13.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D518V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CHRNB3 MUTATED         0        1        1        2         1         0
  CHRNB3 WILD-TYPE       1        8       26       24        30        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHRNB3 MUTATED           0          1          0          1        3
  CHRNB3 WILD-TYPE         3         48         36         23       21
D518V3, multiclass
            clus
vv           CHRNB3 MUTATED CHRNB3 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                1               26
  STAGE II                2               24
  STAGE IIA               1               30
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                3               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CHRNB3 MUTATED     1   2   3   4
  CHRNB3 WILD-TYPE  10  70 119  71
D518V4, multiclass
    clus
vv   CHRNB3 MUTATED CHRNB3 WILD-TYPE
  T1              1               10
  T2              2               70
  T3              3              119
  T4              4               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CHRNB3 MUTATED    4  2  3  1
  CHRNB3 WILD-TYPE 89 79 47 52
D518V5, multiclass
    clus
vv   CHRNB3 MUTATED CHRNB3 WILD-TYPE
  N0              4               89
  N1              2               79
  N2              3               47
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D518V6, binary
                  cls
clus                 0   1
  CHRNB3 MUTATED     8   2
  CHRNB3 WILD-TYPE 249  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNB3 MUTATED      8    2
  CHRNB3 WILD-TYPE  249   16
   clus
vv  CHRNB3 MUTATED CHRNB3 WILD-TYPE
  0              8              249
  1              2               16
[1] 2 2
[1] FALSE
D518V7, binary
                  cls
clus                 0   1
  CHRNB3 MUTATED     5   6
  CHRNB3 WILD-TYPE 105 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNB3 MUTATED      5    6
  CHRNB3 WILD-TYPE  105  173
        clus
vv       CHRNB3 MUTATED CHRNB3 WILD-TYPE
  FEMALE              5              105
  MALE                6              173
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CHRNB3 MUTATED                                       3
  CHRNB3 WILD-TYPE                                    47
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CHRNB3 MUTATED                                                        6
  CHRNB3 WILD-TYPE                                                    129
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CHRNB3 MUTATED                                                                   1
  CHRNB3 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CHRNB3 MUTATED                                                  1
  CHRNB3 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CHRNB3 MUTATED                                                          0
  CHRNB3 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CHRNB3 MUTATED                                                           0
  CHRNB3 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CHRNB3 MUTATED                                          0
  CHRNB3 WILD-TYPE                                        3
D518V8, multiclass
                                                                   clus
vv                                                                  CHRNB3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  CHRNB3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D518V9, binary
                  cls
clus                 0   1
  CHRNB3 MUTATED     0  11
  CHRNB3 WILD-TYPE   5 273
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNB3 MUTATED      0   11
  CHRNB3 WILD-TYPE    5  273
     clus
vv    CHRNB3 MUTATED CHRNB3 WILD-TYPE
  NO               0                5
  YES             11              273
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CHRNB3 MUTATED     6   0   1   3
  CHRNB3 WILD-TYPE 221  10   9  21
D518V10, multiclass
    clus
vv   CHRNB3 MUTATED CHRNB3 WILD-TYPE
  R0              6              221
  R1              0               10
  R2              1                9
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D518V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CHRNB3 MUTATED       3                         0     5
  CHRNB3 WILD-TYPE    73                         4   163
D518V12, multiclass
                           clus
vv                          CHRNB3 MUTATED CHRNB3 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  5              163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(519) Variable = NARG2 MUTATION ANALYSIS
D519V1, survival
                 sevent
clus2               0   1
  NARG2 MUTATED     9   2
  NARG2 WILD-TYPE 172  78
  NARG2 MUTATED NARG2 WILD-TYPE 
             11             250 
  NARG2 MUTATED NARG2 WILD-TYPE 
              2              78 
$`NARG2 MUTATED`
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MJ 
        6.61        34.68        13.45        11.57         0.10        12.62 
TCGA-CG-5721 TCGA-D7-A4YU TCGA-HJ-7597 TCGA-HU-A4GX TCGA-HU-A4H4 
        6.02        16.44        26.47        10.19        23.84 

$`NARG2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
       18.35        30.90         6.18         9.57        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       19.36        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  NARG2 MUTATED NARG2 WILD-TYPE 
            0.1             0.0 
  NARG2 MUTATED NARG2 WILD-TYPE 
          34.68          105.07 
  NARG2 MUTATED NARG2 WILD-TYPE 
         12.620          12.625 
[1] "0.1 - 34.7 (12.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.8"
D519V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NARG2 MUTATED         0        0        2        1         1         1
  NARG2 WILD-TYPE       1        9       25       25        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NARG2 MUTATED           1          0          2          2        1
  NARG2 WILD-TYPE         2         49         34         22       23
D519V3, multiclass
            clus
vv           NARG2 MUTATED NARG2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              1               2
  STAGE IIIA             0              49
  STAGE IIIB             2              34
  STAGE IIIC             2              22
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NARG2 MUTATED     0   4   4   3
  NARG2 WILD-TYPE  11  68 118  72
D519V4, multiclass
    clus
vv   NARG2 MUTATED NARG2 WILD-TYPE
  T1             0              11
  T2             4              68
  T3             4             118
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  NARG2 MUTATED    4  2  2  3
  NARG2 WILD-TYPE 89 79 48 50
D519V5, multiclass
    clus
vv   NARG2 MUTATED NARG2 WILD-TYPE
  N0             4              89
  N1             2              79
  N2             2              48
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D519V6, binary
                 cls
clus                0   1
  NARG2 MUTATED    10   0
  NARG2 WILD-TYPE 247  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NARG2 MUTATED     10    0
  NARG2 WILD-TYPE  247   18
   clus
vv  NARG2 MUTATED NARG2 WILD-TYPE
  0            10             247
  1             0              18
[1] 2 2
[1] FALSE
D519V7, binary
                 cls
clus                0   1
  NARG2 MUTATED     6   5
  NARG2 WILD-TYPE 104 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NARG2 MUTATED      6    5
  NARG2 WILD-TYPE  104  174
        clus
vv       NARG2 MUTATED NARG2 WILD-TYPE
  FEMALE             6             104
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NARG2 MUTATED                                       1
  NARG2 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NARG2 MUTATED                                                        6
  NARG2 WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NARG2 MUTATED                                                                   1
  NARG2 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NARG2 MUTATED                                                  2
  NARG2 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NARG2 MUTATED                                                          0
  NARG2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NARG2 MUTATED                                                           0
  NARG2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NARG2 MUTATED                                          1
  NARG2 WILD-TYPE                                        2
D519V8, multiclass
                                                                   clus
vv                                                                  NARG2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  NARG2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D519V9, binary
                 cls
clus                0   1
  NARG2 MUTATED     0  11
  NARG2 WILD-TYPE   5 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NARG2 MUTATED      0   11
  NARG2 WILD-TYPE    5  273
     clus
vv    NARG2 MUTATED NARG2 WILD-TYPE
  NO              0               5
  YES            11             273
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NARG2 MUTATED     9   0   0   1
  NARG2 WILD-TYPE 218  10  10  23
D519V10, multiclass
    clus
vv   NARG2 MUTATED NARG2 WILD-TYPE
  R0             9             218
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D519V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NARG2 MUTATED       4                         0     6
  NARG2 WILD-TYPE    72                         4   162
D519V12, multiclass
                           clus
vv                          NARG2 MUTATED NARG2 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(520) Variable = FLG MUTATION ANALYSIS
D520V1, survival
               sevent
clus2             0   1
  FLG MUTATED    39  14
  FLG WILD-TYPE 142  66
  FLG MUTATED FLG WILD-TYPE 
           53           208 
  FLG MUTATED FLG WILD-TYPE 
           14            66 
$`FLG MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
        6.97        30.90        34.68        39.12        26.10        32.78 
TCGA-BR-6802 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-8367 
       30.90        14.43        12.26        20.55         6.18        26.33 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A4PD TCGA-BR-A4PE 
        1.12        15.81        15.81         9.86        20.65        20.42 
TCGA-BR-A4QL TCGA-CD-5801 TCGA-CD-5813 TCGA-CD-8528 TCGA-CD-8536 TCGA-CD-A486 
       11.57        13.18         0.39         0.10         0.10         3.42 
TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5721 TCGA-CG-5726 
        6.58         1.02        18.97        22.98         6.02        28.96 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-6526 
       79.07         4.01        69.04        21.07         7.99        17.19 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8579 
       15.22        15.98        11.31        12.33        16.80        20.91 
TCGA-FP-7735 TCGA-FP-7829 TCGA-HU-8610 TCGA-HU-A4G8 TCGA-HU-A4GF TCGA-HU-A4GH 
        3.48        19.53         0.76        11.84        25.81        11.77 
TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-8462 
        6.25        23.84         8.88        27.42        18.81 

$`FLG WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       13.68        19.33         9.17        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       17.49         0.69         9.60         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
       16.31         2.20        15.58         7.40        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 
        5.39        25.18         9.21        20.22        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       13.51         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.15         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.07         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00         9.01         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5728 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       12.03        65.10        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 
       10.26        12.79        10.55        24.72        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        14.66        21.14        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       14.47        72.23        21.27        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
       10.62        24.30         5.59        12.30        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       22.75        29.98         8.98         0.10         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        12.30         9.67 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45         3.39         2.53 

  FLG MUTATED FLG WILD-TYPE 
          0.1           0.0 
  FLG MUTATED FLG WILD-TYPE 
        79.07        105.07 
  FLG MUTATED FLG WILD-TYPE 
        15.81         12.43 
[1] "0.1 - 79.1 (15.8)"  "0.0 - 105.1 (12.4)"
[1] "hr=" "1.7"
D520V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FLG MUTATED         1        3        6        4         7        14
  FLG WILD-TYPE       0        6       21       22        24        30
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FLG MUTATED           1         10          4          0        7
  FLG WILD-TYPE         2         39         32         24       17
D520V3, multiclass
            clus
vv           FLG MUTATED FLG WILD-TYPE
  STAGE I              1             0
  STAGE IA             3             6
  STAGE IB             6            21
  STAGE II             4            22
  STAGE IIA            7            24
  STAGE IIB           14            30
  STAGE III            1             2
  STAGE IIIA          10            39
  STAGE IIIB           4            32
  STAGE IIIC           0            24
  STAGE IV             7            17
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3 T4
  FLG MUTATED    6 17 25 11
  FLG WILD-TYPE  5 55 97 64
D520V4, multiclass
    clus
vv   FLG MUTATED FLG WILD-TYPE
  T1           6             5
  T2          17            55
  T3          25            97
  T4          11            64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  FLG MUTATED   23 19 13  4
  FLG WILD-TYPE 70 62 37 49
D520V5, multiclass
    clus
vv   FLG MUTATED FLG WILD-TYPE
  N0          23            70
  N1          19            62
  N2          13            37
  N3           4            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D520V6, binary
               cls
clus              0   1
  FLG MUTATED    55   4
  FLG WILD-TYPE 202  14
[1] "tbl2"
               cls
clus            [,1] [,2]
  FLG MUTATED     55    4
  FLG WILD-TYPE  202   14
   clus
vv  FLG MUTATED FLG WILD-TYPE
  0          55           202
  1           4            14
[1] 2 2
[1] FALSE
D520V7, binary
               cls
clus              0   1
  FLG MUTATED    26  36
  FLG WILD-TYPE  84 143
[1] "tbl2"
               cls
clus            [,1] [,2]
  FLG MUTATED     26   36
  FLG WILD-TYPE   84  143
        clus
vv       FLG MUTATED FLG WILD-TYPE
  FEMALE          26            84
  MALE            36           143
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FLG MUTATED                                       5
  FLG WILD-TYPE                                    45
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FLG MUTATED                                                       28
  FLG WILD-TYPE                                                    107
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FLG MUTATED                                                                  11
  FLG WILD-TYPE                                                                29
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FLG MUTATED                                                 13
  FLG WILD-TYPE                                               25
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FLG MUTATED                                                          4
  FLG WILD-TYPE                                                       12
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FLG MUTATED                                                           0
  FLG WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FLG MUTATED                                          0
  FLG WILD-TYPE                                        3
D520V8, multiclass
                                                                   clus
vv                                                                  FLG MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                     28
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)          11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                           13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  FLG WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      107
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             25
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D520V9, binary
               cls
clus              0   1
  FLG MUTATED     2  60
  FLG WILD-TYPE   3 224
[1] "tbl2"
               cls
clus            [,1] [,2]
  FLG MUTATED      2   60
  FLG WILD-TYPE    3  224
     clus
vv    FLG MUTATED FLG WILD-TYPE
  NO            2             3
  YES          60           224
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  FLG MUTATED    47   1   3   7
  FLG WILD-TYPE 180   9   7  17
D520V10, multiclass
    clus
vv   FLG MUTATED FLG WILD-TYPE
  R0          47           180
  R1           1             9
  R2           3             7
  RX           7            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D520V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FLG MUTATED      16                         2    31
  FLG WILD-TYPE    60                         2   137
D520V12, multiclass
                           clus
vv                          FLG MUTATED FLG WILD-TYPE
  ASIAN                              16            60
  BLACK OR AFRICAN AMERICAN           2             2
  WHITE                              31           137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(521) Variable = PCBP2 MUTATION ANALYSIS
D521V1, survival
                 sevent
clus2               0   1
  PCBP2 MUTATED     3   0
  PCBP2 WILD-TYPE 178  80
  PCBP2 MUTATED PCBP2 WILD-TYPE 
              3             258 
  PCBP2 MUTATED PCBP2 WILD-TYPE 
              0              80 
$`PCBP2 MUTATED`
TCGA-BR-8368 TCGA-BR-8487 TCGA-HU-A4G9 
        4.31         1.12        24.20 

$`PCBP2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  PCBP2 MUTATED PCBP2 WILD-TYPE 
           1.12            0.00 
  PCBP2 MUTATED PCBP2 WILD-TYPE 
          24.20          105.07 
  PCBP2 MUTATED PCBP2 WILD-TYPE 
           4.31           12.64 
[1] "1.1 - 24.2 (4.3)"   "0.0 - 105.1 (12.6)"
[1] "hr="     "3300000"
D521V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PCBP2 MUTATED         0        1        1        1         1         0
  PCBP2 WILD-TYPE       1        8       26       25        30        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCBP2 MUTATED           0          0          0          0        0
  PCBP2 WILD-TYPE         3         49         36         24       24
D521V3, multiclass
            clus
vv           PCBP2 MUTATED PCBP2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PCBP2 MUTATED     1   2   1   0
  PCBP2 WILD-TYPE  10  70 121  75
D521V4, multiclass
    clus
vv   PCBP2 MUTATED PCBP2 WILD-TYPE
  T1             1              10
  T2             2              70
  T3             1             121
  T4             0              75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PCBP2 MUTATED    3  1  0  0
  PCBP2 WILD-TYPE 90 80 50 53
D521V5, multiclass
    clus
vv   PCBP2 MUTATED PCBP2 WILD-TYPE
  N0             3              90
  N1             1              80
  N2             0              50
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D521V6, binary
                 cls
clus                0   1
  PCBP2 MUTATED     4   0
  PCBP2 WILD-TYPE 253  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP2 MUTATED      4    0
  PCBP2 WILD-TYPE  253   18
   clus
vv  PCBP2 MUTATED PCBP2 WILD-TYPE
  0             4             253
  1             0              18
[1] 2 2
[1] FALSE
D521V7, binary
                 cls
clus                0   1
  PCBP2 MUTATED     3   1
  PCBP2 WILD-TYPE 107 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP2 MUTATED      3    1
  PCBP2 WILD-TYPE  107  178
        clus
vv       PCBP2 MUTATED PCBP2 WILD-TYPE
  FEMALE             3             107
  MALE               1             178
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PCBP2 MUTATED                                       0
  PCBP2 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PCBP2 MUTATED                                                        2
  PCBP2 WILD-TYPE                                                    133
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PCBP2 MUTATED                                                                   0
  PCBP2 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PCBP2 MUTATED                                                  1
  PCBP2 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PCBP2 MUTATED                                                          1
  PCBP2 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PCBP2 MUTATED                                                           0
  PCBP2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PCBP2 MUTATED                                          0
  PCBP2 WILD-TYPE                                        3
D521V8, multiclass
                                                                   clus
vv                                                                  PCBP2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  PCBP2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D521V9, binary
                 cls
clus                0   1
  PCBP2 MUTATED     1   3
  PCBP2 WILD-TYPE   4 281
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP2 MUTATED      1    3
  PCBP2 WILD-TYPE    4  281
     clus
vv    PCBP2 MUTATED PCBP2 WILD-TYPE
  NO              1               4
  YES             3             281
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PCBP2 MUTATED     4   0   0   0
  PCBP2 WILD-TYPE 223  10  10  24
D521V10, multiclass
    clus
vv   PCBP2 MUTATED PCBP2 WILD-TYPE
  R0             4             223
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D521V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PCBP2 MUTATED       1                         0     2
  PCBP2 WILD-TYPE    75                         4   166
D521V12, multiclass
                           clus
vv                          PCBP2 MUTATED PCBP2 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 2             166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(522) Variable = PIAS3 MUTATION ANALYSIS
D522V1, survival
                 sevent
clus2               0   1
  PIAS3 MUTATED     2   2
  PIAS3 WILD-TYPE 179  78
  PIAS3 MUTATED PIAS3 WILD-TYPE 
              4             257 
  PIAS3 MUTATED PIAS3 WILD-TYPE 
              2              78 
$`PIAS3 MUTATED`
TCGA-BR-8078 TCGA-BR-8363 TCGA-CG-4305 TCGA-HJ-7597 
       12.26         0.26        15.95        26.47 

$`PIAS3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        19.50        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 
        5.03        13.58         0.56        11.08         5.52         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  PIAS3 MUTATED PIAS3 WILD-TYPE 
           0.26            0.00 
  PIAS3 MUTATED PIAS3 WILD-TYPE 
          26.47          105.07 
  PIAS3 MUTATED PIAS3 WILD-TYPE 
         14.105          12.620 
[1] "0.3 - 26.5 (14.1)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.6"
D522V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIAS3 MUTATED         0        0        2        1         0         1
  PIAS3 WILD-TYPE       1        9       25       25        31        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIAS3 MUTATED           0          0          0          0        0
  PIAS3 WILD-TYPE         3         49         36         24       24
D522V3, multiclass
            clus
vv           PIAS3 MUTATED PIAS3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               1              25
  STAGE IIA              0              31
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PIAS3 MUTATED     0   3   0   1
  PIAS3 WILD-TYPE  11  69 122  74
D522V4, multiclass
    clus
vv   PIAS3 MUTATED PIAS3 WILD-TYPE
  T1             0              11
  T2             3              69
  T3             0             122
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PIAS3 MUTATED    3  1  0  0
  PIAS3 WILD-TYPE 90 80 50 53
D522V5, multiclass
    clus
vv   PIAS3 MUTATED PIAS3 WILD-TYPE
  N0             3              90
  N1             1              80
  N2             0              50
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D522V6, binary
                 cls
clus                0   1
  PIAS3 MUTATED     4   0
  PIAS3 WILD-TYPE 253  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS3 MUTATED      4    0
  PIAS3 WILD-TYPE  253   18
   clus
vv  PIAS3 MUTATED PIAS3 WILD-TYPE
  0             4             253
  1             0              18
[1] 2 2
[1] FALSE
D522V7, binary
                 cls
clus                0   1
  PIAS3 MUTATED     4   1
  PIAS3 WILD-TYPE 106 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS3 MUTATED      4    1
  PIAS3 WILD-TYPE  106  178
        clus
vv       PIAS3 MUTATED PIAS3 WILD-TYPE
  FEMALE             4             106
  MALE               1             178
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PIAS3 MUTATED                                       0
  PIAS3 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIAS3 MUTATED                                                        4
  PIAS3 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIAS3 MUTATED                                                                   0
  PIAS3 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PIAS3 MUTATED                                                  0
  PIAS3 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PIAS3 MUTATED                                                          0
  PIAS3 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PIAS3 MUTATED                                                           0
  PIAS3 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PIAS3 MUTATED                                          1
  PIAS3 WILD-TYPE                                        2
D522V8, multiclass
                                                                   clus
vv                                                                  PIAS3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  PIAS3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D522V9, binary
                 cls
clus                0   1
  PIAS3 MUTATED     0   5
  PIAS3 WILD-TYPE   5 279
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS3 MUTATED      0    5
  PIAS3 WILD-TYPE    5  279
     clus
vv    PIAS3 MUTATED PIAS3 WILD-TYPE
  NO              0               5
  YES             5             279
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PIAS3 MUTATED     4   0   0   1
  PIAS3 WILD-TYPE 223  10  10  23
D522V10, multiclass
    clus
vv   PIAS3 MUTATED PIAS3 WILD-TYPE
  R0             4             223
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D522V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIAS3 MUTATED       0                         0     4
  PIAS3 WILD-TYPE    76                         4   164
D522V12, multiclass
                           clus
vv                          PIAS3 MUTATED PIAS3 WILD-TYPE
  ASIAN                                 0              76
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(523) Variable = SERPINA1 MUTATION ANALYSIS
D523V1, survival
                    sevent
clus2                  0   1
  SERPINA1 MUTATED     2   2
  SERPINA1 WILD-TYPE 179  78
  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
                 4                257 
  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
                 2                 78 
$`SERPINA1 MUTATED`
TCGA-BR-4184 TCGA-BR-8683 TCGA-CD-8536 TCGA-CG-5721 
        6.97         9.86         0.10         6.02 

$`SERPINA1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       15.81        16.44        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
               0.1                0.0 
  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
              9.86             105.07 
  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
             6.495             12.760 
[1] "0.1 - 9.9 (6.5)"    "0.0 - 105.1 (12.8)"
[1] "hr=" "4.7"
D523V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SERPINA1 MUTATED         0        0        0        1         0         0
  SERPINA1 WILD-TYPE       1        9       27       25        31        44
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINA1 MUTATED           0          2          1          0        2
  SERPINA1 WILD-TYPE         3         47         35         24       22
D523V3, multiclass
            clus
vv           SERPINA1 MUTATED SERPINA1 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  0                 27
  STAGE II                  1                 25
  STAGE IIA                 0                 31
  STAGE IIB                 0                 44
  STAGE III                 0                  3
  STAGE IIIA                2                 47
  STAGE IIIB                1                 35
  STAGE IIIC                0                 24
  STAGE IV                  2                 22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SERPINA1 MUTATED     0   0   2   4
  SERPINA1 WILD-TYPE  11  72 120  71
D523V4, multiclass
    clus
vv   SERPINA1 MUTATED SERPINA1 WILD-TYPE
  T1                0                 11
  T2                0                 72
  T3                2                120
  T4                4                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  SERPINA1 MUTATED    2  3  2  0
  SERPINA1 WILD-TYPE 91 78 48 53
D523V5, multiclass
    clus
vv   SERPINA1 MUTATED SERPINA1 WILD-TYPE
  N0                2                 91
  N1                3                 78
  N2                2                 48
  N3                0                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D523V6, binary
                    cls
clus                   0   1
  SERPINA1 MUTATED     5   1
  SERPINA1 WILD-TYPE 252  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINA1 MUTATED      5    1
  SERPINA1 WILD-TYPE  252   17
   clus
vv  SERPINA1 MUTATED SERPINA1 WILD-TYPE
  0                5                252
  1                1                 17
[1] 2 2
[1] FALSE
D523V7, binary
                    cls
clus                   0   1
  SERPINA1 MUTATED     2   5
  SERPINA1 WILD-TYPE 108 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINA1 MUTATED      2    5
  SERPINA1 WILD-TYPE  108  174
        clus
vv       SERPINA1 MUTATED SERPINA1 WILD-TYPE
  FEMALE                2                108
  MALE                  5                174
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SERPINA1 MUTATED                                       1
  SERPINA1 WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SERPINA1 MUTATED                                                        4
  SERPINA1 WILD-TYPE                                                    131
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SERPINA1 MUTATED                                                                   1
  SERPINA1 WILD-TYPE                                                                39
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SERPINA1 MUTATED                                                  1
  SERPINA1 WILD-TYPE                                               37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SERPINA1 MUTATED                                                          0
  SERPINA1 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SERPINA1 MUTATED                                                           0
  SERPINA1 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SERPINA1 MUTATED                                          0
  SERPINA1 WILD-TYPE                                        3
D523V8, multiclass
                                                                   clus
vv                                                                  SERPINA1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  SERPINA1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D523V9, binary
                    cls
clus                   0   1
  SERPINA1 MUTATED     0   7
  SERPINA1 WILD-TYPE   5 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINA1 MUTATED      0    7
  SERPINA1 WILD-TYPE    5  277
     clus
vv    SERPINA1 MUTATED SERPINA1 WILD-TYPE
  NO                 0                  5
  YES                7                277
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  SERPINA1 MUTATED     3   0   1   3
  SERPINA1 WILD-TYPE 224  10   9  21
D523V10, multiclass
    clus
vv   SERPINA1 MUTATED SERPINA1 WILD-TYPE
  R0                3                224
  R1                0                 10
  R2                1                  9
  RX                3                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D523V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SERPINA1 MUTATED       2                         0     3
  SERPINA1 WILD-TYPE    74                         4   165
D523V12, multiclass
                           clus
vv                          SERPINA1 MUTATED SERPINA1 WILD-TYPE
  ASIAN                                    2                 74
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    3                165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(524) Variable = PIWIL2 MUTATION ANALYSIS
D524V1, survival
                  sevent
clus2                0   1
  PIWIL2 MUTATED     5   1
  PIWIL2 WILD-TYPE 176  79
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
               6              255 
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
               1               79 
$`PIWIL2 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8368 TCGA-BR-A4QL TCGA-CG-5721 TCGA-HU-A4GT 
       30.90        34.68         4.31        11.57         6.02         6.51 

$`PIWIL2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       18.35         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         0.10         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
            4.31             0.00 
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
           34.68           105.07 
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
            9.04            12.66 
[1] "4.3 - 34.7 (9.0)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "2.2"
D524V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIWIL2 MUTATED         0        0        1        0         2         0
  PIWIL2 WILD-TYPE       1        9       26       26        29        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIWIL2 MUTATED           0          0          1          0        1
  PIWIL2 WILD-TYPE         3         49         35         24       23
D524V3, multiclass
            clus
vv           PIWIL2 MUTATED PIWIL2 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               2               29
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              1               35
  STAGE IIIC              0               24
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PIWIL2 MUTATED     0   2   3   1
  PIWIL2 WILD-TYPE  11  70 119  74
D524V4, multiclass
    clus
vv   PIWIL2 MUTATED PIWIL2 WILD-TYPE
  T1              0               11
  T2              2               70
  T3              3              119
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  PIWIL2 MUTATED    3  1  0  1
  PIWIL2 WILD-TYPE 90 80 50 52
D524V5, multiclass
    clus
vv   PIWIL2 MUTATED PIWIL2 WILD-TYPE
  N0              3               90
  N1              1               80
  N2              0               50
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D524V6, binary
                  cls
clus                 0   1
  PIWIL2 MUTATED     6   0
  PIWIL2 WILD-TYPE 251  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIWIL2 MUTATED      6    0
  PIWIL2 WILD-TYPE  251   18
   clus
vv  PIWIL2 MUTATED PIWIL2 WILD-TYPE
  0              6              251
  1              0               18
[1] 2 2
[1] FALSE
D524V7, binary
                  cls
clus                 0   1
  PIWIL2 MUTATED     5   1
  PIWIL2 WILD-TYPE 105 178
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIWIL2 MUTATED      5    1
  PIWIL2 WILD-TYPE  105  178
        clus
vv       PIWIL2 MUTATED PIWIL2 WILD-TYPE
  FEMALE              5              105
  MALE                1              178
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PIWIL2 MUTATED                                       0
  PIWIL2 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIWIL2 MUTATED                                                        4
  PIWIL2 WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIWIL2 MUTATED                                                                   1
  PIWIL2 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PIWIL2 MUTATED                                                  1
  PIWIL2 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PIWIL2 MUTATED                                                          0
  PIWIL2 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PIWIL2 MUTATED                                                           0
  PIWIL2 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PIWIL2 MUTATED                                          0
  PIWIL2 WILD-TYPE                                        3
D524V8, multiclass
                                                                   clus
vv                                                                  PIWIL2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  PIWIL2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D524V9, binary
                  cls
clus                 0   1
  PIWIL2 MUTATED     0   6
  PIWIL2 WILD-TYPE   5 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIWIL2 MUTATED      0    6
  PIWIL2 WILD-TYPE    5  278
     clus
vv    PIWIL2 MUTATED PIWIL2 WILD-TYPE
  NO               0                5
  YES              6              278
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PIWIL2 MUTATED     5   0   0   1
  PIWIL2 WILD-TYPE 222  10  10  23
D524V10, multiclass
    clus
vv   PIWIL2 MUTATED PIWIL2 WILD-TYPE
  R0              5              222
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D524V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIWIL2 MUTATED       1                         0     4
  PIWIL2 WILD-TYPE    75                         4   164
D524V12, multiclass
                           clus
vv                          PIWIL2 MUTATED PIWIL2 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(525) Variable = TMEM79 MUTATION ANALYSIS
D525V1, survival
                  sevent
clus2                0   1
  TMEM79 MUTATED     3   2
  TMEM79 WILD-TYPE 178  78
  TMEM79 MUTATED TMEM79 WILD-TYPE 
               5              256 
  TMEM79 MUTATED TMEM79 WILD-TYPE 
               2               78 
$`TMEM79 MUTATED`
TCGA-BR-4184 TCGA-BR-8284 TCGA-CD-A4MJ TCGA-HU-A4G8 TCGA-HU-A4H8 
        6.97         8.05        12.62        11.84         8.88 

$`TMEM79 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 
       12.43        11.61         6.58        12.20         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
       19.36        23.84        12.30         9.67        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  TMEM79 MUTATED TMEM79 WILD-TYPE 
            6.97             0.00 
  TMEM79 MUTATED TMEM79 WILD-TYPE 
           12.62           105.07 
  TMEM79 MUTATED TMEM79 WILD-TYPE 
           8.880           12.775 
[1] "7.0 - 12.6 (8.9)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "2.1"
D525V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEM79 MUTATED         1        0        2        0         0         1
  TMEM79 WILD-TYPE       0        9       25       26        31        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM79 MUTATED           0          1          0          1        0
  TMEM79 WILD-TYPE         3         48         36         23       24
D525V3, multiclass
            clus
vv           TMEM79 MUTATED TMEM79 WILD-TYPE
  STAGE I                 1                0
  STAGE IA                0                9
  STAGE IB                2               25
  STAGE II                0               26
  STAGE IIA               0               31
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TMEM79 MUTATED     2   1   2   1
  TMEM79 WILD-TYPE   9  71 120  74
D525V4, multiclass
    clus
vv   TMEM79 MUTATED TMEM79 WILD-TYPE
  T1              2                9
  T2              1               71
  T3              2              120
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  TMEM79 MUTATED    1  4  0  1
  TMEM79 WILD-TYPE 92 77 50 52
D525V5, multiclass
    clus
vv   TMEM79 MUTATED TMEM79 WILD-TYPE
  N0              1               92
  N1              4               77
  N2              0               50
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D525V6, binary
                  cls
clus                 0   1
  TMEM79 MUTATED     4   0
  TMEM79 WILD-TYPE 253  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM79 MUTATED      4    0
  TMEM79 WILD-TYPE  253   18
   clus
vv  TMEM79 MUTATED TMEM79 WILD-TYPE
  0              4              253
  1              0               18
[1] 2 2
[1] FALSE
D525V7, binary
                  cls
clus                 0   1
  TMEM79 MUTATED     2   4
  TMEM79 WILD-TYPE 108 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM79 MUTATED      2    4
  TMEM79 WILD-TYPE  108  175
        clus
vv       TMEM79 MUTATED TMEM79 WILD-TYPE
  FEMALE              2              108
  MALE                4              175
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TMEM79 MUTATED                                       1
  TMEM79 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TMEM79 MUTATED                                                        3
  TMEM79 WILD-TYPE                                                    132
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TMEM79 MUTATED                                                                   1
  TMEM79 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TMEM79 MUTATED                                                  1
  TMEM79 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TMEM79 MUTATED                                                          0
  TMEM79 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TMEM79 MUTATED                                                           0
  TMEM79 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TMEM79 MUTATED                                          0
  TMEM79 WILD-TYPE                                        3
D525V8, multiclass
                                                                   clus
vv                                                                  TMEM79 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  TMEM79 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D525V9, binary
                  cls
clus                 0   1
  TMEM79 MUTATED     0   6
  TMEM79 WILD-TYPE   5 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM79 MUTATED      0    6
  TMEM79 WILD-TYPE    5  278
     clus
vv    TMEM79 MUTATED TMEM79 WILD-TYPE
  NO               0                5
  YES              6              278
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TMEM79 MUTATED     3   0   0   1
  TMEM79 WILD-TYPE 224  10  10  23
D525V10, multiclass
    clus
vv   TMEM79 MUTATED TMEM79 WILD-TYPE
  R0              3              224
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D525V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMEM79 MUTATED       3                         1     2
  TMEM79 WILD-TYPE    73                         3   166
D525V12, multiclass
                           clus
vv                          TMEM79 MUTATED TMEM79 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  2              166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(526) Variable = HIST1H1B MUTATION ANALYSIS
D526V1, survival
                    sevent
clus2                  0   1
  HIST1H1B MUTATED     3   4
  HIST1H1B WILD-TYPE 178  76
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 7                254 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 4                 76 
$`HIST1H1B MUTATED`
TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8284 TCGA-BR-A4J1 TCGA-CG-4300 TCGA-CG-5726 
       34.68        24.76         8.05         0.72        20.02        28.96 
TCGA-HU-A4GT 
        6.51 

$`HIST1H1B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8286 
       14.43         0.69        12.26         9.60        20.55        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
       12.89         8.98        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20         0.10        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         0.10         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
              0.72               0.00 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
             34.68             105.07 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
            20.020             12.605 
[1] "0.7 - 34.7 (20.0)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D526V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HIST1H1B MUTATED         1        2        0        0         2         0
  HIST1H1B WILD-TYPE       0        7       27       26        29        44
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H1B MUTATED           0          2          1          1        0
  HIST1H1B WILD-TYPE         3         47         35         23       24
D526V3, multiclass
            clus
vv           HIST1H1B MUTATED HIST1H1B WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                  2                  7
  STAGE IB                  0                 27
  STAGE II                  0                 26
  STAGE IIA                 2                 29
  STAGE IIB                 0                 44
  STAGE III                 0                  3
  STAGE IIIA                2                 47
  STAGE IIIB                1                 35
  STAGE IIIC                1                 23
  STAGE IV                  0                 24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HIST1H1B MUTATED     3   0   3   3
  HIST1H1B WILD-TYPE   8  72 119  72
D526V4, multiclass
    clus
vv   HIST1H1B MUTATED HIST1H1B WILD-TYPE
  T1                3                  8
  T2                0                 72
  T3                3                119
  T4                3                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  HIST1H1B MUTATED    5  2  1  1
  HIST1H1B WILD-TYPE 88 79 49 52
D526V5, multiclass
    clus
vv   HIST1H1B MUTATED HIST1H1B WILD-TYPE
  N0                5                 88
  N1                2                 79
  N2                1                 49
  N3                1                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D526V6, binary
                    cls
clus                   0   1
  HIST1H1B MUTATED     8   0
  HIST1H1B WILD-TYPE 249  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED      8    0
  HIST1H1B WILD-TYPE  249   18
   clus
vv  HIST1H1B MUTATED HIST1H1B WILD-TYPE
  0                8                249
  1                0                 18
[1] 2 2
[1] FALSE
D526V7, binary
                    cls
clus                   0   1
  HIST1H1B MUTATED     4   5
  HIST1H1B WILD-TYPE 106 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED      4    5
  HIST1H1B WILD-TYPE  106  174
        clus
vv       HIST1H1B MUTATED HIST1H1B WILD-TYPE
  FEMALE                4                106
  MALE                  5                174
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  HIST1H1B MUTATED                                       0
  HIST1H1B WILD-TYPE                                    50
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HIST1H1B MUTATED                                                        5
  HIST1H1B WILD-TYPE                                                    130
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HIST1H1B MUTATED                                                                   2
  HIST1H1B WILD-TYPE                                                                38
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  HIST1H1B MUTATED                                                  1
  HIST1H1B WILD-TYPE                                               37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  HIST1H1B MUTATED                                                          0
  HIST1H1B WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  HIST1H1B MUTATED                                                           1
  HIST1H1B WILD-TYPE                                                         5
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  HIST1H1B MUTATED                                          0
  HIST1H1B WILD-TYPE                                        3
D526V8, multiclass
                                                                   clus
vv                                                                  HIST1H1B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  HIST1H1B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D526V9, binary
                    cls
clus                   0   1
  HIST1H1B MUTATED     0   9
  HIST1H1B WILD-TYPE   5 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED      0    9
  HIST1H1B WILD-TYPE    5  275
     clus
vv    HIST1H1B MUTATED HIST1H1B WILD-TYPE
  NO                 0                  5
  YES                9                275
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  HIST1H1B MUTATED     8   0   0   1
  HIST1H1B WILD-TYPE 219  10  10  23
D526V10, multiclass
    clus
vv   HIST1H1B MUTATED HIST1H1B WILD-TYPE
  R0                8                219
  R1                0                 10
  R2                0                 10
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D526V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HIST1H1B MUTATED       2                         1     4
  HIST1H1B WILD-TYPE    74                         3   164
D526V12, multiclass
                           clus
vv                          HIST1H1B MUTATED HIST1H1B WILD-TYPE
  ASIAN                                    2                 74
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                    4                164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(527) Variable = FGF13 MUTATION ANALYSIS
D527V1, survival
                 sevent
clus2               0   1
  FGF13 MUTATED     7   1
  FGF13 WILD-TYPE 174  79
  FGF13 MUTATED FGF13 WILD-TYPE 
              8             253 
  FGF13 MUTATED FGF13 WILD-TYPE 
              1              79 
$`FGF13 MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-6852 TCGA-BR-8078 TCGA-CD-8531 TCGA-CG-5723 
       26.70        30.90        32.94        12.26         0.10       105.07 
TCGA-D7-A4Z0 TCGA-HU-A4H8 
       14.76         8.88 

$`FGF13 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.10         0.13         0.16         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       15.16        13.78         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        9.67        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  FGF13 MUTATED FGF13 WILD-TYPE 
            0.1             0.0 
  FGF13 MUTATED FGF13 WILD-TYPE 
         105.07           79.07 
  FGF13 MUTATED FGF13 WILD-TYPE 
          20.73           12.59 
[1] "0.1 - 105.1 (20.7)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "5.3"
D527V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FGF13 MUTATED         0        0        1        1         1         3
  FGF13 WILD-TYPE       1        9       26       25        30        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FGF13 MUTATED           0          1          0          0        0
  FGF13 WILD-TYPE         3         48         36         24       24
D527V3, multiclass
            clus
vv           FGF13 MUTATED FGF13 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              3              41
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FGF13 MUTATED     2   3   2   2
  FGF13 WILD-TYPE   9  69 120  73
D527V4, multiclass
    clus
vv   FGF13 MUTATED FGF13 WILD-TYPE
  T1             2               9
  T2             3              69
  T3             2             120
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  FGF13 MUTATED    3  3  1  0
  FGF13 WILD-TYPE 90 78 49 53
D527V5, multiclass
    clus
vv   FGF13 MUTATED FGF13 WILD-TYPE
  N0             3              90
  N1             3              78
  N2             1              49
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D527V6, binary
                 cls
clus                0   1
  FGF13 MUTATED     9   0
  FGF13 WILD-TYPE 248  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGF13 MUTATED      9    0
  FGF13 WILD-TYPE  248   18
   clus
vv  FGF13 MUTATED FGF13 WILD-TYPE
  0             9             248
  1             0              18
[1] 2 2
[1] FALSE
D527V7, binary
                 cls
clus                0   1
  FGF13 MUTATED     7   2
  FGF13 WILD-TYPE 103 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGF13 MUTATED      7    2
  FGF13 WILD-TYPE  103  177
        clus
vv       FGF13 MUTATED FGF13 WILD-TYPE
  FEMALE             7             103
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FGF13 MUTATED                                       2
  FGF13 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FGF13 MUTATED                                                        5
  FGF13 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FGF13 MUTATED                                                                   0
  FGF13 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FGF13 MUTATED                                                  1
  FGF13 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FGF13 MUTATED                                                          1
  FGF13 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FGF13 MUTATED                                                           0
  FGF13 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FGF13 MUTATED                                          0
  FGF13 WILD-TYPE                                        3
D527V8, multiclass
                                                                   clus
vv                                                                  FGF13 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  FGF13 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D527V9, binary
                 cls
clus                0   1
  FGF13 MUTATED     0   9
  FGF13 WILD-TYPE   5 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGF13 MUTATED      0    9
  FGF13 WILD-TYPE    5  275
     clus
vv    FGF13 MUTATED FGF13 WILD-TYPE
  NO              0               5
  YES             9             275
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FGF13 MUTATED     7   0   0   2
  FGF13 WILD-TYPE 220  10  10  22
D527V10, multiclass
    clus
vv   FGF13 MUTATED FGF13 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D527V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FGF13 MUTATED       2                         0     6
  FGF13 WILD-TYPE    74                         4   162
D527V12, multiclass
                           clus
vv                          FGF13 MUTATED FGF13 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(528) Variable = SCAMP2 MUTATION ANALYSIS
D528V1, survival
                  sevent
clus2                0   1
  SCAMP2 MUTATED     4   0
  SCAMP2 WILD-TYPE 177  80
  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
               4              257 
  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
               0               80 
$`SCAMP2 MUTATED`
TCGA-BR-7851 TCGA-BR-8382 TCGA-CG-4305 TCGA-HU-A4GT 
       12.43        15.85        15.95         6.51 

$`SCAMP2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       19.17        14.79         0.26         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
            6.51             0.00 
  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
           15.95           105.07 
  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
           14.14            12.62 
[1] "6.5 - 15.9 (14.1)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "9100000"
D528V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SCAMP2 MUTATED         0        0        0        2         1         1
  SCAMP2 WILD-TYPE       1        9       27       24        30        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SCAMP2 MUTATED           0          0          0          1        0
  SCAMP2 WILD-TYPE         3         49         36         23       24
D528V3, multiclass
            clus
vv           SCAMP2 MUTATED SCAMP2 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                2               24
  STAGE IIA               1               30
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SCAMP2 MUTATED     0   1   2   2
  SCAMP2 WILD-TYPE  11  71 120  73
D528V4, multiclass
    clus
vv   SCAMP2 MUTATED SCAMP2 WILD-TYPE
  T1              0               11
  T2              1               71
  T3              2              120
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  SCAMP2 MUTATED    3  2  0  1
  SCAMP2 WILD-TYPE 90 79 50 52
D528V5, multiclass
    clus
vv   SCAMP2 MUTATED SCAMP2 WILD-TYPE
  N0              3               90
  N1              2               79
  N2              0               50
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D528V6, binary
                  cls
clus                 0   1
  SCAMP2 MUTATED     6   0
  SCAMP2 WILD-TYPE 251  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCAMP2 MUTATED      6    0
  SCAMP2 WILD-TYPE  251   18
   clus
vv  SCAMP2 MUTATED SCAMP2 WILD-TYPE
  0              6              251
  1              0               18
[1] 2 2
[1] FALSE
D528V7, binary
                  cls
clus                 0   1
  SCAMP2 MUTATED     3   3
  SCAMP2 WILD-TYPE 107 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCAMP2 MUTATED      3    3
  SCAMP2 WILD-TYPE  107  176
        clus
vv       SCAMP2 MUTATED SCAMP2 WILD-TYPE
  FEMALE              3              107
  MALE                3              176
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SCAMP2 MUTATED                                       1
  SCAMP2 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SCAMP2 MUTATED                                                        3
  SCAMP2 WILD-TYPE                                                    132
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SCAMP2 MUTATED                                                                   1
  SCAMP2 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SCAMP2 MUTATED                                                  1
  SCAMP2 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SCAMP2 MUTATED                                                          0
  SCAMP2 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SCAMP2 MUTATED                                                           0
  SCAMP2 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SCAMP2 MUTATED                                          0
  SCAMP2 WILD-TYPE                                        3
D528V8, multiclass
                                                                   clus
vv                                                                  SCAMP2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  SCAMP2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D528V9, binary
                  cls
clus                 0   1
  SCAMP2 MUTATED     0   6
  SCAMP2 WILD-TYPE   5 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCAMP2 MUTATED      0    6
  SCAMP2 WILD-TYPE    5  278
     clus
vv    SCAMP2 MUTATED SCAMP2 WILD-TYPE
  NO               0                5
  YES              6              278
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SCAMP2 MUTATED     5   0   0   1
  SCAMP2 WILD-TYPE 222  10  10  23
D528V10, multiclass
    clus
vv   SCAMP2 MUTATED SCAMP2 WILD-TYPE
  R0              5              222
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D528V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SCAMP2 MUTATED       2                         0     3
  SCAMP2 WILD-TYPE    74                         4   165
D528V12, multiclass
                           clus
vv                          SCAMP2 MUTATED SCAMP2 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  3              165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(529) Variable = SLC22A16 MUTATION ANALYSIS
D529V1, survival
                    sevent
clus2                  0   1
  SLC22A16 MUTATED     9   1
  SLC22A16 WILD-TYPE 172  79
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                10                251 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                 1                 79 
$`SLC22A16 MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8372 TCGA-CD-8529 TCGA-CD-A4MJ 
       11.70         6.97        34.68        19.17         0.13        12.62 
TCGA-F1-6874 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GN 
       14.47        11.41        11.84        29.98 

$`SLC22A16 WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       26.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.10         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        5.52        26.47         5.92        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        11.77         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
              0.13               0.00 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
             34.68             105.07 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
             12.23              12.66 
[1] "0.1 - 34.7 (12.2)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "3.6"
D529V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC22A16 MUTATED         0        0        3        0         2         2
  SLC22A16 WILD-TYPE       1        9       24       26        29        42
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC22A16 MUTATED           0          1          0          1        1
  SLC22A16 WILD-TYPE         3         48         36         23       23
D529V3, multiclass
            clus
vv           SLC22A16 MUTATED SLC22A16 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  3                 24
  STAGE II                  0                 26
  STAGE IIA                 2                 29
  STAGE IIB                 2                 42
  STAGE III                 0                  3
  STAGE IIIA                1                 48
  STAGE IIIB                0                 36
  STAGE IIIC                1                 23
  STAGE IV                  1                 23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SLC22A16 MUTATED     0   4   3   3
  SLC22A16 WILD-TYPE  11  68 119  72
D529V4, multiclass
    clus
vv   SLC22A16 MUTATED SLC22A16 WILD-TYPE
  T1                0                 11
  T2                4                 68
  T3                3                119
  T4                3                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  SLC22A16 MUTATED    6  3  0  1
  SLC22A16 WILD-TYPE 87 78 50 52
D529V5, multiclass
    clus
vv   SLC22A16 MUTATED SLC22A16 WILD-TYPE
  N0                6                 87
  N1                3                 78
  N2                0                 50
  N3                1                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D529V6, binary
                    cls
clus                   0   1
  SLC22A16 MUTATED     9   1
  SLC22A16 WILD-TYPE 248  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED      9    1
  SLC22A16 WILD-TYPE  248   17
   clus
vv  SLC22A16 MUTATED SLC22A16 WILD-TYPE
  0                9                248
  1                1                 17
[1] 2 2
[1] FALSE
D529V7, binary
                    cls
clus                   0   1
  SLC22A16 MUTATED     4   7
  SLC22A16 WILD-TYPE 106 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED      4    7
  SLC22A16 WILD-TYPE  106  172
        clus
vv       SLC22A16 MUTATED SLC22A16 WILD-TYPE
  FEMALE                4                106
  MALE                  7                172
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SLC22A16 MUTATED                                       3
  SLC22A16 WILD-TYPE                                    47
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC22A16 MUTATED                                                        5
  SLC22A16 WILD-TYPE                                                    130
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC22A16 MUTATED                                                                   1
  SLC22A16 WILD-TYPE                                                                39
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SLC22A16 MUTATED                                                  1
  SLC22A16 WILD-TYPE                                               37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SLC22A16 MUTATED                                                          1
  SLC22A16 WILD-TYPE                                                       15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SLC22A16 MUTATED                                                           0
  SLC22A16 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SLC22A16 MUTATED                                          0
  SLC22A16 WILD-TYPE                                        3
D529V8, multiclass
                                                                   clus
vv                                                                  SLC22A16 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  SLC22A16 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D529V9, binary
                    cls
clus                   0   1
  SLC22A16 MUTATED     0  11
  SLC22A16 WILD-TYPE   5 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED      0   11
  SLC22A16 WILD-TYPE    5  273
     clus
vv    SLC22A16 MUTATED SLC22A16 WILD-TYPE
  NO                 0                  5
  YES               11                273
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  SLC22A16 MUTATED     7   0   0   2
  SLC22A16 WILD-TYPE 220  10  10  22
D529V10, multiclass
    clus
vv   SLC22A16 MUTATED SLC22A16 WILD-TYPE
  R0                7                220
  R1                0                 10
  R2                0                 10
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D529V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC22A16 MUTATED       5                         0     6
  SLC22A16 WILD-TYPE    71                         4   162
D529V12, multiclass
                           clus
vv                          SLC22A16 MUTATED SLC22A16 WILD-TYPE
  ASIAN                                    5                 71
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    6                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(530) Variable = GLYR1 MUTATION ANALYSIS
D530V1, survival
                 sevent
clus2               0   1
  GLYR1 MUTATED     8   1
  GLYR1 WILD-TYPE 173  79
  GLYR1 MUTATED GLYR1 WILD-TYPE 
              9             252 
  GLYR1 MUTATED GLYR1 WILD-TYPE 
              1              79 
$`GLYR1 MUTATED`
TCGA-BR-4184 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8591 TCGA-BR-A4QL TCGA-BR-A4QM 
        6.97        24.76        23.93        13.45        11.57         5.13 
TCGA-CD-A487 TCGA-CG-4437 TCGA-HU-A4H8 
        9.34         8.05         8.88 

$`GLYR1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5798 
       13.51        20.65        20.42         1.15        13.64         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        7.99        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  GLYR1 MUTATED GLYR1 WILD-TYPE 
           5.13            0.00 
  GLYR1 MUTATED GLYR1 WILD-TYPE 
          24.76          105.07 
  GLYR1 MUTATED GLYR1 WILD-TYPE 
           9.34           12.71 
[1] "5.1 - 24.8 (9.3)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "2.3"
D530V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GLYR1 MUTATED         0        1        3        1         0         1
  GLYR1 WILD-TYPE       1        8       24       25        31        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLYR1 MUTATED           0          3          1          1        1
  GLYR1 WILD-TYPE         3         46         35         23       23
D530V3, multiclass
            clus
vv           GLYR1 MUTATED GLYR1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               3              24
  STAGE II               1              25
  STAGE IIA              0              31
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             3              46
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GLYR1 MUTATED     2   4   4   2
  GLYR1 WILD-TYPE   9  68 118  73
D530V4, multiclass
    clus
vv   GLYR1 MUTATED GLYR1 WILD-TYPE
  T1             2               9
  T2             4              68
  T3             4             118
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  GLYR1 MUTATED    4  4  1  3
  GLYR1 WILD-TYPE 89 77 49 50
D530V5, multiclass
    clus
vv   GLYR1 MUTATED GLYR1 WILD-TYPE
  N0             4              89
  N1             4              77
  N2             1              49
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D530V6, binary
                 cls
clus                0   1
  GLYR1 MUTATED    12   0
  GLYR1 WILD-TYPE 245  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLYR1 MUTATED     12    0
  GLYR1 WILD-TYPE  245   18
   clus
vv  GLYR1 MUTATED GLYR1 WILD-TYPE
  0            12             245
  1             0              18
[1] 2 2
[1] FALSE
D530V7, binary
                 cls
clus                0   1
  GLYR1 MUTATED     5   8
  GLYR1 WILD-TYPE 105 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLYR1 MUTATED      5    8
  GLYR1 WILD-TYPE  105  171
        clus
vv       GLYR1 MUTATED GLYR1 WILD-TYPE
  FEMALE             5             105
  MALE               8             171
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GLYR1 MUTATED                                       1
  GLYR1 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GLYR1 MUTATED                                                        7
  GLYR1 WILD-TYPE                                                    128
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GLYR1 MUTATED                                                                   2
  GLYR1 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GLYR1 MUTATED                                                  1
  GLYR1 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GLYR1 MUTATED                                                          1
  GLYR1 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GLYR1 MUTATED                                                           1
  GLYR1 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GLYR1 MUTATED                                          0
  GLYR1 WILD-TYPE                                        3
D530V8, multiclass
                                                                   clus
vv                                                                  GLYR1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  GLYR1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D530V9, binary
                 cls
clus                0   1
  GLYR1 MUTATED     1  12
  GLYR1 WILD-TYPE   4 272
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLYR1 MUTATED      1   12
  GLYR1 WILD-TYPE    4  272
     clus
vv    GLYR1 MUTATED GLYR1 WILD-TYPE
  NO              1               4
  YES            12             272
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GLYR1 MUTATED     9   1   0   3
  GLYR1 WILD-TYPE 218   9  10  21
D530V10, multiclass
    clus
vv   GLYR1 MUTATED GLYR1 WILD-TYPE
  R0             9             218
  R1             1               9
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D530V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GLYR1 MUTATED       2                         0     8
  GLYR1 WILD-TYPE    74                         4   160
D530V12, multiclass
                           clus
vv                          GLYR1 MUTATED GLYR1 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 8             160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(531) Variable = LRRC43 MUTATION ANALYSIS
D531V1, survival
                  sevent
clus2                0   1
  LRRC43 MUTATED     6   1
  LRRC43 WILD-TYPE 175  79
  LRRC43 MUTATED LRRC43 WILD-TYPE 
               7              254 
  LRRC43 MUTATED LRRC43 WILD-TYPE 
               1               79 
$`LRRC43 MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8487 TCGA-CD-8529 
       26.70        30.90        34.68        23.93         1.12         0.13 
TCGA-FP-A4BE 
       11.08 

$`LRRC43 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 
       31.20        32.94        12.82         9.21        24.76        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  LRRC43 MUTATED LRRC43 WILD-TYPE 
            0.13             0.00 
  LRRC43 MUTATED LRRC43 WILD-TYPE 
           34.68           105.07 
  LRRC43 MUTATED LRRC43 WILD-TYPE 
          23.930           12.605 
[1] "0.1 - 34.7 (23.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "3.2"
D531V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LRRC43 MUTATED         1        0        1        1         3         1
  LRRC43 WILD-TYPE       0        9       26       25        28        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRC43 MUTATED           0          0          0          0        1
  LRRC43 WILD-TYPE         3         49         36         24       23
D531V3, multiclass
            clus
vv           LRRC43 MUTATED LRRC43 WILD-TYPE
  STAGE I                 1                0
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                1               25
  STAGE IIA               3               28
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LRRC43 MUTATED     1   3   4   2
  LRRC43 WILD-TYPE  10  69 118  73
D531V4, multiclass
    clus
vv   LRRC43 MUTATED LRRC43 WILD-TYPE
  T1              1               10
  T2              3               69
  T3              4              118
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  LRRC43 MUTATED    6  2  0  0
  LRRC43 WILD-TYPE 87 79 50 53
D531V5, multiclass
    clus
vv   LRRC43 MUTATED LRRC43 WILD-TYPE
  N0              6               87
  N1              2               79
  N2              0               50
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D531V6, binary
                  cls
clus                 0   1
  LRRC43 MUTATED     7   1
  LRRC43 WILD-TYPE 250  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC43 MUTATED      7    1
  LRRC43 WILD-TYPE  250   17
   clus
vv  LRRC43 MUTATED LRRC43 WILD-TYPE
  0              7              250
  1              1               17
[1] 2 2
[1] FALSE
D531V7, binary
                  cls
clus                 0   1
  LRRC43 MUTATED     6   4
  LRRC43 WILD-TYPE 104 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC43 MUTATED      6    4
  LRRC43 WILD-TYPE  104  175
        clus
vv       LRRC43 MUTATED LRRC43 WILD-TYPE
  FEMALE              6              104
  MALE                4              175
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  LRRC43 MUTATED                                       1
  LRRC43 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LRRC43 MUTATED                                                        7
  LRRC43 WILD-TYPE                                                    128
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LRRC43 MUTATED                                                                   0
  LRRC43 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  LRRC43 MUTATED                                                  0
  LRRC43 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  LRRC43 MUTATED                                                          2
  LRRC43 WILD-TYPE                                                       14
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  LRRC43 MUTATED                                                           0
  LRRC43 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  LRRC43 MUTATED                                          0
  LRRC43 WILD-TYPE                                        3
D531V8, multiclass
                                                                   clus
vv                                                                  LRRC43 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  LRRC43 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D531V9, binary
                  cls
clus                 0   1
  LRRC43 MUTATED     1   9
  LRRC43 WILD-TYPE   4 275
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC43 MUTATED      1    9
  LRRC43 WILD-TYPE    4  275
     clus
vv    LRRC43 MUTATED LRRC43 WILD-TYPE
  NO               1                4
  YES              9              275
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  LRRC43 MUTATED     8   0   0   2
  LRRC43 WILD-TYPE 219  10  10  22
D531V10, multiclass
    clus
vv   LRRC43 MUTATED LRRC43 WILD-TYPE
  R0              8              219
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D531V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LRRC43 MUTATED       1                         2     6
  LRRC43 WILD-TYPE    75                         2   162
D531V12, multiclass
                           clus
vv                          LRRC43 MUTATED LRRC43 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              2                2
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(532) Variable = NLRC5 MUTATION ANALYSIS
D532V1, survival
                 sevent
clus2               0   1
  NLRC5 MUTATED    11   4
  NLRC5 WILD-TYPE 170  76
  NLRC5 MUTATED NLRC5 WILD-TYPE 
             15             246 
  NLRC5 MUTATED NLRC5 WILD-TYPE 
              4              76 
$`NLRC5 MUTATED`
TCGA-BR-4184 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-8363 TCGA-BR-8591 
        6.97        24.76        23.93        12.43         0.26        13.45 
TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 
        0.10         6.58         9.01         6.02       105.07        65.10 
TCGA-D7-A4YY TCGA-F1-A448 TCGA-HU-8602 
       13.78        21.27        11.41 

$`NLRC5 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       15.42        28.01        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        15.81         9.34         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
        0.16         0.10         0.10         0.13         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       19.07        12.03         0.00        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        79.07         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       15.16        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       26.47         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  NLRC5 MUTATED NLRC5 WILD-TYPE 
            0.1             0.0 
  NLRC5 MUTATED NLRC5 WILD-TYPE 
         105.07           79.07 
  NLRC5 MUTATED NLRC5 WILD-TYPE 
          12.43           12.64 
[1] "0.1 - 105.1 (12.4)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.5"
D532V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NLRC5 MUTATED         0        1        4        2         1         2
  NLRC5 WILD-TYPE       1        8       23       24        30        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NLRC5 MUTATED           0          1          2          1        2
  NLRC5 WILD-TYPE         3         48         34         23       22
D532V3, multiclass
            clus
vv           NLRC5 MUTATED NLRC5 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               4              23
  STAGE II               2              24
  STAGE IIA              1              30
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             2              34
  STAGE IIIC             1              23
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NLRC5 MUTATED     2   5   5   5
  NLRC5 WILD-TYPE   9  67 117  70
D532V4, multiclass
    clus
vv   NLRC5 MUTATED NLRC5 WILD-TYPE
  T1             2               9
  T2             5              67
  T3             5             117
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  NLRC5 MUTATED    9  3  0  4
  NLRC5 WILD-TYPE 84 78 50 49
D532V5, multiclass
    clus
vv   NLRC5 MUTATED NLRC5 WILD-TYPE
  N0             9              84
  N1             3              78
  N2             0              50
  N3             4              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D532V6, binary
                 cls
clus                0   1
  NLRC5 MUTATED    17   1
  NLRC5 WILD-TYPE 240  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC5 MUTATED     17    1
  NLRC5 WILD-TYPE  240   17
   clus
vv  NLRC5 MUTATED NLRC5 WILD-TYPE
  0            17             240
  1             1              17
[1] 2 2
[1] FALSE
D532V7, binary
                 cls
clus                0   1
  NLRC5 MUTATED     8  11
  NLRC5 WILD-TYPE 102 168
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC5 MUTATED      8   11
  NLRC5 WILD-TYPE  102  168
        clus
vv       NLRC5 MUTATED NLRC5 WILD-TYPE
  FEMALE             8             102
  MALE              11             168
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NLRC5 MUTATED                                       3
  NLRC5 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NLRC5 MUTATED                                                       10
  NLRC5 WILD-TYPE                                                    125
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NLRC5 MUTATED                                                                   4
  NLRC5 WILD-TYPE                                                                36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NLRC5 MUTATED                                                  0
  NLRC5 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NLRC5 MUTATED                                                          1
  NLRC5 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NLRC5 MUTATED                                                           1
  NLRC5 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NLRC5 MUTATED                                          0
  NLRC5 WILD-TYPE                                        3
D532V8, multiclass
                                                                   clus
vv                                                                  NLRC5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  NLRC5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D532V9, binary
                 cls
clus                0   1
  NLRC5 MUTATED     0  19
  NLRC5 WILD-TYPE   5 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC5 MUTATED      0   19
  NLRC5 WILD-TYPE    5  265
     clus
vv    NLRC5 MUTATED NLRC5 WILD-TYPE
  NO              0               5
  YES            19             265
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NLRC5 MUTATED    13   0   1   4
  NLRC5 WILD-TYPE 214  10   9  20
D532V10, multiclass
    clus
vv   NLRC5 MUTATED NLRC5 WILD-TYPE
  R0            13             214
  R1             0              10
  R2             1               9
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D532V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NLRC5 MUTATED       3                         0    11
  NLRC5 WILD-TYPE    73                         4   157
D532V12, multiclass
                           clus
vv                          NLRC5 MUTATED NLRC5 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                11             157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(533) Variable = EAF2 MUTATION ANALYSIS
D533V1, survival
                sevent
clus2              0   1
  EAF2 MUTATED     6   0
  EAF2 WILD-TYPE 175  80
  EAF2 MUTATED EAF2 WILD-TYPE 
             6            255 
  EAF2 MUTATED EAF2 WILD-TYPE 
             0             80 
$`EAF2 MUTATED`
TCGA-BR-6452 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CG-4305 TCGA-HU-A4G9 TCGA-HU-A4GN 
       34.68        13.45        11.57        15.95        24.20        29.98 

$`EAF2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        11.84         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  EAF2 MUTATED EAF2 WILD-TYPE 
         11.57           0.00 
  EAF2 MUTATED EAF2 WILD-TYPE 
         34.68         105.07 
  EAF2 MUTATED EAF2 WILD-TYPE 
        20.075         12.560 
[1] "11.6 - 34.7 (20.1)" "0.0 - 105.1 (12.6)"
[1] "hr="     "2.6e+07"
D533V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EAF2 MUTATED         0        1        0        1         2         0
  EAF2 WILD-TYPE       1        8       27       25        29        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EAF2 MUTATED           0          0          1          1        1
  EAF2 WILD-TYPE         3         49         35         23       23
D533V3, multiclass
            clus
vv           EAF2 MUTATED EAF2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              0             27
  STAGE II              1             25
  STAGE IIA             2             29
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            1             35
  STAGE IIIC            1             23
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EAF2 MUTATED     1   2   2   2
  EAF2 WILD-TYPE  10  70 120  73
D533V4, multiclass
    clus
vv   EAF2 MUTATED EAF2 WILD-TYPE
  T1            1             10
  T2            2             70
  T3            2            120
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  EAF2 MUTATED    2  2  1  2
  EAF2 WILD-TYPE 91 79 49 51
D533V5, multiclass
    clus
vv   EAF2 MUTATED EAF2 WILD-TYPE
  N0            2             91
  N1            2             79
  N2            1             49
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D533V6, binary
                cls
clus               0   1
  EAF2 MUTATED     7   0
  EAF2 WILD-TYPE 250  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAF2 MUTATED      7    0
  EAF2 WILD-TYPE  250   18
   clus
vv  EAF2 MUTATED EAF2 WILD-TYPE
  0            7            250
  1            0             18
[1] 2 2
[1] FALSE
D533V7, binary
                cls
clus               0   1
  EAF2 MUTATED     4   3
  EAF2 WILD-TYPE 106 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAF2 MUTATED      4    3
  EAF2 WILD-TYPE  106  176
        clus
vv       EAF2 MUTATED EAF2 WILD-TYPE
  FEMALE            4            106
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  EAF2 MUTATED                                       0
  EAF2 WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EAF2 MUTATED                                                        5
  EAF2 WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EAF2 MUTATED                                                                   0
  EAF2 WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  EAF2 MUTATED                                                  2
  EAF2 WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  EAF2 MUTATED                                                          0
  EAF2 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  EAF2 MUTATED                                                           0
  EAF2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  EAF2 MUTATED                                          0
  EAF2 WILD-TYPE                                        3
D533V8, multiclass
                                                                   clus
vv                                                                  EAF2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  EAF2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D533V9, binary
                cls
clus               0   1
  EAF2 MUTATED     0   7
  EAF2 WILD-TYPE   5 277
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAF2 MUTATED      0    7
  EAF2 WILD-TYPE    5  277
     clus
vv    EAF2 MUTATED EAF2 WILD-TYPE
  NO             0              5
  YES            7            277
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EAF2 MUTATED     6   0   0   1
  EAF2 WILD-TYPE 221  10  10  23
D533V10, multiclass
    clus
vv   EAF2 MUTATED EAF2 WILD-TYPE
  R0            6            221
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D533V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EAF2 MUTATED       2                         0     4
  EAF2 WILD-TYPE    74                         4   164
D533V12, multiclass
                           clus
vv                          EAF2 MUTATED EAF2 WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                4            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(534) Variable = PHF20 MUTATION ANALYSIS
D534V1, survival
                 sevent
clus2               0   1
  PHF20 MUTATED     4   3
  PHF20 WILD-TYPE 177  77
  PHF20 MUTATED PHF20 WILD-TYPE 
              7             254 
  PHF20 MUTATED PHF20 WILD-TYPE 
              3              77 
$`PHF20 MUTATED`
TCGA-BR-4184 TCGA-BR-8078 TCGA-CD-A4MG TCGA-CG-5717 TCGA-CG-5721 TCGA-HU-A4GH 
        6.97        12.26         6.58         6.97         6.02        11.77 
TCGA-HU-A4GT 
        6.51 

$`PHF20 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
       30.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       25.81        29.98         8.98         0.10         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  PHF20 MUTATED PHF20 WILD-TYPE 
           6.02            0.00 
  PHF20 MUTATED PHF20 WILD-TYPE 
          12.26          105.07 
  PHF20 MUTATED PHF20 WILD-TYPE 
           6.97           12.79 
[1] "6.0 - 12.3 (7.0)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "3"  
D534V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PHF20 MUTATED         1        1        0        1         3         1
  PHF20 WILD-TYPE       0        8       27       25        28        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PHF20 MUTATED           0          2          0          0        1
  PHF20 WILD-TYPE         3         47         36         24       23
D534V3, multiclass
            clus
vv           PHF20 MUTATED PHF20 WILD-TYPE
  STAGE I                1               0
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              3              28
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PHF20 MUTATED     2   1   4   3
  PHF20 WILD-TYPE   9  71 118  72
D534V4, multiclass
    clus
vv   PHF20 MUTATED PHF20 WILD-TYPE
  T1             2               9
  T2             1              71
  T3             4             118
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PHF20 MUTATED    6  4  0  0
  PHF20 WILD-TYPE 87 77 50 53
D534V5, multiclass
    clus
vv   PHF20 MUTATED PHF20 WILD-TYPE
  N0             6              87
  N1             4              77
  N2             0              50
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D534V6, binary
                 cls
clus                0   1
  PHF20 MUTATED     9   0
  PHF20 WILD-TYPE 248  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF20 MUTATED      9    0
  PHF20 WILD-TYPE  248   18
   clus
vv  PHF20 MUTATED PHF20 WILD-TYPE
  0             9             248
  1             0              18
[1] 2 2
[1] FALSE
D534V7, binary
                 cls
clus                0   1
  PHF20 MUTATED     3   8
  PHF20 WILD-TYPE 107 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF20 MUTATED      3    8
  PHF20 WILD-TYPE  107  171
        clus
vv       PHF20 MUTATED PHF20 WILD-TYPE
  FEMALE             3             107
  MALE               8             171
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PHF20 MUTATED                                       1
  PHF20 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PHF20 MUTATED                                                        7
  PHF20 WILD-TYPE                                                    128
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PHF20 MUTATED                                                                   1
  PHF20 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PHF20 MUTATED                                                  2
  PHF20 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PHF20 MUTATED                                                          0
  PHF20 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PHF20 MUTATED                                                           0
  PHF20 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PHF20 MUTATED                                          0
  PHF20 WILD-TYPE                                        3
D534V8, multiclass
                                                                   clus
vv                                                                  PHF20 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  PHF20 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D534V9, binary
                 cls
clus                0   1
  PHF20 MUTATED     0  11
  PHF20 WILD-TYPE   5 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF20 MUTATED      0   11
  PHF20 WILD-TYPE    5  273
     clus
vv    PHF20 MUTATED PHF20 WILD-TYPE
  NO              0               5
  YES            11             273
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PHF20 MUTATED     7   0   0   3
  PHF20 WILD-TYPE 220  10  10  21
D534V10, multiclass
    clus
vv   PHF20 MUTATED PHF20 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D534V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHF20 MUTATED       3                         1     5
  PHF20 WILD-TYPE    73                         3   163
D534V12, multiclass
                           clus
vv                          PHF20 MUTATED PHF20 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(535) Variable = UBXN6 MUTATION ANALYSIS
D535V1, survival
                 sevent
clus2               0   1
  UBXN6 MUTATED     8   4
  UBXN6 WILD-TYPE 173  76
  UBXN6 MUTATED UBXN6 WILD-TYPE 
             12             249 
  UBXN6 MUTATED UBXN6 WILD-TYPE 
              4              76 
$`UBXN6 MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4437 
       26.70        30.90         1.12         6.58        12.62         8.05 
TCGA-CG-5733 TCGA-D7-A4YV TCGA-F1-A448 TCGA-HU-A4GN TCGA-HU-A4H3 TCGA-HU-A4H8 
       21.07         5.92        21.27        29.98        19.36         8.88 

$`UBXN6 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       11.61        12.20         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         7.99        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       28.96        79.07        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        11.77         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  UBXN6 MUTATED UBXN6 WILD-TYPE 
           1.12            0.00 
  UBXN6 MUTATED UBXN6 WILD-TYPE 
          30.90          105.07 
  UBXN6 MUTATED UBXN6 WILD-TYPE 
          15.99           12.59 
[1] "1.1 - 30.9 (16.0)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D535V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UBXN6 MUTATED         0        0        2        1         3         2
  UBXN6 WILD-TYPE       1        9       25       25        28        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UBXN6 MUTATED           0          1          1          1        0
  UBXN6 WILD-TYPE         3         48         35         23       24
D535V3, multiclass
            clus
vv           UBXN6 MUTATED UBXN6 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               1              25
  STAGE IIA              3              28
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  UBXN6 MUTATED     1   5   4   2
  UBXN6 WILD-TYPE  10  67 118  73
D535V4, multiclass
    clus
vv   UBXN6 MUTATED UBXN6 WILD-TYPE
  T1             1              10
  T2             5              67
  T3             4             118
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  UBXN6 MUTATED    4  4  1  2
  UBXN6 WILD-TYPE 89 77 49 51
D535V5, multiclass
    clus
vv   UBXN6 MUTATED UBXN6 WILD-TYPE
  N0             4              89
  N1             4              77
  N2             1              49
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D535V6, binary
                 cls
clus                0   1
  UBXN6 MUTATED    12   0
  UBXN6 WILD-TYPE 245  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN6 MUTATED     12    0
  UBXN6 WILD-TYPE  245   18
   clus
vv  UBXN6 MUTATED UBXN6 WILD-TYPE
  0            12             245
  1             0              18
[1] 2 2
[1] FALSE
D535V7, binary
                 cls
clus                0   1
  UBXN6 MUTATED     6   6
  UBXN6 WILD-TYPE 104 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN6 MUTATED      6    6
  UBXN6 WILD-TYPE  104  173
        clus
vv       UBXN6 MUTATED UBXN6 WILD-TYPE
  FEMALE             6             104
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  UBXN6 MUTATED                                       3
  UBXN6 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  UBXN6 MUTATED                                                        3
  UBXN6 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  UBXN6 MUTATED                                                                   2
  UBXN6 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  UBXN6 MUTATED                                                  3
  UBXN6 WILD-TYPE                                               35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  UBXN6 MUTATED                                                          1
  UBXN6 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  UBXN6 MUTATED                                                           0
  UBXN6 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  UBXN6 MUTATED                                          0
  UBXN6 WILD-TYPE                                        3
D535V8, multiclass
                                                                   clus
vv                                                                  UBXN6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  UBXN6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D535V9, binary
                 cls
clus                0   1
  UBXN6 MUTATED     0  12
  UBXN6 WILD-TYPE   5 272
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN6 MUTATED      0   12
  UBXN6 WILD-TYPE    5  272
     clus
vv    UBXN6 MUTATED UBXN6 WILD-TYPE
  NO              0               5
  YES            12             272
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  UBXN6 MUTATED     9   0   0   1
  UBXN6 WILD-TYPE 218  10  10  23
D535V10, multiclass
    clus
vv   UBXN6 MUTATED UBXN6 WILD-TYPE
  R0             9             218
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D535V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UBXN6 MUTATED       5                         0     5
  UBXN6 WILD-TYPE    71                         4   163
D535V12, multiclass
                           clus
vv                          UBXN6 MUTATED UBXN6 WILD-TYPE
  ASIAN                                 5              71
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(536) Variable = ZNF367 MUTATION ANALYSIS
D536V1, survival
                  sevent
clus2                0   1
  ZNF367 MUTATED     2   1
  ZNF367 WILD-TYPE 179  79
  ZNF367 MUTATED ZNF367 WILD-TYPE 
               3              258 
  ZNF367 MUTATED ZNF367 WILD-TYPE 
               1               79 
$`ZNF367 MUTATED`
TCGA-BR-8372 TCGA-CD-A4MG TCGA-CD-A4MI 
       19.17         6.58         0.10 

$`ZNF367 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       11.31        12.43        11.61        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  ZNF367 MUTATED ZNF367 WILD-TYPE 
             0.1              0.0 
  ZNF367 MUTATED ZNF367 WILD-TYPE 
           19.17           105.07 
  ZNF367 MUTATED ZNF367 WILD-TYPE 
            6.58            12.64 
[1] "0.1 - 19.2 (6.6)"   "0.0 - 105.1 (12.6)"
[1] "hr=" "1.8"
D536V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF367 MUTATED         0        0        1        0         1         0
  ZNF367 WILD-TYPE       1        9       26       26        30        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF367 MUTATED           0          0          1          1        0
  ZNF367 WILD-TYPE         3         49         35         23       24
D536V3, multiclass
            clus
vv           ZNF367 MUTATED ZNF367 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              1               35
  STAGE IIIC              1               23
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF367 MUTATED     0   1   2   1
  ZNF367 WILD-TYPE  11  71 120  74
D536V4, multiclass
    clus
vv   ZNF367 MUTATED ZNF367 WILD-TYPE
  T1              0               11
  T2              1               71
  T3              2              120
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZNF367 MUTATED    2  1  0  1
  ZNF367 WILD-TYPE 91 80 50 52
D536V5, multiclass
    clus
vv   ZNF367 MUTATED ZNF367 WILD-TYPE
  N0              2               91
  N1              1               80
  N2              0               50
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D536V6, binary
                  cls
clus                 0   1
  ZNF367 MUTATED     4   0
  ZNF367 WILD-TYPE 253  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF367 MUTATED      4    0
  ZNF367 WILD-TYPE  253   18
   clus
vv  ZNF367 MUTATED ZNF367 WILD-TYPE
  0              4              253
  1              0               18
[1] 2 2
[1] FALSE
D536V7, binary
                  cls
clus                 0   1
  ZNF367 MUTATED     0   4
  ZNF367 WILD-TYPE 110 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF367 MUTATED      0    4
  ZNF367 WILD-TYPE  110  175
        clus
vv       ZNF367 MUTATED ZNF367 WILD-TYPE
  FEMALE              0              110
  MALE                4              175
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZNF367 MUTATED                                       1
  ZNF367 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF367 MUTATED                                                        2
  ZNF367 WILD-TYPE                                                    133
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF367 MUTATED                                                                   1
  ZNF367 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZNF367 MUTATED                                                  0
  ZNF367 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZNF367 MUTATED                                                          0
  ZNF367 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZNF367 MUTATED                                                           0
  ZNF367 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZNF367 MUTATED                                          0
  ZNF367 WILD-TYPE                                        3
D536V8, multiclass
                                                                   clus
vv                                                                  ZNF367 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ZNF367 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D536V9, binary
                  cls
clus                 0   1
  ZNF367 MUTATED     0   4
  ZNF367 WILD-TYPE   5 280
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF367 MUTATED      0    4
  ZNF367 WILD-TYPE    5  280
     clus
vv    ZNF367 MUTATED ZNF367 WILD-TYPE
  NO               0                5
  YES              4              280
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF367 MUTATED     2   0   0   0
  ZNF367 WILD-TYPE 225  10  10  24
D536V10, multiclass
[1] "Remove cluster labels:" "ZNF367 MUTATED"        
clus
  ZNF367 MUTATED ZNF367 WILD-TYPE 
               2              269 
      TCGA-B7-5816       TCGA-B7-5818       TCGA-BR-4183       TCGA-BR-4184 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-4187       TCGA-BR-4188       TCGA-BR-4191       TCGA-BR-4201 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-4253       TCGA-BR-4255       TCGA-BR-4256       TCGA-BR-4257 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-4267       TCGA-BR-4279       TCGA-BR-4280       TCGA-BR-4292 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-4294       TCGA-BR-4357       TCGA-BR-4361       TCGA-BR-4362 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-4363       TCGA-BR-4366       TCGA-BR-4368       TCGA-BR-4369 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-4370       TCGA-BR-4371       TCGA-BR-6452       TCGA-BR-6453 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-6454       TCGA-BR-6455       TCGA-BR-6456       TCGA-BR-6457 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-6458       TCGA-BR-6563       TCGA-BR-6564       TCGA-BR-6565 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-6566       TCGA-BR-6705       TCGA-BR-6706       TCGA-BR-6707 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-6710       TCGA-BR-6801       TCGA-BR-6802       TCGA-BR-6803 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-6852       TCGA-BR-7196       TCGA-BR-7197       TCGA-BR-7703 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-7707       TCGA-BR-7715       TCGA-BR-7716       TCGA-BR-7717 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-7722       TCGA-BR-7723       TCGA-BR-7851       TCGA-BR-7901 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-7957       TCGA-BR-7958       TCGA-BR-7959       TCGA-BR-8058 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8059       TCGA-BR-8077       TCGA-BR-8078       TCGA-BR-8080 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8081       TCGA-BR-8284       TCGA-BR-8286       TCGA-BR-8289 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8291       TCGA-BR-8295       TCGA-BR-8296       TCGA-BR-8297 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8360       TCGA-BR-8361       TCGA-BR-8363       TCGA-BR-8364 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8365       TCGA-BR-8366       TCGA-BR-8367       TCGA-BR-8368 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8369       TCGA-BR-8370       TCGA-BR-8371       TCGA-BR-8373 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8380       TCGA-BR-8381       TCGA-BR-8382       TCGA-BR-8384 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8483       TCGA-BR-8484       TCGA-BR-8485       TCGA-BR-8486 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8487       TCGA-BR-8588       TCGA-BR-8589       TCGA-BR-8590 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8591       TCGA-BR-8592       TCGA-BR-8676       TCGA-BR-8677 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8678       TCGA-BR-8679       TCGA-BR-8680       TCGA-BR-8682 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8683       TCGA-BR-8686       TCGA-BR-8687       TCGA-BR-8690 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-A44T       TCGA-BR-A44U       TCGA-BR-A452       TCGA-BR-A453 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-A4CQ       TCGA-BR-A4CR       TCGA-BR-A4CS       TCGA-BR-A4IU 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-A4IV       TCGA-BR-A4IY       TCGA-BR-A4IZ       TCGA-BR-A4J1 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-A4J2       TCGA-BR-A4J4       TCGA-BR-A4J6       TCGA-BR-A4J7 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-A4J8       TCGA-BR-A4PD       TCGA-BR-A4PE       TCGA-BR-A4PF 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-A4QI       TCGA-BR-A4QL       TCGA-BR-A4QM       TCGA-CD-5800 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CD-5801       TCGA-CD-5804       TCGA-CD-8524       TCGA-CD-8525 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CD-8526       TCGA-CD-8527       TCGA-CD-8528       TCGA-CD-8529 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CD-8530       TCGA-CD-8531       TCGA-CD-8532       TCGA-CD-8534 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CD-8535       TCGA-CD-8536       TCGA-CD-A487       TCGA-CG-4300 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CG-4301       TCGA-CG-4304       TCGA-CG-4305       TCGA-CG-4306 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CG-4436       TCGA-CG-4437       TCGA-CG-4438       TCGA-CG-4440 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CG-4441       TCGA-CG-4443       TCGA-CG-4444       TCGA-CG-4449 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CG-4455       TCGA-CG-4462       TCGA-CG-4465       TCGA-CG-4466 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CG-4469       TCGA-CG-4474       TCGA-CG-4475       TCGA-CG-4476 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CG-4477       TCGA-CG-5717       TCGA-CG-5718       TCGA-CG-5719 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CG-5720       TCGA-CG-5721       TCGA-CG-5722       TCGA-CG-5723 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CG-5724       TCGA-CG-5726       TCGA-CG-5727       TCGA-CG-5728 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CG-5730       TCGA-CG-5732       TCGA-CG-5733       TCGA-CG-5734 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-D7-5577       TCGA-D7-5578       TCGA-D7-5579       TCGA-D7-6518 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-D7-6519       TCGA-D7-6520       TCGA-D7-6521       TCGA-D7-6522 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-D7-6524       TCGA-D7-6525       TCGA-D7-6526       TCGA-D7-6527 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-D7-6528       TCGA-D7-6815       TCGA-D7-6817       TCGA-D7-6818 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-D7-6820       TCGA-D7-6822       TCGA-D7-8570       TCGA-D7-8572 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-D7-8573       TCGA-D7-8574       TCGA-D7-8575       TCGA-D7-8576 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-D7-8578       TCGA-D7-8579       TCGA-D7-A4YT       TCGA-D7-A4YU 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-D7-A4YV       TCGA-D7-A4YX       TCGA-D7-A4YY       TCGA-D7-A4Z0 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-EQ-5647       TCGA-EQ-A4SO       TCGA-F1-6177       TCGA-F1-6874 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-F1-6875       TCGA-F1-A448       TCGA-FP-7735       TCGA-FP-7829 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-FP-7998       TCGA-FP-8099       TCGA-FP-8209       TCGA-FP-8211 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-FP-8631       TCGA-FP-A4BE       TCGA-FP-A4BF       TCGA-HF-7132 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-HF-7133       TCGA-HF-7136       TCGA-HJ-7597       TCGA-HU-8243 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-HU-8245       TCGA-HU-8249       TCGA-HU-8602       TCGA-HU-8604 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-HU-8608       TCGA-HU-8610       TCGA-HU-A4G2       TCGA-HU-A4G3 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-HU-A4G6       TCGA-HU-A4G9       TCGA-HU-A4GC       TCGA-HU-A4GD 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-HU-A4GF       TCGA-HU-A4GH       TCGA-HU-A4GN       TCGA-HU-A4GP 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-HU-A4GQ       TCGA-HU-A4GT       TCGA-HU-A4GU       TCGA-HU-A4GX 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-HU-A4GY       TCGA-HU-A4H0       TCGA-HU-A4H2       TCGA-HU-A4H3 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-HU-A4H4       TCGA-HU-A4H5       TCGA-HU-A4H6       TCGA-HU-A4H8 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-HU-A4HD       TCGA-IN-7806       TCGA-IN-8462       TCGA-IN-8663 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-IP-7968 
"ZNF367 WILD-TYPE" 
D536V11, continuous
[1] "Remove cluster labels:" "ZNF367 MUTATED"        
clus
  ZNF367 MUTATED ZNF367 WILD-TYPE 
               2              249 
      TCGA-B7-5816       TCGA-BR-4183       TCGA-BR-4184       TCGA-BR-4188 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-4191       TCGA-BR-4253       TCGA-BR-4255       TCGA-BR-4256 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-4267       TCGA-BR-4279       TCGA-BR-4280       TCGA-BR-4361 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-4362       TCGA-BR-4368       TCGA-BR-6452       TCGA-BR-6453 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-6454       TCGA-BR-6455       TCGA-BR-6456       TCGA-BR-6457 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-6458       TCGA-BR-6563       TCGA-BR-6564       TCGA-BR-6565 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-6566       TCGA-BR-6705       TCGA-BR-6706       TCGA-BR-6707 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-6710       TCGA-BR-6801       TCGA-BR-6802       TCGA-BR-6803 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-6852       TCGA-BR-7196       TCGA-BR-7197       TCGA-BR-7703 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-7707       TCGA-BR-7715       TCGA-BR-7716       TCGA-BR-7717 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-7722       TCGA-BR-7723       TCGA-BR-7851       TCGA-BR-7901 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-7957       TCGA-BR-7958       TCGA-BR-7959       TCGA-BR-8058 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8059       TCGA-BR-8077       TCGA-BR-8078       TCGA-BR-8080 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8081       TCGA-BR-8284       TCGA-BR-8286       TCGA-BR-8289 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8291       TCGA-BR-8295       TCGA-BR-8296       TCGA-BR-8297 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8360       TCGA-BR-8361       TCGA-BR-8363       TCGA-BR-8364 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8365       TCGA-BR-8366       TCGA-BR-8367       TCGA-BR-8368 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8369       TCGA-BR-8370       TCGA-BR-8371       TCGA-BR-8373 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8380       TCGA-BR-8381       TCGA-BR-8382       TCGA-BR-8384 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8483       TCGA-BR-8484       TCGA-BR-8485       TCGA-BR-8486 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8487       TCGA-BR-8588       TCGA-BR-8589       TCGA-BR-8590 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8591       TCGA-BR-8592       TCGA-BR-8676       TCGA-BR-8677 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8678       TCGA-BR-8679       TCGA-BR-8680       TCGA-BR-8682 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-8683       TCGA-BR-8686       TCGA-BR-8687       TCGA-BR-8690 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-A44T       TCGA-BR-A44U       TCGA-BR-A452       TCGA-BR-A453 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-A4CQ       TCGA-BR-A4CR       TCGA-BR-A4CS       TCGA-BR-A4IU 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-A4IV       TCGA-BR-A4IY       TCGA-BR-A4IZ       TCGA-BR-A4J1 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-A4J2       TCGA-BR-A4J4       TCGA-BR-A4J6       TCGA-BR-A4J8 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-A4PD       TCGA-BR-A4PE       TCGA-BR-A4PF       TCGA-BR-A4QI 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-BR-A4QL       TCGA-BR-A4QM       TCGA-CD-5804       TCGA-CD-8525 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CD-8526       TCGA-CD-8531       TCGA-CD-8535       TCGA-CD-A487 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CG-4301       TCGA-CG-4304       TCGA-CG-4305       TCGA-CG-4436 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CG-4437       TCGA-CG-4438       TCGA-CG-4440       TCGA-CG-4441 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CG-4443       TCGA-CG-4444       TCGA-CG-4449       TCGA-CG-4455 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CG-4462       TCGA-CG-4465       TCGA-CG-4466       TCGA-CG-4469 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CG-4474       TCGA-CG-4475       TCGA-CG-4476       TCGA-CG-4477 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CG-5717       TCGA-CG-5718       TCGA-CG-5719       TCGA-CG-5720 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CG-5721       TCGA-CG-5722       TCGA-CG-5723       TCGA-CG-5724 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CG-5726       TCGA-CG-5727       TCGA-CG-5728       TCGA-CG-5730 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-CG-5732       TCGA-CG-5733       TCGA-CG-5734       TCGA-D7-5577 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-D7-5578       TCGA-D7-5579       TCGA-D7-6518       TCGA-D7-6519 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-D7-6520       TCGA-D7-6521       TCGA-D7-6522       TCGA-D7-6524 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-D7-6525       TCGA-D7-6526       TCGA-D7-6527       TCGA-D7-6528 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-D7-6815       TCGA-D7-6817       TCGA-D7-6818       TCGA-D7-6820 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-D7-6822       TCGA-D7-8570       TCGA-D7-8572       TCGA-D7-8573 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-D7-8574       TCGA-D7-8575       TCGA-D7-8576       TCGA-D7-8578 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-D7-8579       TCGA-D7-A4YT       TCGA-D7-A4YU       TCGA-D7-A4YV 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-D7-A4YX       TCGA-D7-A4YY       TCGA-D7-A4Z0       TCGA-EQ-5647 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-EQ-8122       TCGA-EQ-A4SO       TCGA-F1-6177       TCGA-F1-6874 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-F1-6875       TCGA-F1-A448       TCGA-FP-7735       TCGA-FP-7829 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-FP-7916       TCGA-FP-7998       TCGA-FP-8099       TCGA-FP-8209 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-FP-8210       TCGA-FP-8211       TCGA-FP-8631       TCGA-FP-A4BE 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-FP-A4BF       TCGA-HF-7132       TCGA-HF-7133       TCGA-HF-7136 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-HJ-7597       TCGA-HU-8243       TCGA-HU-8245       TCGA-HU-8249 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-HU-8602       TCGA-HU-8604       TCGA-HU-8608       TCGA-HU-8610 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-HU-A4G2       TCGA-HU-A4G3       TCGA-HU-A4G6       TCGA-HU-A4G8 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-HU-A4G9       TCGA-HU-A4GC       TCGA-HU-A4GD       TCGA-HU-A4GF 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-HU-A4GH       TCGA-HU-A4GN       TCGA-HU-A4GP       TCGA-HU-A4GQ 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-HU-A4GT       TCGA-HU-A4GU       TCGA-HU-A4GX       TCGA-HU-A4GY 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-HU-A4H0       TCGA-HU-A4H2       TCGA-HU-A4H3       TCGA-HU-A4H4 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-HU-A4H5       TCGA-HU-A4H6       TCGA-HU-A4H8       TCGA-HU-A4HD 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-IN-7806       TCGA-IN-7808       TCGA-IN-8462       TCGA-IN-8663 
"ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" "ZNF367 WILD-TYPE" 
      TCGA-IP-7968 
"ZNF367 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF367 MUTATED       2                         0     1
  ZNF367 WILD-TYPE    74                         4   167
D536V12, multiclass
                           clus
vv                          ZNF367 MUTATED ZNF367 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  1              167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(537) Variable = NEK8 MUTATION ANALYSIS
D537V1, survival
                sevent
clus2              0   1
  NEK8 MUTATED     8   3
  NEK8 WILD-TYPE 173  77
  NEK8 MUTATED NEK8 WILD-TYPE 
            11            250 
  NEK8 MUTATED NEK8 WILD-TYPE 
             3             77 
$`NEK8 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8690 
       30.90        34.68        24.76         4.31        15.85        10.68 
TCGA-CG-5721 TCGA-CG-5733 TCGA-HJ-7597 TCGA-HU-A4GX TCGA-HU-A4H3 
        6.02        21.07        26.47        10.19        19.36 

$`NEK8 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       18.35         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 
       30.90        31.20        32.94        12.82         9.21        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
        8.22        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10         4.01        69.04         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  NEK8 MUTATED NEK8 WILD-TYPE 
          4.31           0.00 
  NEK8 MUTATED NEK8 WILD-TYPE 
         34.68         105.07 
  NEK8 MUTATED NEK8 WILD-TYPE 
        19.360         12.575 
[1] "4.3 - 34.7 (19.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.6"
D537V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NEK8 MUTATED         0        1        2        0         1         0
  NEK8 WILD-TYPE       1        8       25       26        30        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NEK8 MUTATED           0          1          1          3        1
  NEK8 WILD-TYPE         3         48         35         21       23
D537V3, multiclass
            clus
vv           NEK8 MUTATED NEK8 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              2             25
  STAGE II              0             26
  STAGE IIA             1             30
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            3             21
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NEK8 MUTATED     1   4   2   4
  NEK8 WILD-TYPE  10  68 120  71
D537V4, multiclass
    clus
vv   NEK8 MUTATED NEK8 WILD-TYPE
  T1            1             10
  T2            4             68
  T3            2            120
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  NEK8 MUTATED    4  1  2  3
  NEK8 WILD-TYPE 89 80 48 50
D537V5, multiclass
    clus
vv   NEK8 MUTATED NEK8 WILD-TYPE
  N0            4             89
  N1            1             80
  N2            2             48
  N3            3             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D537V6, binary
                cls
clus               0   1
  NEK8 MUTATED    10   0
  NEK8 WILD-TYPE 247  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK8 MUTATED     10    0
  NEK8 WILD-TYPE  247   18
   clus
vv  NEK8 MUTATED NEK8 WILD-TYPE
  0           10            247
  1            0             18
[1] 2 2
[1] FALSE
D537V7, binary
                cls
clus               0   1
  NEK8 MUTATED     9   2
  NEK8 WILD-TYPE 101 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK8 MUTATED      9    2
  NEK8 WILD-TYPE  101  177
        clus
vv       NEK8 MUTATED NEK8 WILD-TYPE
  FEMALE            9            101
  MALE              2            177
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NEK8 MUTATED                                       2
  NEK8 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NEK8 MUTATED                                                        5
  NEK8 WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NEK8 MUTATED                                                                   2
  NEK8 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NEK8 MUTATED                                                  0
  NEK8 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NEK8 MUTATED                                                          0
  NEK8 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NEK8 MUTATED                                                           1
  NEK8 WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NEK8 MUTATED                                          1
  NEK8 WILD-TYPE                                        2
D537V8, multiclass
                                                                   clus
vv                                                                  NEK8 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  NEK8 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D537V9, binary
                cls
clus               0   1
  NEK8 MUTATED     0  11
  NEK8 WILD-TYPE   5 273
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK8 MUTATED      0   11
  NEK8 WILD-TYPE    5  273
     clus
vv    NEK8 MUTATED NEK8 WILD-TYPE
  NO             0              5
  YES           11            273
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NEK8 MUTATED    10   0   0   1
  NEK8 WILD-TYPE 217  10  10  23
D537V10, multiclass
    clus
vv   NEK8 MUTATED NEK8 WILD-TYPE
  R0           10            217
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D537V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NEK8 MUTATED       2                         0     7
  NEK8 WILD-TYPE    74                         4   161
D537V12, multiclass
                           clus
vv                          NEK8 MUTATED NEK8 WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                7            161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(538) Variable = ZNF292 MUTATION ANALYSIS
D538V1, survival
                  sevent
clus2                0   1
  ZNF292 MUTATED    15   3
  ZNF292 WILD-TYPE 166  77
  ZNF292 MUTATED ZNF292 WILD-TYPE 
              18              243 
  ZNF292 MUTATED ZNF292 WILD-TYPE 
               3               77 
$`ZNF292 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-8081 TCGA-BR-8286 
        6.97        34.68        32.78        30.90        20.55        12.95 
TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-8531 TCGA-CD-8536 
       19.17         1.12        13.45        15.81         0.10         0.10 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-D7-5577 TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-A4GX 
        6.58         0.10        12.36        11.08        26.47        10.19 

$`ZNF292 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       25.61        18.05        19.89         8.98        21.11        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       12.26         9.60         8.05         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 
        0.10         0.13         0.16         0.10         0.13         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ 
        9.34        11.31        12.43        11.61        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 
       65.10         4.01        69.04        21.07         7.99        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 
        5.03        13.58         0.56         5.52         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  ZNF292 MUTATED ZNF292 WILD-TYPE 
             0.1              0.0 
  ZNF292 MUTATED ZNF292 WILD-TYPE 
           34.68           105.07 
  ZNF292 MUTATED ZNF292 WILD-TYPE 
          12.655           12.620 
[1] "0.1 - 34.7 (12.7)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.1"
D538V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF292 MUTATED         0        0        2        2         5         1
  ZNF292 WILD-TYPE       1        9       25       24        26        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF292 MUTATED           0          4          1          3        1
  ZNF292 WILD-TYPE         3         45         35         21       23
D538V3, multiclass
            clus
vv           ZNF292 MUTATED ZNF292 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                2               25
  STAGE II                2               24
  STAGE IIA               5               26
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              4               45
  STAGE IIIB              1               35
  STAGE IIIC              3               21
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF292 MUTATED     0   3  11   5
  ZNF292 WILD-TYPE  11  69 111  70
D538V4, multiclass
    clus
vv   ZNF292 MUTATED ZNF292 WILD-TYPE
  T1              0               11
  T2              3               69
  T3             11              111
  T4              5               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZNF292 MUTATED   10  5  3  3
  ZNF292 WILD-TYPE 83 76 47 50
D538V5, multiclass
    clus
vv   ZNF292 MUTATED ZNF292 WILD-TYPE
  N0             10               83
  N1              5               76
  N2              3               47
  N3              3               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D538V6, binary
                  cls
clus                 0   1
  ZNF292 MUTATED    18   1
  ZNF292 WILD-TYPE 239  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF292 MUTATED     18    1
  ZNF292 WILD-TYPE  239   17
   clus
vv  ZNF292 MUTATED ZNF292 WILD-TYPE
  0             18              239
  1              1               17
[1] 2 2
[1] FALSE
D538V7, binary
                  cls
clus                 0   1
  ZNF292 MUTATED     9  12
  ZNF292 WILD-TYPE 101 167
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF292 MUTATED      9   12
  ZNF292 WILD-TYPE  101  167
        clus
vv       ZNF292 MUTATED ZNF292 WILD-TYPE
  FEMALE              9              101
  MALE               12              167
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZNF292 MUTATED                                       3
  ZNF292 WILD-TYPE                                    47
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF292 MUTATED                                                       14
  ZNF292 WILD-TYPE                                                    121
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF292 MUTATED                                                                   1
  ZNF292 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZNF292 MUTATED                                                  2
  ZNF292 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZNF292 MUTATED                                                          0
  ZNF292 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZNF292 MUTATED                                                           0
  ZNF292 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZNF292 MUTATED                                          1
  ZNF292 WILD-TYPE                                        2
D538V8, multiclass
                                                                   clus
vv                                                                  ZNF292 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        14
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       1
                                                                   clus
vv                                                                  ZNF292 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         121
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D538V9, binary
                  cls
clus                 0   1
  ZNF292 MUTATED     0  21
  ZNF292 WILD-TYPE   5 263
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF292 MUTATED      0   21
  ZNF292 WILD-TYPE    5  263
     clus
vv    ZNF292 MUTATED ZNF292 WILD-TYPE
  NO               0                5
  YES             21              263
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF292 MUTATED    16   0   0   3
  ZNF292 WILD-TYPE 211  10  10  21
D538V10, multiclass
    clus
vv   ZNF292 MUTATED ZNF292 WILD-TYPE
  R0             16              211
  R1              0               10
  R2              0               10
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D538V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF292 MUTATED       6                         1    13
  ZNF292 WILD-TYPE    70                         3   155
D538V12, multiclass
                           clus
vv                          ZNF292 MUTATED ZNF292 WILD-TYPE
  ASIAN                                  6               70
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                 13              155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(539) Variable = NT5DC1 MUTATION ANALYSIS
D539V1, survival
                  sevent
clus2                0   1
  NT5DC1 MUTATED     3   3
  NT5DC1 WILD-TYPE 178  77
  NT5DC1 MUTATED NT5DC1 WILD-TYPE 
               6              255 
  NT5DC1 MUTATED NT5DC1 WILD-TYPE 
               3               77 
$`NT5DC1 MUTATED`
TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8487 TCGA-CD-8536 TCGA-CD-A4MG TCGA-D7-A4YV 
       34.68         0.26         1.12         0.10         6.58         5.92 

$`NT5DC1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        19.50        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  NT5DC1 MUTATED NT5DC1 WILD-TYPE 
             0.1              0.0 
  NT5DC1 MUTATED NT5DC1 WILD-TYPE 
           34.68           105.07 
  NT5DC1 MUTATED NT5DC1 WILD-TYPE 
            3.52            12.76 
[1] "0.1 - 34.7 (3.5)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "2.9"
D539V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NT5DC1 MUTATED         0        0        1        1         3         1
  NT5DC1 WILD-TYPE       1        9       26       25        28        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NT5DC1 MUTATED           0          0          0          0        0
  NT5DC1 WILD-TYPE         3         49         36         24       24
D539V3, multiclass
            clus
vv           NT5DC1 MUTATED NT5DC1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                1               25
  STAGE IIA               3               28
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NT5DC1 MUTATED     0   1   5   0
  NT5DC1 WILD-TYPE  11  71 117  75
D539V4, multiclass
    clus
vv   NT5DC1 MUTATED NT5DC1 WILD-TYPE
  T1              0               11
  T2              1               71
  T3              5              117
  T4              0               75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  NT5DC1 MUTATED    5  1  0  0
  NT5DC1 WILD-TYPE 88 80 50 53
D539V5, multiclass
    clus
vv   NT5DC1 MUTATED NT5DC1 WILD-TYPE
  N0              5               88
  N1              1               80
  N2              0               50
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D539V6, binary
                  cls
clus                 0   1
  NT5DC1 MUTATED     6   0
  NT5DC1 WILD-TYPE 251  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5DC1 MUTATED      6    0
  NT5DC1 WILD-TYPE  251   18
   clus
vv  NT5DC1 MUTATED NT5DC1 WILD-TYPE
  0              6              251
  1              0               18
[1] 2 2
[1] FALSE
D539V7, binary
                  cls
clus                 0   1
  NT5DC1 MUTATED     4   2
  NT5DC1 WILD-TYPE 106 177
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5DC1 MUTATED      4    2
  NT5DC1 WILD-TYPE  106  177
        clus
vv       NT5DC1 MUTATED NT5DC1 WILD-TYPE
  FEMALE              4              106
  MALE                2              177
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NT5DC1 MUTATED                                       1
  NT5DC1 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NT5DC1 MUTATED                                                        4
  NT5DC1 WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NT5DC1 MUTATED                                                                   0
  NT5DC1 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NT5DC1 MUTATED                                                  1
  NT5DC1 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NT5DC1 MUTATED                                                          0
  NT5DC1 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NT5DC1 MUTATED                                                           0
  NT5DC1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NT5DC1 MUTATED                                          0
  NT5DC1 WILD-TYPE                                        3
D539V8, multiclass
                                                                   clus
vv                                                                  NT5DC1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  NT5DC1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D539V9, binary
                  cls
clus                 0   1
  NT5DC1 MUTATED     0   6
  NT5DC1 WILD-TYPE   5 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5DC1 MUTATED      0    6
  NT5DC1 WILD-TYPE    5  278
     clus
vv    NT5DC1 MUTATED NT5DC1 WILD-TYPE
  NO               0                5
  YES              6              278
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NT5DC1 MUTATED     5   0   0   0
  NT5DC1 WILD-TYPE 222  10  10  24
D539V10, multiclass
    clus
vv   NT5DC1 MUTATED NT5DC1 WILD-TYPE
  R0              5              222
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D539V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NT5DC1 MUTATED       2                         0     4
  NT5DC1 WILD-TYPE    74                         4   164
D539V12, multiclass
                           clus
vv                          NT5DC1 MUTATED NT5DC1 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(540) Variable = DUSP9 MUTATION ANALYSIS
D540V1, survival
                 sevent
clus2               0   1
  DUSP9 MUTATED     3   1
  DUSP9 WILD-TYPE 178  79
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              4             257 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              1              79 
$`DUSP9 MUTATED`
TCGA-BR-4280 TCGA-BR-8081 TCGA-CD-8535 TCGA-HU-A4GH 
        6.61        20.55         0.13        11.77 

$`DUSP9 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       17.49        14.43         0.69        12.26         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  DUSP9 MUTATED DUSP9 WILD-TYPE 
           0.13            0.00 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
          20.55          105.07 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
           9.19           12.66 
[1] "0.1 - 20.6 (9.2)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.2"
D540V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DUSP9 MUTATED         0        1        0        0         0         1
  DUSP9 WILD-TYPE       1        8       27       26        31        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DUSP9 MUTATED           1          2          0          0        0
  DUSP9 WILD-TYPE         2         47         36         24       24
D540V3, multiclass
            clus
vv           DUSP9 MUTATED DUSP9 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              0              31
  STAGE IIB              1              43
  STAGE III              1               2
  STAGE IIIA             2              47
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DUSP9 MUTATED     1   1   1   2
  DUSP9 WILD-TYPE  10  71 121  73
D540V4, multiclass
    clus
vv   DUSP9 MUTATED DUSP9 WILD-TYPE
  T1             1              10
  T2             1              71
  T3             1             121
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  DUSP9 MUTATED    3  2  0  0
  DUSP9 WILD-TYPE 90 79 50 53
D540V5, multiclass
    clus
vv   DUSP9 MUTATED DUSP9 WILD-TYPE
  N0             3              90
  N1             2              79
  N2             0              50
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D540V6, binary
                 cls
clus                0   1
  DUSP9 MUTATED     5   0
  DUSP9 WILD-TYPE 252  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP9 MUTATED      5    0
  DUSP9 WILD-TYPE  252   18
   clus
vv  DUSP9 MUTATED DUSP9 WILD-TYPE
  0             5             252
  1             0              18
[1] 2 2
[1] FALSE
D540V7, binary
                 cls
clus                0   1
  DUSP9 MUTATED     3   2
  DUSP9 WILD-TYPE 107 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP9 MUTATED      3    2
  DUSP9 WILD-TYPE  107  177
        clus
vv       DUSP9 MUTATED DUSP9 WILD-TYPE
  FEMALE             3             107
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DUSP9 MUTATED                                       0
  DUSP9 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DUSP9 MUTATED                                                        4
  DUSP9 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DUSP9 MUTATED                                                                   0
  DUSP9 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DUSP9 MUTATED                                                  1
  DUSP9 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DUSP9 MUTATED                                                          0
  DUSP9 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DUSP9 MUTATED                                                           0
  DUSP9 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DUSP9 MUTATED                                          0
  DUSP9 WILD-TYPE                                        3
D540V8, multiclass
                                                                   clus
vv                                                                  DUSP9 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  DUSP9 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D540V9, binary
                 cls
clus                0   1
  DUSP9 MUTATED     0   5
  DUSP9 WILD-TYPE   5 279
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP9 MUTATED      0    5
  DUSP9 WILD-TYPE    5  279
     clus
vv    DUSP9 MUTATED DUSP9 WILD-TYPE
  NO              0               5
  YES             5             279
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DUSP9 MUTATED     3   0   0   2
  DUSP9 WILD-TYPE 224  10  10  22
D540V10, multiclass
    clus
vv   DUSP9 MUTATED DUSP9 WILD-TYPE
  R0             3             224
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D540V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DUSP9 MUTATED       2                         0     3
  DUSP9 WILD-TYPE    74                         4   165
D540V12, multiclass
                           clus
vv                          DUSP9 MUTATED DUSP9 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(541) Variable = ABCA5 MUTATION ANALYSIS
D541V1, survival
                 sevent
clus2               0   1
  ABCA5 MUTATED    15   3
  ABCA5 WILD-TYPE 166  77
  ABCA5 MUTATED ABCA5 WILD-TYPE 
             18             243 
  ABCA5 MUTATED ABCA5 WILD-TYPE 
              3              77 
$`ABCA5 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-7703 TCGA-BR-8360 TCGA-BR-8368 
        6.97        34.68        15.95        24.76         6.18         4.31 
TCGA-BR-8372 TCGA-BR-8680 TCGA-BR-A4PE TCGA-CD-5801 TCGA-CD-A4MH TCGA-D7-5579 
       19.17        15.81        20.42        13.18        12.20        11.93 
TCGA-D7-6820 TCGA-HJ-7597 TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H8 
       11.31        26.47        11.84         6.51         6.25         8.88 

$`ABCA5 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6455 TCGA-BR-6456 
       30.90         6.18         9.57         6.61        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 
       31.20        32.94        12.82         9.21        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
       16.31         2.20        15.58         7.40        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        19.36        13.51        20.65         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
       11.57         5.13         2.83         3.25        13.15         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        12.36        12.66        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 
       10.26        15.22        15.98        12.79        10.55        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.52         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  ABCA5 MUTATED ABCA5 WILD-TYPE 
           4.31            0.00 
  ABCA5 MUTATED ABCA5 WILD-TYPE 
          34.68          105.07 
  ABCA5 MUTATED ABCA5 WILD-TYPE 
         12.065          12.660 
[1] "4.3 - 34.7 (12.1)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.9"
D541V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCA5 MUTATED         0        1        4        0         5         3
  ABCA5 WILD-TYPE       1        8       23       26        26        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ABCA5 MUTATED           0          4          0          1        2
  ABCA5 WILD-TYPE         3         45         36         23       22
D541V3, multiclass
            clus
vv           ABCA5 MUTATED ABCA5 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               4              23
  STAGE II               0              26
  STAGE IIA              5              26
  STAGE IIB              3              41
  STAGE III              0               3
  STAGE IIIA             4              45
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCA5 MUTATED     2   5   9   4
  ABCA5 WILD-TYPE   9  67 113  71
D541V4, multiclass
    clus
vv   ABCA5 MUTATED ABCA5 WILD-TYPE
  T1             2               9
  T2             5              67
  T3             9             113
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ABCA5 MUTATED    9  7  3  1
  ABCA5 WILD-TYPE 84 74 47 52
D541V5, multiclass
    clus
vv   ABCA5 MUTATED ABCA5 WILD-TYPE
  N0             9              84
  N1             7              74
  N2             3              47
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D541V6, binary
                 cls
clus                0   1
  ABCA5 MUTATED    17   1
  ABCA5 WILD-TYPE 240  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA5 MUTATED     17    1
  ABCA5 WILD-TYPE  240   17
   clus
vv  ABCA5 MUTATED ABCA5 WILD-TYPE
  0            17             240
  1             1              17
[1] 2 2
[1] FALSE
D541V7, binary
                 cls
clus                0   1
  ABCA5 MUTATED     9  11
  ABCA5 WILD-TYPE 101 168
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA5 MUTATED      9   11
  ABCA5 WILD-TYPE  101  168
        clus
vv       ABCA5 MUTATED ABCA5 WILD-TYPE
  FEMALE             9             101
  MALE              11             168
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ABCA5 MUTATED                                       2
  ABCA5 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ABCA5 MUTATED                                                       10
  ABCA5 WILD-TYPE                                                    125
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ABCA5 MUTATED                                                                   1
  ABCA5 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ABCA5 MUTATED                                                  4
  ABCA5 WILD-TYPE                                               34
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ABCA5 MUTATED                                                          1
  ABCA5 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ABCA5 MUTATED                                                           1
  ABCA5 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ABCA5 MUTATED                                          1
  ABCA5 WILD-TYPE                                        2
D541V8, multiclass
                                                                   clus
vv                                                                  ABCA5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  ABCA5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D541V9, binary
                 cls
clus                0   1
  ABCA5 MUTATED     0  20
  ABCA5 WILD-TYPE   5 264
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA5 MUTATED      0   20
  ABCA5 WILD-TYPE    5  264
     clus
vv    ABCA5 MUTATED ABCA5 WILD-TYPE
  NO              0               5
  YES            20             264
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ABCA5 MUTATED    14   1   0   3
  ABCA5 WILD-TYPE 213   9  10  21
D541V10, multiclass
    clus
vv   ABCA5 MUTATED ABCA5 WILD-TYPE
  R0            14             213
  R1             1               9
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D541V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ABCA5 MUTATED       7                         0    13
  ABCA5 WILD-TYPE    69                         4   155
D541V12, multiclass
                           clus
vv                          ABCA5 MUTATED ABCA5 WILD-TYPE
  ASIAN                                 7              69
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                13             155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(542) Variable = GFOD1 MUTATION ANALYSIS
D542V1, survival
                 sevent
clus2               0   1
  GFOD1 MUTATED     8   2
  GFOD1 WILD-TYPE 173  78
  GFOD1 MUTATED GFOD1 WILD-TYPE 
             10             251 
  GFOD1 MUTATED GFOD1 WILD-TYPE 
              2              78 
$`GFOD1 MUTATED`
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8297 TCGA-CG-4469 TCGA-CG-5721 TCGA-CG-5723 
       30.90        32.94         7.40         7.07         6.02       105.07 
TCGA-CG-5726 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-IP-7968 
       28.96        11.41        11.84         2.53 

$`GFOD1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
        8.98        21.11        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 
       12.95         2.66        16.31         2.20        15.58         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 
       12.03         0.00         9.01        18.97        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
        6.97        36.00         1.02         0.99         0.99        12.03 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        5.52        26.47         5.92        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       27.42        21.21         3.45        18.81         3.39 

  GFOD1 MUTATED GFOD1 WILD-TYPE 
           2.53            0.00 
  GFOD1 MUTATED GFOD1 WILD-TYPE 
         105.07           79.07 
  GFOD1 MUTATED GFOD1 WILD-TYPE 
         11.625          12.660 
[1] "2.5 - 105.1 (11.6)" "0.0 - 79.1 (12.7)" 
[1] "hr=" "2.7"
D542V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GFOD1 MUTATED         0        1        1        1         1         2
  GFOD1 WILD-TYPE       1        8       26       25        30        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GFOD1 MUTATED           0          2          1          1        2
  GFOD1 WILD-TYPE         3         47         35         23       22
D542V3, multiclass
            clus
vv           GFOD1 MUTATED GFOD1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GFOD1 MUTATED     1   2   5   4
  GFOD1 WILD-TYPE  10  70 117  71
D542V4, multiclass
    clus
vv   GFOD1 MUTATED GFOD1 WILD-TYPE
  T1             1              10
  T2             2              70
  T3             5             117
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  GFOD1 MUTATED    5  3  2  2
  GFOD1 WILD-TYPE 88 78 48 51
D542V5, multiclass
    clus
vv   GFOD1 MUTATED GFOD1 WILD-TYPE
  N0             5              88
  N1             3              78
  N2             2              48
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D542V6, binary
                 cls
clus                0   1
  GFOD1 MUTATED    12   0
  GFOD1 WILD-TYPE 245  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFOD1 MUTATED     12    0
  GFOD1 WILD-TYPE  245   18
   clus
vv  GFOD1 MUTATED GFOD1 WILD-TYPE
  0            12             245
  1             0              18
[1] 2 2
[1] FALSE
D542V7, binary
                 cls
clus                0   1
  GFOD1 MUTATED     5   8
  GFOD1 WILD-TYPE 105 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFOD1 MUTATED      5    8
  GFOD1 WILD-TYPE  105  171
        clus
vv       GFOD1 MUTATED GFOD1 WILD-TYPE
  FEMALE             5             105
  MALE               8             171
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GFOD1 MUTATED                                       3
  GFOD1 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GFOD1 MUTATED                                                        6
  GFOD1 WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GFOD1 MUTATED                                                                   4
  GFOD1 WILD-TYPE                                                                36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GFOD1 MUTATED                                                  0
  GFOD1 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GFOD1 MUTATED                                                          0
  GFOD1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GFOD1 MUTATED                                                           0
  GFOD1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GFOD1 MUTATED                                          0
  GFOD1 WILD-TYPE                                        3
D542V8, multiclass
                                                                   clus
vv                                                                  GFOD1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  GFOD1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D542V9, binary
                 cls
clus                0   1
  GFOD1 MUTATED     0  13
  GFOD1 WILD-TYPE   5 271
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFOD1 MUTATED      0   13
  GFOD1 WILD-TYPE    5  271
     clus
vv    GFOD1 MUTATED GFOD1 WILD-TYPE
  NO              0               5
  YES            13             271
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GFOD1 MUTATED     9   1   0   2
  GFOD1 WILD-TYPE 218   9  10  22
D542V10, multiclass
    clus
vv   GFOD1 MUTATED GFOD1 WILD-TYPE
  R0             9             218
  R1             1               9
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D542V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GFOD1 MUTATED       2                         0     6
  GFOD1 WILD-TYPE    74                         4   162
D542V12, multiclass
                           clus
vv                          GFOD1 MUTATED GFOD1 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(543) Variable = ZNF334 MUTATION ANALYSIS
D543V1, survival
                  sevent
clus2                0   1
  ZNF334 MUTATED     9   1
  ZNF334 WILD-TYPE 172  79
  ZNF334 MUTATED ZNF334 WILD-TYPE 
              10              251 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
               1               79 
$`ZNF334 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8081 TCGA-BR-8680 TCGA-CG-5723 
        6.97        34.68        32.94        20.55        15.81       105.07 
TCGA-HU-8602 TCGA-HU-A4GH TCGA-HU-A4GT TCGA-HU-A4GU 
       11.41        11.77         6.51         6.25 

$`ZNF334 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69        12.26         9.60         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN 
       11.84        24.20         3.25        22.75        25.81        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  ZNF334 MUTATED ZNF334 WILD-TYPE 
            6.25             0.00 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
          105.07            79.07 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
           13.79            12.62 
[1] "6.2 - 105.1 (13.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "5.4"
D543V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF334 MUTATED         0        1        1        1         3         3
  ZNF334 WILD-TYPE       1        8       26       25        28        41
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF334 MUTATED           0          1          0          0        2
  ZNF334 WILD-TYPE         3         48         36         24       22
D543V3, multiclass
            clus
vv           ZNF334 MUTATED ZNF334 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                1               26
  STAGE II                1               25
  STAGE IIA               3               28
  STAGE IIB               3               41
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF334 MUTATED     1   2   5   4
  ZNF334 WILD-TYPE  10  70 117  71
D543V4, multiclass
    clus
vv   ZNF334 MUTATED ZNF334 WILD-TYPE
  T1              1               10
  T2              2               70
  T3              5              117
  T4              4               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZNF334 MUTATED    7  3  2  0
  ZNF334 WILD-TYPE 86 78 48 53
D543V5, multiclass
    clus
vv   ZNF334 MUTATED ZNF334 WILD-TYPE
  N0              7               86
  N1              3               78
  N2              2               48
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D543V6, binary
                  cls
clus                 0   1
  ZNF334 MUTATED    10   1
  ZNF334 WILD-TYPE 247  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF334 MUTATED     10    1
  ZNF334 WILD-TYPE  247   17
   clus
vv  ZNF334 MUTATED ZNF334 WILD-TYPE
  0             10              247
  1              1               17
[1] 2 2
[1] FALSE
D543V7, binary
                  cls
clus                 0   1
  ZNF334 MUTATED     6   6
  ZNF334 WILD-TYPE 104 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF334 MUTATED      6    6
  ZNF334 WILD-TYPE  104  173
        clus
vv       ZNF334 MUTATED ZNF334 WILD-TYPE
  FEMALE              6              104
  MALE                6              173
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZNF334 MUTATED                                       2
  ZNF334 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF334 MUTATED                                                        6
  ZNF334 WILD-TYPE                                                    129
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF334 MUTATED                                                                   1
  ZNF334 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZNF334 MUTATED                                                  3
  ZNF334 WILD-TYPE                                               35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZNF334 MUTATED                                                          0
  ZNF334 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZNF334 MUTATED                                                           0
  ZNF334 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZNF334 MUTATED                                          0
  ZNF334 WILD-TYPE                                        3
D543V8, multiclass
                                                                   clus
vv                                                                  ZNF334 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ZNF334 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D543V9, binary
                  cls
clus                 0   1
  ZNF334 MUTATED     0  12
  ZNF334 WILD-TYPE   5 272
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF334 MUTATED      0   12
  ZNF334 WILD-TYPE    5  272
     clus
vv    ZNF334 MUTATED ZNF334 WILD-TYPE
  NO               0                5
  YES             12              272
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF334 MUTATED    10   0   0   2
  ZNF334 WILD-TYPE 217  10  10  22
D543V10, multiclass
    clus
vv   ZNF334 MUTATED ZNF334 WILD-TYPE
  R0             10              217
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D543V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF334 MUTATED       5                         0     5
  ZNF334 WILD-TYPE    71                         4   163
D543V12, multiclass
                           clus
vv                          ZNF334 MUTATED ZNF334 WILD-TYPE
  ASIAN                                  5               71
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  5              163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(544) Variable = MUT MUTATION ANALYSIS
D544V1, survival
               sevent
clus2             0   1
  MUT MUTATED     4   2
  MUT WILD-TYPE 177  78
  MUT MUTATED MUT WILD-TYPE 
            6           255 
  MUT MUTATED MUT WILD-TYPE 
            2            78 
$`MUT MUTATED`
TCGA-BR-4280 TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8680 TCGA-HU-A4G8 TCGA-HU-A4G9 
        6.61         0.26        19.17        15.81        11.84        24.20 

$`MUT WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        19.50        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.30         5.59        12.30         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  MUT MUTATED MUT WILD-TYPE 
         0.26          0.00 
  MUT MUTATED MUT WILD-TYPE 
        24.20        105.07 
  MUT MUTATED MUT WILD-TYPE 
       13.825        12.620 
[1] "0.3 - 24.2 (13.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D544V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MUT MUTATED         0        1        1        0         0         1
  MUT WILD-TYPE       1        8       26       26        31        43
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MUT MUTATED           1          0          0          1        1
  MUT WILD-TYPE         2         49         36         23       23
D544V3, multiclass
            clus
vv           MUT MUTATED MUT WILD-TYPE
  STAGE I              0             1
  STAGE IA             1             8
  STAGE IB             1            26
  STAGE II             0            26
  STAGE IIA            0            31
  STAGE IIB            1            43
  STAGE III            1             2
  STAGE IIIA           0            49
  STAGE IIIB           0            36
  STAGE IIIC           1            23
  STAGE IV             1            23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MUT MUTATED     1   2   1   2
  MUT WILD-TYPE  10  70 121  73
D544V4, multiclass
    clus
vv   MUT MUTATED MUT WILD-TYPE
  T1           1            10
  T2           2            70
  T3           1           121
  T4           2            73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  MUT MUTATED    2  2  1  1
  MUT WILD-TYPE 91 79 49 52
D544V5, multiclass
    clus
vv   MUT MUTATED MUT WILD-TYPE
  N0           2            91
  N1           2            79
  N2           1            49
  N3           1            52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D544V6, binary
               cls
clus              0   1
  MUT MUTATED     5   1
  MUT WILD-TYPE 252  17
[1] "tbl2"
               cls
clus            [,1] [,2]
  MUT MUTATED      5    1
  MUT WILD-TYPE  252   17
   clus
vv  MUT MUTATED MUT WILD-TYPE
  0           5           252
  1           1            17
[1] 2 2
[1] FALSE
D544V7, binary
               cls
clus              0   1
  MUT MUTATED     4   2
  MUT WILD-TYPE 106 177
[1] "tbl2"
               cls
clus            [,1] [,2]
  MUT MUTATED      4    2
  MUT WILD-TYPE  106  177
        clus
vv       MUT MUTATED MUT WILD-TYPE
  FEMALE           4           106
  MALE             2           177
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MUT MUTATED                                       1
  MUT WILD-TYPE                                    49
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MUT MUTATED                                                        3
  MUT WILD-TYPE                                                    132
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MUT MUTATED                                                                   0
  MUT WILD-TYPE                                                                40
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MUT MUTATED                                                  2
  MUT WILD-TYPE                                               36
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MUT MUTATED                                                          0
  MUT WILD-TYPE                                                       16
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MUT MUTATED                                                           0
  MUT WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MUT MUTATED                                          0
  MUT WILD-TYPE                                        3
D544V8, multiclass
                                                                   clus
vv                                                                  MUT MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  MUT WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D544V9, binary
               cls
clus              0   1
  MUT MUTATED     0   6
  MUT WILD-TYPE   5 278
[1] "tbl2"
               cls
clus            [,1] [,2]
  MUT MUTATED      0    6
  MUT WILD-TYPE    5  278
     clus
vv    MUT MUTATED MUT WILD-TYPE
  NO            0             5
  YES           6           278
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  MUT MUTATED     4   0   0   1
  MUT WILD-TYPE 223  10  10  23
D544V10, multiclass
    clus
vv   MUT MUTATED MUT WILD-TYPE
  R0           4           223
  R1           0            10
  R2           0            10
  RX           1            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D544V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MUT MUTATED       3                         0     3
  MUT WILD-TYPE    73                         4   165
D544V12, multiclass
                           clus
vv                          MUT MUTATED MUT WILD-TYPE
  ASIAN                               3            73
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                               3           165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(545) Variable = MGST2 MUTATION ANALYSIS
D545V1, survival
                 sevent
clus2               0   1
  MGST2 MUTATED     3   0
  MGST2 WILD-TYPE 178  80
  MGST2 MUTATED MGST2 WILD-TYPE 
              3             258 
  MGST2 MUTATED MGST2 WILD-TYPE 
              0              80 
$`MGST2 MUTATED`
TCGA-BR-6852 TCGA-BR-8078 TCGA-CD-A4MJ 
       32.94        12.26        12.62 

$`MGST2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        30.90        31.20        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 
       12.43        11.61         6.58        12.20         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  MGST2 MUTATED MGST2 WILD-TYPE 
          12.26            0.00 
  MGST2 MUTATED MGST2 WILD-TYPE 
          32.94          105.07 
  MGST2 MUTATED MGST2 WILD-TYPE 
         12.620          12.625 
[1] "12.3 - 32.9 (12.6)" "0.0 - 105.1 (12.6)"
[1] "hr="     "9200000"
D545V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MGST2 MUTATED         0        0        1        0         1         1
  MGST2 WILD-TYPE       1        9       26       26        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MGST2 MUTATED           0          0          0          0        0
  MGST2 WILD-TYPE         3         49         36         24       24
D545V3, multiclass
            clus
vv           MGST2 MUTATED MGST2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MGST2 MUTATED     0   1   1   1
  MGST2 WILD-TYPE  11  71 121  74
D545V4, multiclass
    clus
vv   MGST2 MUTATED MGST2 WILD-TYPE
  T1             0              11
  T2             1              71
  T3             1             121
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  MGST2 MUTATED    3  0  0  0
  MGST2 WILD-TYPE 90 81 50 53
D545V5, multiclass
    clus
vv   MGST2 MUTATED MGST2 WILD-TYPE
  N0             3              90
  N1             0              81
  N2             0              50
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D545V6, binary
                 cls
clus                0   1
  MGST2 MUTATED     3   0
  MGST2 WILD-TYPE 254  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGST2 MUTATED      3    0
  MGST2 WILD-TYPE  254   18
   clus
vv  MGST2 MUTATED MGST2 WILD-TYPE
  0             3             254
  1             0              18
[1] 2 2
[1] FALSE
D545V7, binary
                 cls
clus                0   1
  MGST2 MUTATED     2   1
  MGST2 WILD-TYPE 108 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGST2 MUTATED      2    1
  MGST2 WILD-TYPE  108  178
        clus
vv       MGST2 MUTATED MGST2 WILD-TYPE
  FEMALE             2             108
  MALE               1             178
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MGST2 MUTATED                                       0
  MGST2 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MGST2 MUTATED                                                        3
  MGST2 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MGST2 MUTATED                                                                   0
  MGST2 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MGST2 MUTATED                                                  0
  MGST2 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MGST2 MUTATED                                                          0
  MGST2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MGST2 MUTATED                                                           0
  MGST2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MGST2 MUTATED                                          0
  MGST2 WILD-TYPE                                        3
D545V8, multiclass
                                                                   clus
vv                                                                  MGST2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  MGST2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D545V9, binary
                 cls
clus                0   1
  MGST2 MUTATED     0   3
  MGST2 WILD-TYPE   5 281
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGST2 MUTATED      0    3
  MGST2 WILD-TYPE    5  281
     clus
vv    MGST2 MUTATED MGST2 WILD-TYPE
  NO              0               5
  YES             3             281
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MGST2 MUTATED     2   0   0   0
  MGST2 WILD-TYPE 225  10  10  24
D545V10, multiclass
[1] "Remove cluster labels:" "MGST2 MUTATED"         
clus
  MGST2 MUTATED MGST2 WILD-TYPE 
              2             269 
     TCGA-B7-5816      TCGA-B7-5818      TCGA-BR-4183      TCGA-BR-4184 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-4187      TCGA-BR-4188      TCGA-BR-4191      TCGA-BR-4201 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256      TCGA-BR-4257 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4292 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-4294      TCGA-BR-4357      TCGA-BR-4361      TCGA-BR-4362 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-4363      TCGA-BR-4366      TCGA-BR-4368      TCGA-BR-4369 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-4370      TCGA-BR-4371      TCGA-BR-6452      TCGA-BR-6453 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703      TCGA-BR-7707 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-7715      TCGA-BR-7716      TCGA-BR-7717      TCGA-BR-7722 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-7723      TCGA-BR-7851      TCGA-BR-7901      TCGA-BR-7957 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-7958      TCGA-BR-7959      TCGA-BR-8058      TCGA-BR-8059 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8077      TCGA-BR-8080      TCGA-BR-8081      TCGA-BR-8284 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8286      TCGA-BR-8289      TCGA-BR-8291      TCGA-BR-8295 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8296      TCGA-BR-8297      TCGA-BR-8360      TCGA-BR-8361 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8363      TCGA-BR-8364      TCGA-BR-8365      TCGA-BR-8366 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8367      TCGA-BR-8368      TCGA-BR-8369      TCGA-BR-8370 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8371      TCGA-BR-8372      TCGA-BR-8373      TCGA-BR-8380 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8381      TCGA-BR-8382      TCGA-BR-8384      TCGA-BR-8483 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8484      TCGA-BR-8485      TCGA-BR-8486      TCGA-BR-8487 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8588      TCGA-BR-8589      TCGA-BR-8590      TCGA-BR-8591 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8592      TCGA-BR-8676      TCGA-BR-8677      TCGA-BR-8678 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8679      TCGA-BR-8680      TCGA-BR-8682      TCGA-BR-8683 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8686      TCGA-BR-8687      TCGA-BR-8690      TCGA-BR-A44T 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A44U      TCGA-BR-A452      TCGA-BR-A453      TCGA-BR-A4CQ 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A4CR      TCGA-BR-A4CS      TCGA-BR-A4IU      TCGA-BR-A4IV 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A4IY      TCGA-BR-A4IZ      TCGA-BR-A4J1      TCGA-BR-A4J2 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A4J4      TCGA-BR-A4J6      TCGA-BR-A4J7      TCGA-BR-A4J8 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A4PD      TCGA-BR-A4PE      TCGA-BR-A4PF      TCGA-BR-A4QI 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A4QL      TCGA-BR-A4QM      TCGA-CD-5800      TCGA-CD-5801 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CD-5804      TCGA-CD-8524      TCGA-CD-8525      TCGA-CD-8526 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CD-8527      TCGA-CD-8528      TCGA-CD-8529      TCGA-CD-8530 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CD-8531      TCGA-CD-8532      TCGA-CD-8534      TCGA-CD-8535 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CD-8536      TCGA-CD-A487      TCGA-CG-4300      TCGA-CG-4301 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-4304      TCGA-CG-4305      TCGA-CG-4306      TCGA-CG-4436 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-4437      TCGA-CG-4438      TCGA-CG-4440      TCGA-CG-4441 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-4442      TCGA-CG-4443      TCGA-CG-4444      TCGA-CG-4449 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-4455      TCGA-CG-4462      TCGA-CG-4465      TCGA-CG-4466 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-4469      TCGA-CG-4474      TCGA-CG-4475      TCGA-CG-4476 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-4477      TCGA-CG-5717      TCGA-CG-5718      TCGA-CG-5719 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-5720      TCGA-CG-5721      TCGA-CG-5722      TCGA-CG-5723 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-5724      TCGA-CG-5726      TCGA-CG-5727      TCGA-CG-5728 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-5730      TCGA-CG-5732      TCGA-CG-5733      TCGA-CG-5734 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-5577      TCGA-D7-5578      TCGA-D7-5579      TCGA-D7-6518 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-6519      TCGA-D7-6520      TCGA-D7-6521      TCGA-D7-6522 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-6524      TCGA-D7-6525      TCGA-D7-6526      TCGA-D7-6527 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-6528      TCGA-D7-6815      TCGA-D7-6817      TCGA-D7-6818 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-6820      TCGA-D7-6822      TCGA-D7-8570      TCGA-D7-8572 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-8573      TCGA-D7-8574      TCGA-D7-8575      TCGA-D7-8576 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-8578      TCGA-D7-8579      TCGA-D7-A4YT      TCGA-D7-A4YU 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-A4YV      TCGA-D7-A4YX      TCGA-D7-A4YY      TCGA-D7-A4Z0 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-EQ-5647      TCGA-EQ-A4SO      TCGA-F1-6177      TCGA-F1-6874 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-F1-6875      TCGA-F1-A448      TCGA-FP-7735      TCGA-FP-7829 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-FP-7998      TCGA-FP-8099      TCGA-FP-8209      TCGA-FP-8211 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-FP-8631      TCGA-FP-A4BE      TCGA-FP-A4BF      TCGA-HF-7132 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HF-7133      TCGA-HF-7136      TCGA-HJ-7597      TCGA-HU-8243 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-8245      TCGA-HU-8249      TCGA-HU-8602      TCGA-HU-8604 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-8608      TCGA-HU-8610      TCGA-HU-A4G2      TCGA-HU-A4G3 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4G6      TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4GF      TCGA-HU-A4GH      TCGA-HU-A4GN      TCGA-HU-A4GP 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4GQ      TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4GY      TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4H4      TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4HD      TCGA-IN-7806      TCGA-IN-8462      TCGA-IN-8663 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-IP-7968 
"MGST2 WILD-TYPE" 
D545V11, continuous
[1] "Remove cluster labels:" "MGST2 MUTATED"         
clus
  MGST2 MUTATED MGST2 WILD-TYPE 
              2             249 
     TCGA-B7-5816      TCGA-BR-4183      TCGA-BR-4184      TCGA-BR-4188 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-4191      TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4361 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-4362      TCGA-BR-4368      TCGA-BR-6452      TCGA-BR-6453 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703      TCGA-BR-7707 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-7715      TCGA-BR-7716      TCGA-BR-7717      TCGA-BR-7722 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-7723      TCGA-BR-7851      TCGA-BR-7901      TCGA-BR-7957 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-7958      TCGA-BR-7959      TCGA-BR-8058      TCGA-BR-8059 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8077      TCGA-BR-8080      TCGA-BR-8081      TCGA-BR-8284 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8286      TCGA-BR-8289      TCGA-BR-8291      TCGA-BR-8295 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8296      TCGA-BR-8297      TCGA-BR-8360      TCGA-BR-8361 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8363      TCGA-BR-8364      TCGA-BR-8365      TCGA-BR-8366 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8367      TCGA-BR-8368      TCGA-BR-8369      TCGA-BR-8370 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8371      TCGA-BR-8372      TCGA-BR-8373      TCGA-BR-8380 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8381      TCGA-BR-8382      TCGA-BR-8384      TCGA-BR-8483 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8484      TCGA-BR-8485      TCGA-BR-8486      TCGA-BR-8487 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8588      TCGA-BR-8589      TCGA-BR-8590      TCGA-BR-8591 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8592      TCGA-BR-8676      TCGA-BR-8677      TCGA-BR-8678 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8679      TCGA-BR-8680      TCGA-BR-8682      TCGA-BR-8683 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8686      TCGA-BR-8687      TCGA-BR-8690      TCGA-BR-A44T 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A44U      TCGA-BR-A452      TCGA-BR-A453      TCGA-BR-A4CQ 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A4CR      TCGA-BR-A4CS      TCGA-BR-A4IU      TCGA-BR-A4IV 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A4IY      TCGA-BR-A4IZ      TCGA-BR-A4J1      TCGA-BR-A4J2 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A4J4      TCGA-BR-A4J6      TCGA-BR-A4J8      TCGA-BR-A4PD 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A4PE      TCGA-BR-A4PF      TCGA-BR-A4QI      TCGA-BR-A4QL 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A4QM      TCGA-CD-5804      TCGA-CD-8525      TCGA-CD-8526 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CD-8531      TCGA-CD-8535      TCGA-CD-A487      TCGA-CG-4301 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-4304      TCGA-CG-4305      TCGA-CG-4436      TCGA-CG-4437 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-4438      TCGA-CG-4440      TCGA-CG-4441      TCGA-CG-4442 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-4443      TCGA-CG-4444      TCGA-CG-4449      TCGA-CG-4455 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-4462      TCGA-CG-4465      TCGA-CG-4466      TCGA-CG-4469 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-4474      TCGA-CG-4475      TCGA-CG-4476      TCGA-CG-4477 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-5717      TCGA-CG-5718      TCGA-CG-5719      TCGA-CG-5720 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-5721      TCGA-CG-5722      TCGA-CG-5723      TCGA-CG-5724 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-5726      TCGA-CG-5727      TCGA-CG-5728      TCGA-CG-5730 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-5732      TCGA-CG-5733      TCGA-CG-5734      TCGA-D7-5577 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-5578      TCGA-D7-5579      TCGA-D7-6518      TCGA-D7-6519 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-6520      TCGA-D7-6521      TCGA-D7-6522      TCGA-D7-6524 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-6525      TCGA-D7-6526      TCGA-D7-6527      TCGA-D7-6528 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-6815      TCGA-D7-6817      TCGA-D7-6818      TCGA-D7-6820 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-6822      TCGA-D7-8570      TCGA-D7-8572      TCGA-D7-8573 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-8574      TCGA-D7-8575      TCGA-D7-8576      TCGA-D7-8578 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-8579      TCGA-D7-A4YT      TCGA-D7-A4YU      TCGA-D7-A4YV 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-A4YX      TCGA-D7-A4YY      TCGA-D7-A4Z0      TCGA-EQ-5647 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-EQ-8122      TCGA-EQ-A4SO      TCGA-F1-6177      TCGA-F1-6874 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-F1-6875      TCGA-F1-A448      TCGA-FP-7735      TCGA-FP-7829 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-FP-7916      TCGA-FP-7998      TCGA-FP-8099      TCGA-FP-8209 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-FP-8210      TCGA-FP-8211      TCGA-FP-8631      TCGA-FP-A4BE 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-FP-A4BF      TCGA-HF-7132      TCGA-HF-7133      TCGA-HF-7136 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HJ-7597      TCGA-HU-8243      TCGA-HU-8245      TCGA-HU-8249 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-8602      TCGA-HU-8604      TCGA-HU-8608      TCGA-HU-8610 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4G2      TCGA-HU-A4G3      TCGA-HU-A4G6      TCGA-HU-A4G8 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD      TCGA-HU-A4GF 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4GH      TCGA-HU-A4GN      TCGA-HU-A4GP      TCGA-HU-A4GQ 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX      TCGA-HU-A4GY 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3      TCGA-HU-A4H4 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8      TCGA-HU-A4HD 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-IN-7806      TCGA-IN-7808      TCGA-IN-8462      TCGA-IN-8663 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-IP-7968 
"MGST2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MGST2 MUTATED       1                         0     2
  MGST2 WILD-TYPE    75                         4   166
D545V12, multiclass
                           clus
vv                          MGST2 MUTATED MGST2 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 2             166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(546) Variable = GPATCH4 MUTATION ANALYSIS
D546V1, survival
                   sevent
clus2                 0   1
  GPATCH4 MUTATED     4   3
  GPATCH4 WILD-TYPE 177  77
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
                7               254 
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
                3                77 
$`GPATCH4 MUTATED`
TCGA-BR-4201 TCGA-BR-8487 TCGA-CD-8536 TCGA-CD-A4MG TCGA-D7-6526 TCGA-F1-6875 
       30.90         1.12         0.10         6.58        17.19        72.23 
TCGA-HU-A4GN 
       29.98 

$`GPATCH4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       13.35        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       16.24        14.47        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
              0.1               0.0 
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
            72.23            105.07 
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
           17.190            12.605 
[1] "0.1 - 72.2 (17.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D546V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPATCH4 MUTATED         0        1        0        1         3         0
  GPATCH4 WILD-TYPE       1        8       27       25        28        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPATCH4 MUTATED           0          1          0          0        0
  GPATCH4 WILD-TYPE         3         48         36         24       24
D546V3, multiclass
            clus
vv           GPATCH4 MUTATED GPATCH4 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 1                 8
  STAGE IB                 0                27
  STAGE II                 1                25
  STAGE IIA                3                28
  STAGE IIB                0                44
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               0                36
  STAGE IIIC               0                24
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GPATCH4 MUTATED     0   3   5   0
  GPATCH4 WILD-TYPE  11  69 117  75
D546V4, multiclass
    clus
vv   GPATCH4 MUTATED GPATCH4 WILD-TYPE
  T1               0                11
  T2               3                69
  T3               5               117
  T4               0                75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  GPATCH4 MUTATED    4  1  1  0
  GPATCH4 WILD-TYPE 89 80 49 53
D546V5, multiclass
    clus
vv   GPATCH4 MUTATED GPATCH4 WILD-TYPE
  N0               4                89
  N1               1                80
  N2               1                49
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D546V6, binary
                   cls
clus                  0   1
  GPATCH4 MUTATED     7   0
  GPATCH4 WILD-TYPE 250  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH4 MUTATED      7    0
  GPATCH4 WILD-TYPE  250   18
   clus
vv  GPATCH4 MUTATED GPATCH4 WILD-TYPE
  0               7               250
  1               0                18
[1] 2 2
[1] FALSE
D546V7, binary
                   cls
clus                  0   1
  GPATCH4 MUTATED     3   5
  GPATCH4 WILD-TYPE 107 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH4 MUTATED      3    5
  GPATCH4 WILD-TYPE  107  174
        clus
vv       GPATCH4 MUTATED GPATCH4 WILD-TYPE
  FEMALE               3               107
  MALE                 5               174
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GPATCH4 MUTATED                                       1
  GPATCH4 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPATCH4 MUTATED                                                        5
  GPATCH4 WILD-TYPE                                                    130
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPATCH4 MUTATED                                                                   0
  GPATCH4 WILD-TYPE                                                                40
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GPATCH4 MUTATED                                                  2
  GPATCH4 WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GPATCH4 MUTATED                                                          0
  GPATCH4 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GPATCH4 MUTATED                                                           0
  GPATCH4 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GPATCH4 MUTATED                                          0
  GPATCH4 WILD-TYPE                                        3
D546V8, multiclass
                                                                   clus
vv                                                                  GPATCH4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  GPATCH4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D546V9, binary
                   cls
clus                  0   1
  GPATCH4 MUTATED     0   8
  GPATCH4 WILD-TYPE   5 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH4 MUTATED      0    8
  GPATCH4 WILD-TYPE    5  276
     clus
vv    GPATCH4 MUTATED GPATCH4 WILD-TYPE
  NO                0                 5
  YES               8               276
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  GPATCH4 MUTATED     5   0   0   2
  GPATCH4 WILD-TYPE 222  10  10  22
D546V10, multiclass
    clus
vv   GPATCH4 MUTATED GPATCH4 WILD-TYPE
  R0               5               222
  R1               0                10
  R2               0                10
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D546V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPATCH4 MUTATED       3                         1     4
  GPATCH4 WILD-TYPE    73                         3   164
D546V12, multiclass
                           clus
vv                          GPATCH4 MUTATED GPATCH4 WILD-TYPE
  ASIAN                                   3                73
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   4               164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(547) Variable = MAP2K1 MUTATION ANALYSIS
D547V1, survival
                  sevent
clus2                0   1
  MAP2K1 MUTATED     4   1
  MAP2K1 WILD-TYPE 177  79
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
               5              256 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
               1               79 
$`MAP2K1 MUTATED`
TCGA-BR-6566 TCGA-BR-8368 TCGA-BR-8683 TCGA-CG-5723 TCGA-D7-5577 
       32.78         4.31         9.86       105.07        12.36 

$`MAP2K1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       16.44        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04        21.07         7.99        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
            4.31             0.00 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
          105.07            79.07 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
           12.36            12.64 
[1] "4.3 - 105.1 (12.4)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "3.3"
D547V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAP2K1 MUTATED         0        0        1        1         1         0
  MAP2K1 WILD-TYPE       1        9       26       25        30        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP2K1 MUTATED           0          1          1          0        0
  MAP2K1 WILD-TYPE         3         48         35         24       24
D547V3, multiclass
            clus
vv           MAP2K1 MUTATED MAP2K1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                1               25
  STAGE IIA               1               30
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAP2K1 MUTATED     0   3   1   1
  MAP2K1 WILD-TYPE  11  69 121  74
D547V4, multiclass
    clus
vv   MAP2K1 MUTATED MAP2K1 WILD-TYPE
  T1              0               11
  T2              3               69
  T3              1              121
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  MAP2K1 MUTATED    2  1  1  1
  MAP2K1 WILD-TYPE 91 80 49 52
D547V5, multiclass
    clus
vv   MAP2K1 MUTATED MAP2K1 WILD-TYPE
  N0              2               91
  N1              1               80
  N2              1               49
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D547V6, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     5   0
  MAP2K1 WILD-TYPE 252  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      5    0
  MAP2K1 WILD-TYPE  252   18
   clus
vv  MAP2K1 MUTATED MAP2K1 WILD-TYPE
  0              5              252
  1              0               18
[1] 2 2
[1] FALSE
D547V7, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     3   2
  MAP2K1 WILD-TYPE 107 177
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      3    2
  MAP2K1 WILD-TYPE  107  177
        clus
vv       MAP2K1 MUTATED MAP2K1 WILD-TYPE
  FEMALE              3              107
  MALE                2              177
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MAP2K1 MUTATED                                       0
  MAP2K1 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MAP2K1 MUTATED                                                        3
  MAP2K1 WILD-TYPE                                                    132
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MAP2K1 MUTATED                                                                   0
  MAP2K1 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MAP2K1 MUTATED                                                  2
  MAP2K1 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MAP2K1 MUTATED                                                          0
  MAP2K1 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MAP2K1 MUTATED                                                           0
  MAP2K1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MAP2K1 MUTATED                                          0
  MAP2K1 WILD-TYPE                                        3
D547V8, multiclass
                                                                   clus
vv                                                                  MAP2K1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  MAP2K1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D547V9, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     0   5
  MAP2K1 WILD-TYPE   5 279
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      0    5
  MAP2K1 WILD-TYPE    5  279
     clus
vv    MAP2K1 MUTATED MAP2K1 WILD-TYPE
  NO               0                5
  YES              5              279
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MAP2K1 MUTATED     5   0   0   0
  MAP2K1 WILD-TYPE 222  10  10  24
D547V10, multiclass
    clus
vv   MAP2K1 MUTATED MAP2K1 WILD-TYPE
  R0              5              222
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D547V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAP2K1 MUTATED       1                         0     3
  MAP2K1 WILD-TYPE    75                         4   165
D547V12, multiclass
                           clus
vv                          MAP2K1 MUTATED MAP2K1 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  3              165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(548) Variable = TCEAL5 MUTATION ANALYSIS
D548V1, survival
                  sevent
clus2                0   1
  TCEAL5 MUTATED     4   2
  TCEAL5 WILD-TYPE 177  78
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
               6              255 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
               2               78 
$`TCEAL5 MUTATED`
TCGA-BR-8368 TCGA-CD-5801 TCGA-CG-5722 TCGA-CG-5723 TCGA-D7-A4YV TCGA-HU-A4H8 
        4.31        13.18         0.99       105.07         5.92         8.88 

$`TCEAL5 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.15         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        6.02        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       16.44        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
            0.99             0.00 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
          105.07            79.07 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
            7.40            12.66 
[1] "1.0 - 105.1 (7.4)" "0.0 - 79.1 (12.7)"
[1] "hr=" "1.2"
D548V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TCEAL5 MUTATED         0        0        2        1         0         1
  TCEAL5 WILD-TYPE       1        9       25       25        31        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TCEAL5 MUTATED           0          1          0          0        1
  TCEAL5 WILD-TYPE         3         48         36         24       23
D548V3, multiclass
            clus
vv           TCEAL5 MUTATED TCEAL5 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                2               25
  STAGE II                1               25
  STAGE IIA               0               31
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TCEAL5 MUTATED     1   2   3   0
  TCEAL5 WILD-TYPE  10  70 119  75
D548V4, multiclass
    clus
vv   TCEAL5 MUTATED TCEAL5 WILD-TYPE
  T1              1               10
  T2              2               70
  T3              3              119
  T4              0               75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  TCEAL5 MUTATED    1  4  1  0
  TCEAL5 WILD-TYPE 92 77 49 53
D548V5, multiclass
    clus
vv   TCEAL5 MUTATED TCEAL5 WILD-TYPE
  N0              1               92
  N1              4               77
  N2              1               49
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D548V6, binary
                  cls
clus                 0   1
  TCEAL5 MUTATED     5   1
  TCEAL5 WILD-TYPE 252  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      5    1
  TCEAL5 WILD-TYPE  252   17
   clus
vv  TCEAL5 MUTATED TCEAL5 WILD-TYPE
  0              5              252
  1              1               17
[1] 2 2
[1] FALSE
D548V7, binary
                  cls
clus                 0   1
  TCEAL5 MUTATED     3   3
  TCEAL5 WILD-TYPE 107 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      3    3
  TCEAL5 WILD-TYPE  107  176
        clus
vv       TCEAL5 MUTATED TCEAL5 WILD-TYPE
  FEMALE              3              107
  MALE                3              176
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TCEAL5 MUTATED                                       0
  TCEAL5 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TCEAL5 MUTATED                                                        3
  TCEAL5 WILD-TYPE                                                    132
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TCEAL5 MUTATED                                                                   1
  TCEAL5 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TCEAL5 MUTATED                                                  2
  TCEAL5 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TCEAL5 MUTATED                                                          0
  TCEAL5 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TCEAL5 MUTATED                                                           0
  TCEAL5 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TCEAL5 MUTATED                                          0
  TCEAL5 WILD-TYPE                                        3
D548V8, multiclass
                                                                   clus
vv                                                                  TCEAL5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  TCEAL5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D548V9, binary
                  cls
clus                 0   1
  TCEAL5 MUTATED     0   6
  TCEAL5 WILD-TYPE   5 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      0    6
  TCEAL5 WILD-TYPE    5  278
     clus
vv    TCEAL5 MUTATED TCEAL5 WILD-TYPE
  NO               0                5
  YES              6              278
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TCEAL5 MUTATED     5   0   1   0
  TCEAL5 WILD-TYPE 222  10   9  24
D548V10, multiclass
    clus
vv   TCEAL5 MUTATED TCEAL5 WILD-TYPE
  R0              5              222
  R1              0               10
  R2              1                9
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D548V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TCEAL5 MUTATED       2                         0     2
  TCEAL5 WILD-TYPE    74                         4   166
D548V12, multiclass
                           clus
vv                          TCEAL5 MUTATED TCEAL5 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  2              166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(549) Variable = GANAB MUTATION ANALYSIS
D549V1, survival
                 sevent
clus2               0   1
  GANAB MUTATED     8   1
  GANAB WILD-TYPE 173  79
  GANAB MUTATED GANAB WILD-TYPE 
              9             252 
  GANAB MUTATED GANAB WILD-TYPE 
              1              79 
$`GANAB MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8372 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-5721 
       26.70        34.68        19.17         6.58         0.10         6.02 
TCGA-D7-A4YY TCGA-F1-A448 TCGA-HU-8602 
       13.78        21.27        11.41 

$`GANAB WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       11.61        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       15.16        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       26.47         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  GANAB MUTATED GANAB WILD-TYPE 
            0.1             0.0 
  GANAB MUTATED GANAB WILD-TYPE 
          34.68          105.07 
  GANAB MUTATED GANAB WILD-TYPE 
         13.780          12.605 
[1] "0.1 - 34.7 (13.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "3.2"
D549V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GANAB MUTATED         0        0        0        0         2         2
  GANAB WILD-TYPE       1        9       27       26        29        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GANAB MUTATED           0          0          3          1        1
  GANAB WILD-TYPE         3         49         33         23       23
D549V3, multiclass
            clus
vv           GANAB MUTATED GANAB WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             3              33
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GANAB MUTATED     0   0   5   4
  GANAB WILD-TYPE  11  72 117  71
D549V4, multiclass
    clus
vv   GANAB MUTATED GANAB WILD-TYPE
  T1             0              11
  T2             0              72
  T3             5             117
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  GANAB MUTATED    4  3  0  3
  GANAB WILD-TYPE 89 78 50 50
D549V5, multiclass
    clus
vv   GANAB MUTATED GANAB WILD-TYPE
  N0             4              89
  N1             3              78
  N2             0              50
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D549V6, binary
                 cls
clus                0   1
  GANAB MUTATED    10   0
  GANAB WILD-TYPE 247  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GANAB MUTATED     10    0
  GANAB WILD-TYPE  247   18
   clus
vv  GANAB MUTATED GANAB WILD-TYPE
  0            10             247
  1             0              18
[1] 2 2
[1] FALSE
D549V7, binary
                 cls
clus                0   1
  GANAB MUTATED     3   7
  GANAB WILD-TYPE 107 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GANAB MUTATED      3    7
  GANAB WILD-TYPE  107  172
        clus
vv       GANAB MUTATED GANAB WILD-TYPE
  FEMALE             3             107
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GANAB MUTATED                                       3
  GANAB WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GANAB MUTATED                                                        5
  GANAB WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GANAB MUTATED                                                                   1
  GANAB WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GANAB MUTATED                                                  0
  GANAB WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GANAB MUTATED                                                          1
  GANAB WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GANAB MUTATED                                                           0
  GANAB WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GANAB MUTATED                                          0
  GANAB WILD-TYPE                                        3
D549V8, multiclass
                                                                   clus
vv                                                                  GANAB MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  GANAB WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D549V9, binary
                 cls
clus                0   1
  GANAB MUTATED     0  10
  GANAB WILD-TYPE   5 274
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GANAB MUTATED      0   10
  GANAB WILD-TYPE    5  274
     clus
vv    GANAB MUTATED GANAB WILD-TYPE
  NO              0               5
  YES            10             274
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GANAB MUTATED     7   0   0   1
  GANAB WILD-TYPE 220  10  10  23
D549V10, multiclass
    clus
vv   GANAB MUTATED GANAB WILD-TYPE
  R0             7             220
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D549V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GANAB MUTATED       3                         0     6
  GANAB WILD-TYPE    73                         4   162
D549V12, multiclass
                           clus
vv                          GANAB MUTATED GANAB WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(550) Variable = PIAS1 MUTATION ANALYSIS
D550V1, survival
                 sevent
clus2               0   1
  PIAS1 MUTATED     7   2
  PIAS1 WILD-TYPE 174  78
  PIAS1 MUTATED PIAS1 WILD-TYPE 
              9             252 
  PIAS1 MUTATED PIAS1 WILD-TYPE 
              2              78 
$`PIAS1 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6706 TCGA-BR-8361 TCGA-BR-8373 TCGA-BR-8382 
        6.97        34.68        18.05        19.50        14.79        15.85 
TCGA-BR-8487 TCGA-CG-5721 TCGA-CG-5723 
        1.12         6.02       105.07 

$`PIAS1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       32.78        25.61        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8384 
       14.04         3.32        11.80        19.17         0.26         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99         0.99        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  PIAS1 MUTATED PIAS1 WILD-TYPE 
           1.12            0.00 
  PIAS1 MUTATED PIAS1 WILD-TYPE 
         105.07           79.07 
  PIAS1 MUTATED PIAS1 WILD-TYPE 
         15.850          12.575 
[1] "1.1 - 105.1 (15.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "2.3"
D550V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIAS1 MUTATED         1        0        0        1         2         0
  PIAS1 WILD-TYPE       0        9       27       25        29        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIAS1 MUTATED           0          3          0          2        1
  PIAS1 WILD-TYPE         3         46         36         22       23
D550V3, multiclass
            clus
vv           PIAS1 MUTATED PIAS1 WILD-TYPE
  STAGE I                1               0
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              2              29
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             3              46
  STAGE IIIB             0              36
  STAGE IIIC             2              22
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PIAS1 MUTATED     1   1   4   4
  PIAS1 WILD-TYPE  10  71 118  71
D550V4, multiclass
    clus
vv   PIAS1 MUTATED PIAS1 WILD-TYPE
  T1             1              10
  T2             1              71
  T3             4             118
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PIAS1 MUTATED    2  6  1  1
  PIAS1 WILD-TYPE 91 75 49 52
D550V5, multiclass
    clus
vv   PIAS1 MUTATED PIAS1 WILD-TYPE
  N0             2              91
  N1             6              75
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D550V6, binary
                 cls
clus                0   1
  PIAS1 MUTATED     8   0
  PIAS1 WILD-TYPE 249  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS1 MUTATED      8    0
  PIAS1 WILD-TYPE  249   18
   clus
vv  PIAS1 MUTATED PIAS1 WILD-TYPE
  0             8             249
  1             0              18
[1] 2 2
[1] FALSE
D550V7, binary
                 cls
clus                0   1
  PIAS1 MUTATED     5   5
  PIAS1 WILD-TYPE 105 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS1 MUTATED      5    5
  PIAS1 WILD-TYPE  105  174
        clus
vv       PIAS1 MUTATED PIAS1 WILD-TYPE
  FEMALE             5             105
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PIAS1 MUTATED                                       0
  PIAS1 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIAS1 MUTATED                                                        8
  PIAS1 WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIAS1 MUTATED                                                                   2
  PIAS1 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PIAS1 MUTATED                                                  0
  PIAS1 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PIAS1 MUTATED                                                          0
  PIAS1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PIAS1 MUTATED                                                           0
  PIAS1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PIAS1 MUTATED                                          0
  PIAS1 WILD-TYPE                                        3
D550V8, multiclass
                                                                   clus
vv                                                                  PIAS1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  PIAS1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D550V9, binary
                 cls
clus                0   1
  PIAS1 MUTATED     0  10
  PIAS1 WILD-TYPE   5 274
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS1 MUTATED      0   10
  PIAS1 WILD-TYPE    5  274
     clus
vv    PIAS1 MUTATED PIAS1 WILD-TYPE
  NO              0               5
  YES            10             274
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PIAS1 MUTATED     9   0   0   1
  PIAS1 WILD-TYPE 218  10  10  23
D550V10, multiclass
    clus
vv   PIAS1 MUTATED PIAS1 WILD-TYPE
  R0             9             218
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D550V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIAS1 MUTATED       0                         1     7
  PIAS1 WILD-TYPE    76                         3   161
D550V12, multiclass
                           clus
vv                          PIAS1 MUTATED PIAS1 WILD-TYPE
  ASIAN                                 0              76
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 7             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(551) Variable = YLPM1 MUTATION ANALYSIS
D551V1, survival
                 sevent
clus2               0   1
  YLPM1 MUTATED    12   2
  YLPM1 WILD-TYPE 169  78
  YLPM1 MUTATED YLPM1 WILD-TYPE 
             14             247 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
              2              78 
$`YLPM1 MUTATED`
TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-7851 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8360 
        6.97        32.94        12.43        12.26        20.55         6.18 
TCGA-BR-8382 TCGA-BR-8680 TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5733 
       15.85        15.81        15.95         6.02       105.07        21.07 
TCGA-D7-6822 TCGA-HU-A4GT 
       12.33         6.51 

$`YLPM1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        0.69         9.60         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20        15.58         7.40        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        19.17        14.79         0.26         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  YLPM1 MUTATED YLPM1 WILD-TYPE 
           6.02            0.00 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
         105.07           79.07 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
          14.12           12.62 
[1] "6.0 - 105.1 (14.1)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "3.1"
D551V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  YLPM1 MUTATED         1        0        1        2         3         3
  YLPM1 WILD-TYPE       0        9       26       24        28        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  YLPM1 MUTATED           0          2          0          1        3
  YLPM1 WILD-TYPE         3         47         36         23       21
D551V3, multiclass
            clus
vv           YLPM1 MUTATED YLPM1 WILD-TYPE
  STAGE I                1               0
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               2              24
  STAGE IIA              3              28
  STAGE IIB              3              41
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               3              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  YLPM1 MUTATED     2   4   4   7
  YLPM1 WILD-TYPE   9  68 118  68
D551V4, multiclass
    clus
vv   YLPM1 MUTATED YLPM1 WILD-TYPE
  T1             2               9
  T2             4              68
  T3             4             118
  T4             7              68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  YLPM1 MUTATED    7  6  3  1
  YLPM1 WILD-TYPE 86 75 47 52
D551V5, multiclass
    clus
vv   YLPM1 MUTATED YLPM1 WILD-TYPE
  N0             7              86
  N1             6              75
  N2             3              47
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D551V6, binary
                 cls
clus                0   1
  YLPM1 MUTATED    15   1
  YLPM1 WILD-TYPE 242  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YLPM1 MUTATED     15    1
  YLPM1 WILD-TYPE  242   17
   clus
vv  YLPM1 MUTATED YLPM1 WILD-TYPE
  0            15             242
  1             1              17
[1] 2 2
[1] FALSE
D551V7, binary
                 cls
clus                0   1
  YLPM1 MUTATED     8  10
  YLPM1 WILD-TYPE 102 169
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YLPM1 MUTATED      8   10
  YLPM1 WILD-TYPE  102  169
        clus
vv       YLPM1 MUTATED YLPM1 WILD-TYPE
  FEMALE             8             102
  MALE              10             169
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  YLPM1 MUTATED                                       0
  YLPM1 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  YLPM1 MUTATED                                                       11
  YLPM1 WILD-TYPE                                                    124
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  YLPM1 MUTATED                                                                   4
  YLPM1 WILD-TYPE                                                                36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  YLPM1 MUTATED                                                  3
  YLPM1 WILD-TYPE                                               35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  YLPM1 MUTATED                                                          0
  YLPM1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  YLPM1 MUTATED                                                           0
  YLPM1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  YLPM1 MUTATED                                          0
  YLPM1 WILD-TYPE                                        3
D551V8, multiclass
                                                                   clus
vv                                                                  YLPM1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  YLPM1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D551V9, binary
                 cls
clus                0   1
  YLPM1 MUTATED     0  18
  YLPM1 WILD-TYPE   5 266
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YLPM1 MUTATED      0   18
  YLPM1 WILD-TYPE    5  266
     clus
vv    YLPM1 MUTATED YLPM1 WILD-TYPE
  NO              0               5
  YES            18             266
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  YLPM1 MUTATED    14   0   0   4
  YLPM1 WILD-TYPE 213  10  10  20
D551V10, multiclass
    clus
vv   YLPM1 MUTATED YLPM1 WILD-TYPE
  R0            14             213
  R1             0              10
  R2             0              10
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D551V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  YLPM1 MUTATED       2                         1    11
  YLPM1 WILD-TYPE    74                         3   157
D551V12, multiclass
                           clus
vv                          YLPM1 MUTATED YLPM1 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                11             157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(552) Variable = SMAD7 MUTATION ANALYSIS
D552V1, survival
                 sevent
clus2               0   1
  SMAD7 MUTATED     3   0
  SMAD7 WILD-TYPE 178  80
  SMAD7 MUTATED SMAD7 WILD-TYPE 
              3             258 
  SMAD7 MUTATED SMAD7 WILD-TYPE 
              0              80 
$`SMAD7 MUTATED`
TCGA-BR-7703 TCGA-FP-A4BE TCGA-HU-A4H5 
       24.76        11.08        12.30 

$`SMAD7 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        19.36        23.84         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  SMAD7 MUTATED SMAD7 WILD-TYPE 
          11.08            0.00 
  SMAD7 MUTATED SMAD7 WILD-TYPE 
          24.76          105.07 
  SMAD7 MUTATED SMAD7 WILD-TYPE 
          12.30           12.64 
[1] "11.1 - 24.8 (12.3)" "0.0 - 105.1 (12.6)"
[1] "hr="     "9100000"
D552V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMAD7 MUTATED         0        1        1        0         1         0
  SMAD7 WILD-TYPE       1        8       26       26        30        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMAD7 MUTATED           0          0          0          0        1
  SMAD7 WILD-TYPE         3         49         36         24       23
D552V3, multiclass
            clus
vv           SMAD7 MUTATED SMAD7 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SMAD7 MUTATED     1   1   1   1
  SMAD7 WILD-TYPE  10  71 121  74
D552V4, multiclass
    clus
vv   SMAD7 MUTATED SMAD7 WILD-TYPE
  T1             1              10
  T2             1              71
  T3             1             121
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  SMAD7 MUTATED    3  0  1  0
  SMAD7 WILD-TYPE 90 81 49 53
D552V5, multiclass
    clus
vv   SMAD7 MUTATED SMAD7 WILD-TYPE
  N0             3              90
  N1             0              81
  N2             1              49
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D552V6, binary
                 cls
clus                0   1
  SMAD7 MUTATED     5   0
  SMAD7 WILD-TYPE 252  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD7 MUTATED      5    0
  SMAD7 WILD-TYPE  252   18
   clus
vv  SMAD7 MUTATED SMAD7 WILD-TYPE
  0             5             252
  1             0              18
[1] 2 2
[1] FALSE
D552V7, binary
                 cls
clus                0   1
  SMAD7 MUTATED     2   3
  SMAD7 WILD-TYPE 108 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD7 MUTATED      2    3
  SMAD7 WILD-TYPE  108  176
        clus
vv       SMAD7 MUTATED SMAD7 WILD-TYPE
  FEMALE             2             108
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SMAD7 MUTATED                                       0
  SMAD7 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SMAD7 MUTATED                                                        3
  SMAD7 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SMAD7 MUTATED                                                                   0
  SMAD7 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SMAD7 MUTATED                                                  0
  SMAD7 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SMAD7 MUTATED                                                          0
  SMAD7 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SMAD7 MUTATED                                                           2
  SMAD7 WILD-TYPE                                                         4
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SMAD7 MUTATED                                          0
  SMAD7 WILD-TYPE                                        3
D552V8, multiclass
                                                                   clus
vv                                                                  SMAD7 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  SMAD7 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D552V9, binary
                 cls
clus                0   1
  SMAD7 MUTATED     0   5
  SMAD7 WILD-TYPE   5 279
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD7 MUTATED      0    5
  SMAD7 WILD-TYPE    5  279
     clus
vv    SMAD7 MUTATED SMAD7 WILD-TYPE
  NO              0               5
  YES             5             279
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SMAD7 MUTATED     3   0   0   2
  SMAD7 WILD-TYPE 224  10  10  22
D552V10, multiclass
    clus
vv   SMAD7 MUTATED SMAD7 WILD-TYPE
  R0             3             224
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D552V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMAD7 MUTATED       1                         1     3
  SMAD7 WILD-TYPE    75                         3   165
D552V12, multiclass
                           clus
vv                          SMAD7 MUTATED SMAD7 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(553) Variable = PPARGC1B MUTATION ANALYSIS
D553V1, survival
                    sevent
clus2                  0   1
  PPARGC1B MUTATED     6   0
  PPARGC1B WILD-TYPE 175  80
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 6                255 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 0                 80 
$`PPARGC1B MUTATED`
TCGA-BR-7851 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8591 TCGA-HU-8602 TCGA-HU-A4GN 
       12.43        19.50         1.12        13.45        11.41        29.98 

$`PPARGC1B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
        9.21        20.22        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
              1.12               0.00 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
             29.98             105.07 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
             12.94              12.62 
[1] "1.1 - 30.0 (12.9)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "2.5e+07"
D553V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPARGC1B MUTATED         0        0        0        0         2         2
  PPARGC1B WILD-TYPE       1        9       27       26        29        42
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPARGC1B MUTATED           0          0          0          2        0
  PPARGC1B WILD-TYPE         3         49         36         22       24
D553V3, multiclass
            clus
vv           PPARGC1B MUTATED PPARGC1B WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  0                 27
  STAGE II                  0                 26
  STAGE IIA                 2                 29
  STAGE IIB                 2                 42
  STAGE III                 0                  3
  STAGE IIIA                0                 49
  STAGE IIIB                0                 36
  STAGE IIIC                2                 22
  STAGE IV                  0                 24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  PPARGC1B MUTATED     0   1   1   4
  PPARGC1B WILD-TYPE  11  71 121  71
D553V4, multiclass
    clus
vv   PPARGC1B MUTATED PPARGC1B WILD-TYPE
  T1                0                 11
  T2                1                 71
  T3                1                121
  T4                4                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  PPARGC1B MUTATED    3  1  1  1
  PPARGC1B WILD-TYPE 90 80 49 52
D553V5, multiclass
    clus
vv   PPARGC1B MUTATED PPARGC1B WILD-TYPE
  N0                3                 90
  N1                1                 80
  N2                1                 49
  N3                1                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D553V6, binary
                    cls
clus                   0   1
  PPARGC1B MUTATED     7   0
  PPARGC1B WILD-TYPE 250  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1B MUTATED      7    0
  PPARGC1B WILD-TYPE  250   18
   clus
vv  PPARGC1B MUTATED PPARGC1B WILD-TYPE
  0                7                250
  1                0                 18
[1] 2 2
[1] FALSE
D553V7, binary
                    cls
clus                   0   1
  PPARGC1B MUTATED     4   3
  PPARGC1B WILD-TYPE 106 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1B MUTATED      4    3
  PPARGC1B WILD-TYPE  106  176
        clus
vv       PPARGC1B MUTATED PPARGC1B WILD-TYPE
  FEMALE                4                106
  MALE                  3                176
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PPARGC1B MUTATED                                       1
  PPARGC1B WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PPARGC1B MUTATED                                                        4
  PPARGC1B WILD-TYPE                                                    131
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PPARGC1B MUTATED                                                                   1
  PPARGC1B WILD-TYPE                                                                39
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PPARGC1B MUTATED                                                  1
  PPARGC1B WILD-TYPE                                               37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PPARGC1B MUTATED                                                          0
  PPARGC1B WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PPARGC1B MUTATED                                                           0
  PPARGC1B WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PPARGC1B MUTATED                                          0
  PPARGC1B WILD-TYPE                                        3
D553V8, multiclass
                                                                   clus
vv                                                                  PPARGC1B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  PPARGC1B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D553V9, binary
                    cls
clus                   0   1
  PPARGC1B MUTATED     0   7
  PPARGC1B WILD-TYPE   5 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1B MUTATED      0    7
  PPARGC1B WILD-TYPE    5  277
     clus
vv    PPARGC1B MUTATED PPARGC1B WILD-TYPE
  NO                 0                  5
  YES                7                277
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  PPARGC1B MUTATED     6   0   0   1
  PPARGC1B WILD-TYPE 221  10  10  23
D553V10, multiclass
    clus
vv   PPARGC1B MUTATED PPARGC1B WILD-TYPE
  R0                6                221
  R1                0                 10
  R2                0                 10
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D553V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPARGC1B MUTATED       2                         0     5
  PPARGC1B WILD-TYPE    74                         4   163
D553V12, multiclass
                           clus
vv                          PPARGC1B MUTATED PPARGC1B WILD-TYPE
  ASIAN                                    2                 74
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    5                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(554) Variable = TSPYL5 MUTATION ANALYSIS
D554V1, survival
                  sevent
clus2                0   1
  TSPYL5 MUTATED     6   1
  TSPYL5 WILD-TYPE 175  79
  TSPYL5 MUTATED TSPYL5 WILD-TYPE 
               7              254 
  TSPYL5 MUTATED TSPYL5 WILD-TYPE 
               1               79 
$`TSPYL5 MUTATED`
TCGA-BR-8078 TCGA-BR-8382 TCGA-BR-8591 TCGA-CD-A4MG TCGA-CG-5721 TCGA-HU-A4H8 
       12.26        15.85        13.45         6.58         6.02         8.88 
TCGA-IN-8462 
       18.81 

$`TSPYL5 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       19.17        14.79         0.26         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  TSPYL5 MUTATED TSPYL5 WILD-TYPE 
            6.02             0.00 
  TSPYL5 MUTATED TSPYL5 WILD-TYPE 
           18.81           105.07 
  TSPYL5 MUTATED TSPYL5 WILD-TYPE 
           12.26            12.64 
[1] "6.0 - 18.8 (12.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.7"
D554V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TSPYL5 MUTATED         0        0        1        1         1         2
  TSPYL5 WILD-TYPE       1        9       26       25        30        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TSPYL5 MUTATED           0          0          0          2        1
  TSPYL5 WILD-TYPE         3         49         36         22       23
D554V3, multiclass
            clus
vv           TSPYL5 MUTATED TSPYL5 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                1               25
  STAGE IIA               1               30
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              2               22
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TSPYL5 MUTATED     1   2   1   4
  TSPYL5 WILD-TYPE  10  70 121  71
D554V4, multiclass
    clus
vv   TSPYL5 MUTATED TSPYL5 WILD-TYPE
  T1              1               10
  T2              2               70
  T3              1              121
  T4              4               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  TSPYL5 MUTATED    2  4  0  2
  TSPYL5 WILD-TYPE 91 77 50 51
D554V5, multiclass
    clus
vv   TSPYL5 MUTATED TSPYL5 WILD-TYPE
  N0              2               91
  N1              4               77
  N2              0               50
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D554V6, binary
                  cls
clus                 0   1
  TSPYL5 MUTATED     9   0
  TSPYL5 WILD-TYPE 248  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPYL5 MUTATED      9    0
  TSPYL5 WILD-TYPE  248   18
   clus
vv  TSPYL5 MUTATED TSPYL5 WILD-TYPE
  0              9              248
  1              0               18
[1] 2 2
[1] FALSE
D554V7, binary
                  cls
clus                 0   1
  TSPYL5 MUTATED     3   6
  TSPYL5 WILD-TYPE 107 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPYL5 MUTATED      3    6
  TSPYL5 WILD-TYPE  107  173
        clus
vv       TSPYL5 MUTATED TSPYL5 WILD-TYPE
  FEMALE              3              107
  MALE                6              173
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TSPYL5 MUTATED                                       1
  TSPYL5 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TSPYL5 MUTATED                                                        5
  TSPYL5 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TSPYL5 MUTATED                                                                   1
  TSPYL5 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TSPYL5 MUTATED                                                  1
  TSPYL5 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TSPYL5 MUTATED                                                          1
  TSPYL5 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TSPYL5 MUTATED                                                           0
  TSPYL5 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TSPYL5 MUTATED                                          0
  TSPYL5 WILD-TYPE                                        3
D554V8, multiclass
                                                                   clus
vv                                                                  TSPYL5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  TSPYL5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D554V9, binary
                  cls
clus                 0   1
  TSPYL5 MUTATED     1   8
  TSPYL5 WILD-TYPE   4 276
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPYL5 MUTATED      1    8
  TSPYL5 WILD-TYPE    4  276
     clus
vv    TSPYL5 MUTATED TSPYL5 WILD-TYPE
  NO               1                4
  YES              8              276
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TSPYL5 MUTATED     7   0   0   1
  TSPYL5 WILD-TYPE 220  10  10  23
D554V10, multiclass
    clus
vv   TSPYL5 MUTATED TSPYL5 WILD-TYPE
  R0              7              220
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D554V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TSPYL5 MUTATED       2                         0     5
  TSPYL5 WILD-TYPE    74                         4   163
D554V12, multiclass
                           clus
vv                          TSPYL5 MUTATED TSPYL5 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  5              163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(555) Variable = UPK2 MUTATION ANALYSIS
D555V1, survival
                sevent
clus2              0   1
  UPK2 MUTATED     2   1
  UPK2 WILD-TYPE 179  79
  UPK2 MUTATED UPK2 WILD-TYPE 
             3            258 
  UPK2 MUTATED UPK2 WILD-TYPE 
             1             79 
$`UPK2 MUTATED`
TCGA-BR-8081 TCGA-BR-8360 TCGA-CG-4465 
       20.55         6.18         9.01 

$`UPK2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       19.07        12.03         0.00        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  UPK2 MUTATED UPK2 WILD-TYPE 
          6.18           0.00 
  UPK2 MUTATED UPK2 WILD-TYPE 
         20.55         105.07 
  UPK2 MUTATED UPK2 WILD-TYPE 
          9.01          12.64 
[1] "6.2 - 20.6 (9.0)"   "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D555V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UPK2 MUTATED         0        0        0        0         1         1
  UPK2 WILD-TYPE       1        9       27       26        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UPK2 MUTATED           0          0          0          0        1
  UPK2 WILD-TYPE         3         49         36         24       23
D555V3, multiclass
            clus
vv           UPK2 MUTATED UPK2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              0             26
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  UPK2 MUTATED     0   0   1   2
  UPK2 WILD-TYPE  11  72 121  73
D555V4, multiclass
    clus
vv   UPK2 MUTATED UPK2 WILD-TYPE
  T1            0             11
  T2            0             72
  T3            1            121
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  UPK2 MUTATED    2  0  0  1
  UPK2 WILD-TYPE 91 81 50 52
D555V5, multiclass
    clus
vv   UPK2 MUTATED UPK2 WILD-TYPE
  N0            2             91
  N1            0             81
  N2            0             50
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D555V6, binary
                cls
clus               0   1
  UPK2 MUTATED     2   1
  UPK2 WILD-TYPE 255  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  UPK2 MUTATED      2    1
  UPK2 WILD-TYPE  255   17
   clus
vv  UPK2 MUTATED UPK2 WILD-TYPE
  0            2            255
  1            1             17
[1] 2 2
[1] FALSE
D555V7, binary
                cls
clus               0   1
  UPK2 MUTATED     2   1
  UPK2 WILD-TYPE 108 178
[1] "tbl2"
                cls
clus             [,1] [,2]
  UPK2 MUTATED      2    1
  UPK2 WILD-TYPE  108  178
        clus
vv       UPK2 MUTATED UPK2 WILD-TYPE
  FEMALE            2            108
  MALE              1            178
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  UPK2 MUTATED                                       1
  UPK2 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  UPK2 MUTATED                                                        1
  UPK2 WILD-TYPE                                                    134
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  UPK2 MUTATED                                                                   1
  UPK2 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  UPK2 MUTATED                                                  0
  UPK2 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  UPK2 MUTATED                                                          0
  UPK2 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  UPK2 MUTATED                                                           0
  UPK2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  UPK2 MUTATED                                          0
  UPK2 WILD-TYPE                                        3
D555V8, multiclass
                                                                   clus
vv                                                                  UPK2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       1
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  UPK2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D555V9, binary
                cls
clus               0   1
  UPK2 MUTATED     0   3
  UPK2 WILD-TYPE   5 281
[1] "tbl2"
                cls
clus             [,1] [,2]
  UPK2 MUTATED      0    3
  UPK2 WILD-TYPE    5  281
     clus
vv    UPK2 MUTATED UPK2 WILD-TYPE
  NO             0              5
  YES            3            281
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  UPK2 MUTATED     2   0   1   0
  UPK2 WILD-TYPE 225  10   9  24
D555V10, multiclass
    clus
vv   UPK2 MUTATED UPK2 WILD-TYPE
  R0            2            225
  R1            0             10
  R2            1              9
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D555V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UPK2 MUTATED       0                         0     2
  UPK2 WILD-TYPE    76                         4   166
D555V12, multiclass
[1] "Remove cluster labels:" "UPK2 MUTATED"          
clus
  UPK2 MUTATED UPK2 WILD-TYPE 
             2            246 
    TCGA-B7-5816     TCGA-B7-5818     TCGA-BR-4183     TCGA-BR-4184 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-4187     TCGA-BR-4188     TCGA-BR-4191     TCGA-BR-4201 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-4253     TCGA-BR-4255     TCGA-BR-4256     TCGA-BR-4257 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-4267     TCGA-BR-4279     TCGA-BR-4280     TCGA-BR-4292 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-4294     TCGA-BR-4357     TCGA-BR-4361     TCGA-BR-4362 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-4363     TCGA-BR-4366     TCGA-BR-4368     TCGA-BR-4369 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-4370     TCGA-BR-4371     TCGA-BR-6452     TCGA-BR-6453 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-6454     TCGA-BR-6455     TCGA-BR-6456     TCGA-BR-6457 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-6458     TCGA-BR-6563     TCGA-BR-6564     TCGA-BR-6565 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-6566     TCGA-BR-6705     TCGA-BR-6706     TCGA-BR-6707 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-6710     TCGA-BR-6801     TCGA-BR-6802     TCGA-BR-6803 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-6852     TCGA-BR-7196     TCGA-BR-7197     TCGA-BR-7703 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-7707     TCGA-BR-7715     TCGA-BR-7716     TCGA-BR-7717 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-7722     TCGA-BR-7723     TCGA-BR-7851     TCGA-BR-7901 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-7957     TCGA-BR-7958     TCGA-BR-7959     TCGA-BR-8058 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-8059     TCGA-BR-8077     TCGA-BR-8078     TCGA-BR-8080 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-8284     TCGA-BR-8286     TCGA-BR-8289     TCGA-BR-8291 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-8295     TCGA-BR-8296     TCGA-BR-8297     TCGA-BR-8361 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-8363     TCGA-BR-8364     TCGA-BR-8365     TCGA-BR-8366 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-8367     TCGA-BR-8368     TCGA-BR-8369     TCGA-BR-8370 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-8371     TCGA-BR-8372     TCGA-BR-8373     TCGA-BR-8380 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-8381     TCGA-BR-8382     TCGA-BR-8384     TCGA-BR-8483 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-8484     TCGA-BR-8485     TCGA-BR-8486     TCGA-BR-8487 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-8588     TCGA-BR-8589     TCGA-BR-8590     TCGA-BR-8591 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-8592     TCGA-BR-8676     TCGA-BR-8677     TCGA-BR-8678 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-8679     TCGA-BR-8680     TCGA-BR-8682     TCGA-BR-8683 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-8686     TCGA-BR-8687     TCGA-BR-8690     TCGA-BR-A44T 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-A44U     TCGA-BR-A452     TCGA-BR-A453     TCGA-BR-A4CQ 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-A4CR     TCGA-BR-A4CS     TCGA-BR-A4IU     TCGA-BR-A4IV 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-A4IY     TCGA-BR-A4IZ     TCGA-BR-A4J1     TCGA-BR-A4J2 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-A4J4     TCGA-BR-A4J6     TCGA-BR-A4J7     TCGA-BR-A4J8 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-A4PD     TCGA-BR-A4PE     TCGA-BR-A4PF     TCGA-BR-A4QI 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-BR-A4QL     TCGA-BR-A4QM     TCGA-CD-5798     TCGA-CD-5799 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-CD-5800     TCGA-CD-5801     TCGA-CD-5802     TCGA-CD-5803 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-CD-5804     TCGA-CD-5813     TCGA-CD-8524     TCGA-CD-8525 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-CD-8526     TCGA-CD-8527     TCGA-CD-8528     TCGA-CD-8529 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-CD-8530     TCGA-CD-8531     TCGA-CD-8532     TCGA-CD-8534 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-CD-8535     TCGA-CD-8536     TCGA-CD-A486     TCGA-CD-A487 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-CD-A489     TCGA-CD-A48A     TCGA-CD-A48C     TCGA-CD-A4MG 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-CD-A4MH     TCGA-CD-A4MI     TCGA-CD-A4MJ     TCGA-D7-5577 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-D7-5578     TCGA-D7-5579     TCGA-D7-6518     TCGA-D7-6519 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-D7-6520     TCGA-D7-6521     TCGA-D7-6522     TCGA-D7-6524 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-D7-6525     TCGA-D7-6526     TCGA-D7-6527     TCGA-D7-6528 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-D7-6815     TCGA-D7-6817     TCGA-D7-6818     TCGA-D7-6820 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-D7-6822     TCGA-D7-8570     TCGA-D7-8572     TCGA-D7-8573 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-D7-8574     TCGA-D7-8575     TCGA-D7-8576     TCGA-D7-8578 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-D7-8579     TCGA-D7-A4YT     TCGA-D7-A4YU     TCGA-D7-A4YV 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-D7-A4YX     TCGA-D7-A4YY     TCGA-D7-A4Z0     TCGA-EQ-5647 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-EQ-8122     TCGA-EQ-A4SO     TCGA-F1-6177     TCGA-F1-6874 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-F1-6875     TCGA-F1-A448     TCGA-FP-7735     TCGA-FP-7829 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-FP-7916     TCGA-FP-7998     TCGA-FP-8099     TCGA-FP-8209 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-FP-8210     TCGA-FP-8211     TCGA-FP-8631     TCGA-FP-A4BE 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-FP-A4BF     TCGA-HJ-7597     TCGA-HU-8243     TCGA-HU-8245 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-HU-8249     TCGA-HU-8602     TCGA-HU-8604     TCGA-HU-8608 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-HU-8610     TCGA-HU-A4G2     TCGA-HU-A4G3     TCGA-HU-A4G6 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-HU-A4G8     TCGA-HU-A4G9     TCGA-HU-A4GC     TCGA-HU-A4GD 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-HU-A4GF     TCGA-HU-A4GH     TCGA-HU-A4GN     TCGA-HU-A4GP 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-HU-A4GQ     TCGA-HU-A4GT     TCGA-HU-A4GU     TCGA-HU-A4GX 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-HU-A4GY     TCGA-HU-A4H0     TCGA-HU-A4H2     TCGA-HU-A4H3 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-HU-A4H4     TCGA-HU-A4H5     TCGA-HU-A4H6     TCGA-HU-A4H8 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-HU-A4HD     TCGA-IN-7806     TCGA-IN-7808     TCGA-IN-8462 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 
    TCGA-IN-8663     TCGA-IP-7968 
"UPK2 WILD-TYPE" "UPK2 WILD-TYPE" 

Clustering(556) Variable = BCKDHA MUTATION ANALYSIS
D556V1, survival
                  sevent
clus2                0   1
  BCKDHA MUTATED     7   4
  BCKDHA WILD-TYPE 174  76
  BCKDHA MUTATED BCKDHA WILD-TYPE 
              11              250 
  BCKDHA MUTATED BCKDHA WILD-TYPE 
               4               76 
$`BCKDHA MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6566 TCGA-CD-8536 TCGA-CD-A487 TCGA-D7-8578 
        6.97        30.90        32.78         0.10         9.34        21.14 
TCGA-D7-A4YV TCGA-F1-6874 TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-A4H4 
        5.92        14.47        11.08        26.47        23.84 

$`BCKDHA WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.13         3.42        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       18.21        14.66        20.91        14.27        16.44        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
       13.78        14.76         0.62         7.99        16.24        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8243 
       59.54         5.03        13.58         0.56         5.52         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       19.36        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  BCKDHA MUTATED BCKDHA WILD-TYPE 
             0.1              0.0 
  BCKDHA MUTATED BCKDHA WILD-TYPE 
           32.78           105.07 
  BCKDHA MUTATED BCKDHA WILD-TYPE 
          14.470           12.605 
[1] "0.1 - 32.8 (14.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D556V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BCKDHA MUTATED         0        0        3        1         2         3
  BCKDHA WILD-TYPE       1        9       24       25        29        41
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BCKDHA MUTATED           0          2          0          0        0
  BCKDHA WILD-TYPE         3         47         36         24       24
D556V3, multiclass
            clus
vv           BCKDHA MUTATED BCKDHA WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                3               24
  STAGE II                1               25
  STAGE IIA               2               29
  STAGE IIB               3               41
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BCKDHA MUTATED     0   5   6   1
  BCKDHA WILD-TYPE  11  67 116  74
D556V4, multiclass
    clus
vv   BCKDHA MUTATED BCKDHA WILD-TYPE
  T1              0               11
  T2              5               67
  T3              6              116
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  BCKDHA MUTATED    7  3  1  0
  BCKDHA WILD-TYPE 86 78 49 53
D556V5, multiclass
    clus
vv   BCKDHA MUTATED BCKDHA WILD-TYPE
  N0              7               86
  N1              3               78
  N2              1               49
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D556V6, binary
                  cls
clus                 0   1
  BCKDHA MUTATED    10   0
  BCKDHA WILD-TYPE 247  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCKDHA MUTATED     10    0
  BCKDHA WILD-TYPE  247   18
   clus
vv  BCKDHA MUTATED BCKDHA WILD-TYPE
  0             10              247
  1              0               18
[1] 2 2
[1] FALSE
D556V7, binary
                  cls
clus                 0   1
  BCKDHA MUTATED     6   6
  BCKDHA WILD-TYPE 104 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCKDHA MUTATED      6    6
  BCKDHA WILD-TYPE  104  173
        clus
vv       BCKDHA MUTATED BCKDHA WILD-TYPE
  FEMALE              6              104
  MALE                6              173
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  BCKDHA MUTATED                                       1
  BCKDHA WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BCKDHA MUTATED                                                        7
  BCKDHA WILD-TYPE                                                    128
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BCKDHA MUTATED                                                                   1
  BCKDHA WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  BCKDHA MUTATED                                                  2
  BCKDHA WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  BCKDHA MUTATED                                                          0
  BCKDHA WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  BCKDHA MUTATED                                                           0
  BCKDHA WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  BCKDHA MUTATED                                          1
  BCKDHA WILD-TYPE                                        2
D556V8, multiclass
                                                                   clus
vv                                                                  BCKDHA MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       1
                                                                   clus
vv                                                                  BCKDHA WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D556V9, binary
                  cls
clus                 0   1
  BCKDHA MUTATED     0  12
  BCKDHA WILD-TYPE   5 272
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCKDHA MUTATED      0   12
  BCKDHA WILD-TYPE    5  272
     clus
vv    BCKDHA MUTATED BCKDHA WILD-TYPE
  NO               0                5
  YES             12              272
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  BCKDHA MUTATED     9   0   0   3
  BCKDHA WILD-TYPE 218  10  10  21
D556V10, multiclass
    clus
vv   BCKDHA MUTATED BCKDHA WILD-TYPE
  R0              9              218
  R1              0               10
  R2              0               10
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D556V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCKDHA MUTATED       3                         1     8
  BCKDHA WILD-TYPE    73                         3   160
D556V12, multiclass
                           clus
vv                          BCKDHA MUTATED BCKDHA WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  8              160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(557) Variable = BRD3 MUTATION ANALYSIS
D557V1, survival
                sevent
clus2              0   1
  BRD3 MUTATED    11   2
  BRD3 WILD-TYPE 170  78
  BRD3 MUTATED BRD3 WILD-TYPE 
            13            248 
  BRD3 MUTATED BRD3 WILD-TYPE 
             2             78 
$`BRD3 MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8589 
       34.68        12.26        20.55        19.17         1.12        15.81 
TCGA-BR-8680 TCGA-CD-8529 TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5721 TCGA-HU-A4H4 
       15.81         0.13         6.58         1.02         6.02        23.84 
TCGA-HU-A4H8 
        8.88 

$`BRD3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 
       17.49        14.43         0.69         9.60         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.07         0.10         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       12.30         9.67        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  BRD3 MUTATED BRD3 WILD-TYPE 
          0.13           0.00 
  BRD3 MUTATED BRD3 WILD-TYPE 
         34.68         105.07 
  BRD3 MUTATED BRD3 WILD-TYPE 
         12.26          12.64 
[1] "0.1 - 34.7 (12.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.9"
D557V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BRD3 MUTATED         0        0        2        1         3         3
  BRD3 WILD-TYPE       1        9       25       25        28        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BRD3 MUTATED           0          0          1          1        4
  BRD3 WILD-TYPE         3         49         35         23       20
D557V3, multiclass
            clus
vv           BRD3 MUTATED BRD3 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              1             25
  STAGE IIA             3             28
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            1             35
  STAGE IIIC            1             23
  STAGE IV              4             20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BRD3 MUTATED     1   3   4   7
  BRD3 WILD-TYPE  10  69 118  68
D557V4, multiclass
    clus
vv   BRD3 MUTATED BRD3 WILD-TYPE
  T1            1             10
  T2            3             69
  T3            4            118
  T4            7             68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  BRD3 MUTATED    7  5  3  1
  BRD3 WILD-TYPE 86 76 47 52
D557V5, multiclass
    clus
vv   BRD3 MUTATED BRD3 WILD-TYPE
  N0            7             86
  N1            5             76
  N2            3             47
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D557V6, binary
                cls
clus               0   1
  BRD3 MUTATED    13   3
  BRD3 WILD-TYPE 244  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD3 MUTATED     13    3
  BRD3 WILD-TYPE  244   15
   clus
vv  BRD3 MUTATED BRD3 WILD-TYPE
  0           13            244
  1            3             15
[1] 2 2
[1] FALSE
D557V7, binary
                cls
clus               0   1
  BRD3 MUTATED     6  10
  BRD3 WILD-TYPE 104 169
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD3 MUTATED      6   10
  BRD3 WILD-TYPE  104  169
        clus
vv       BRD3 MUTATED BRD3 WILD-TYPE
  FEMALE            6            104
  MALE             10            169
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  BRD3 MUTATED                                       1
  BRD3 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BRD3 MUTATED                                                        8
  BRD3 WILD-TYPE                                                    127
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BRD3 MUTATED                                                                   2
  BRD3 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  BRD3 MUTATED                                                  3
  BRD3 WILD-TYPE                                               35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  BRD3 MUTATED                                                          2
  BRD3 WILD-TYPE                                                       14
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  BRD3 MUTATED                                                           0
  BRD3 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  BRD3 MUTATED                                          0
  BRD3 WILD-TYPE                                        3
D557V8, multiclass
                                                                   clus
vv                                                                  BRD3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  BRD3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D557V9, binary
                cls
clus               0   1
  BRD3 MUTATED     1  15
  BRD3 WILD-TYPE   4 269
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD3 MUTATED      1   15
  BRD3 WILD-TYPE    4  269
     clus
vv    BRD3 MUTATED BRD3 WILD-TYPE
  NO             1              4
  YES           15            269
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BRD3 MUTATED    13   0   1   1
  BRD3 WILD-TYPE 214  10   9  23
D557V10, multiclass
    clus
vv   BRD3 MUTATED BRD3 WILD-TYPE
  R0           13            214
  R1            0             10
  R2            1              9
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D557V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BRD3 MUTATED       5                         0     7
  BRD3 WILD-TYPE    71                         4   161
D557V12, multiclass
                           clus
vv                          BRD3 MUTATED BRD3 WILD-TYPE
  ASIAN                                5             71
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                7            161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(558) Variable = PNMT MUTATION ANALYSIS
D558V1, survival
                sevent
clus2              0   1
  PNMT MUTATED     5   1
  PNMT WILD-TYPE 176  79
  PNMT MUTATED PNMT WILD-TYPE 
             6            255 
  PNMT MUTATED PNMT WILD-TYPE 
             1             79 
$`PNMT MUTATED`
TCGA-BR-7715 TCGA-BR-8081 TCGA-BR-A4J7 TCGA-CG-4306 TCGA-CG-5721 TCGA-HU-A4GU 
       15.42        20.55        19.36         1.02         6.02         6.25 

$`PNMT WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        23.93        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       17.49        14.43         0.69        12.26         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  PNMT MUTATED PNMT WILD-TYPE 
          1.02           0.00 
  PNMT MUTATED PNMT WILD-TYPE 
         20.55         105.07 
  PNMT MUTATED PNMT WILD-TYPE 
        10.835         12.620 
[1] "1.0 - 20.6 (10.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.5"
D558V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PNMT MUTATED         0        0        0        1         1         3
  PNMT WILD-TYPE       1        9       27       25        30        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PNMT MUTATED           0          0          0          0        2
  PNMT WILD-TYPE         3         49         36         24       22
D558V3, multiclass
            clus
vv           PNMT MUTATED PNMT WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              1             25
  STAGE IIA             1             30
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PNMT MUTATED     0   1   3   3
  PNMT WILD-TYPE  11  71 119  72
D558V4, multiclass
    clus
vv   PNMT MUTATED PNMT WILD-TYPE
  T1            0             11
  T2            1             71
  T3            3            119
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  PNMT MUTATED    2  4  1  0
  PNMT WILD-TYPE 91 77 49 53
D558V5, multiclass
    clus
vv   PNMT MUTATED PNMT WILD-TYPE
  N0            2             91
  N1            4             77
  N2            1             49
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D558V6, binary
                cls
clus               0   1
  PNMT MUTATED     7   1
  PNMT WILD-TYPE 250  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  PNMT MUTATED      7    1
  PNMT WILD-TYPE  250   17
   clus
vv  PNMT MUTATED PNMT WILD-TYPE
  0            7            250
  1            1             17
[1] 2 2
[1] FALSE
D558V7, binary
                cls
clus               0   1
  PNMT MUTATED     2   6
  PNMT WILD-TYPE 108 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  PNMT MUTATED      2    6
  PNMT WILD-TYPE  108  173
        clus
vv       PNMT MUTATED PNMT WILD-TYPE
  FEMALE            2            108
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PNMT MUTATED                                       1
  PNMT WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PNMT MUTATED                                                        4
  PNMT WILD-TYPE                                                    131
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PNMT MUTATED                                                                   1
  PNMT WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PNMT MUTATED                                                  0
  PNMT WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PNMT MUTATED                                                          2
  PNMT WILD-TYPE                                                       14
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PNMT MUTATED                                                           0
  PNMT WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PNMT MUTATED                                          0
  PNMT WILD-TYPE                                        3
D558V8, multiclass
                                                                   clus
vv                                                                  PNMT MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  PNMT WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D558V9, binary
                cls
clus               0   1
  PNMT MUTATED     1   7
  PNMT WILD-TYPE   4 277
[1] "tbl2"
                cls
clus             [,1] [,2]
  PNMT MUTATED      1    7
  PNMT WILD-TYPE    4  277
     clus
vv    PNMT MUTATED PNMT WILD-TYPE
  NO             1              4
  YES            7            277
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PNMT MUTATED     6   0   1   1
  PNMT WILD-TYPE 221  10   9  23
D558V10, multiclass
    clus
vv   PNMT MUTATED PNMT WILD-TYPE
  R0            6            221
  R1            0             10
  R2            1              9
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D558V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PNMT MUTATED       2                         0     3
  PNMT WILD-TYPE    74                         4   165
D558V12, multiclass
                           clus
vv                          PNMT MUTATED PNMT WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                3            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(559) Variable = IGSF21 MUTATION ANALYSIS
D559V1, survival
                  sevent
clus2                0   1
  IGSF21 MUTATED     2   1
  IGSF21 WILD-TYPE 179  79
  IGSF21 MUTATED IGSF21 WILD-TYPE 
               3              258 
  IGSF21 MUTATED IGSF21 WILD-TYPE 
               1               79 
$`IGSF21 MUTATED`
TCGA-CG-5723 TCGA-CG-5726 TCGA-HU-A4GN 
      105.07        28.96        29.98 

$`IGSF21 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 
        1.02         0.99         6.02         0.99        12.03        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       24.20         3.25        22.75        25.81        11.77         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  IGSF21 MUTATED IGSF21 WILD-TYPE 
           28.96             0.00 
  IGSF21 MUTATED IGSF21 WILD-TYPE 
          105.07            79.07 
  IGSF21 MUTATED IGSF21 WILD-TYPE 
          29.980           12.575 
[1] "29.0 - 105.1 (30.0)" "0.0 - 79.1 (12.6)"  
[1] "hr=" "3.5"
D559V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IGSF21 MUTATED         0        1        0        1         1         0
  IGSF21 WILD-TYPE       1        8       27       25        30        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IGSF21 MUTATED           0          0          0          0        0
  IGSF21 WILD-TYPE         3         49         36         24       24
D559V3, multiclass
            clus
vv           IGSF21 MUTATED IGSF21 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                0               27
  STAGE II                1               25
  STAGE IIA               1               30
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IGSF21 MUTATED     1   2   0   0
  IGSF21 WILD-TYPE  10  70 122  75
D559V4, multiclass
    clus
vv   IGSF21 MUTATED IGSF21 WILD-TYPE
  T1              1               10
  T2              2               70
  T3              0              122
  T4              0               75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  IGSF21 MUTATED    1  2  0  0
  IGSF21 WILD-TYPE 92 79 50 53
D559V5, multiclass
    clus
vv   IGSF21 MUTATED IGSF21 WILD-TYPE
  N0              1               92
  N1              2               79
  N2              0               50
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D559V6, binary
                  cls
clus                 0   1
  IGSF21 MUTATED     3   0
  IGSF21 WILD-TYPE 254  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGSF21 MUTATED      3    0
  IGSF21 WILD-TYPE  254   18
   clus
vv  IGSF21 MUTATED IGSF21 WILD-TYPE
  0              3              254
  1              0               18
[1] 2 2
[1] FALSE
D559V7, binary
                  cls
clus                 0   1
  IGSF21 MUTATED     0   3
  IGSF21 WILD-TYPE 110 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGSF21 MUTATED      0    3
  IGSF21 WILD-TYPE  110  176
        clus
vv       IGSF21 MUTATED IGSF21 WILD-TYPE
  FEMALE              0              110
  MALE                3              176
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  IGSF21 MUTATED                                       0
  IGSF21 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IGSF21 MUTATED                                                        1
  IGSF21 WILD-TYPE                                                    134
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IGSF21 MUTATED                                                                   1
  IGSF21 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  IGSF21 MUTATED                                                  1
  IGSF21 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  IGSF21 MUTATED                                                          0
  IGSF21 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  IGSF21 MUTATED                                                           0
  IGSF21 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  IGSF21 MUTATED                                          0
  IGSF21 WILD-TYPE                                        3
D559V8, multiclass
                                                                   clus
vv                                                                  IGSF21 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         1
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  IGSF21 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D559V9, binary
                  cls
clus                 0   1
  IGSF21 MUTATED     0   3
  IGSF21 WILD-TYPE   5 281
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGSF21 MUTATED      0    3
  IGSF21 WILD-TYPE    5  281
     clus
vv    IGSF21 MUTATED IGSF21 WILD-TYPE
  NO               0                5
  YES              3              281
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  IGSF21 MUTATED     3   0   0   0
  IGSF21 WILD-TYPE 224  10  10  24
D559V10, multiclass
    clus
vv   IGSF21 MUTATED IGSF21 WILD-TYPE
  R0              3              224
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D559V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IGSF21 MUTATED       1                         0     0
  IGSF21 WILD-TYPE    75                         4   168
D559V12, multiclass
[1] "Remove cluster labels:" "IGSF21 MUTATED"        
clus
  IGSF21 MUTATED IGSF21 WILD-TYPE 
               1              247 
      TCGA-B7-5816       TCGA-B7-5818       TCGA-BR-4183       TCGA-BR-4184 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-4187       TCGA-BR-4188       TCGA-BR-4191       TCGA-BR-4201 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-4253       TCGA-BR-4255       TCGA-BR-4256       TCGA-BR-4257 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-4267       TCGA-BR-4279       TCGA-BR-4280       TCGA-BR-4292 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-4294       TCGA-BR-4357       TCGA-BR-4361       TCGA-BR-4362 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-4363       TCGA-BR-4366       TCGA-BR-4368       TCGA-BR-4369 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-4370       TCGA-BR-4371       TCGA-BR-6452       TCGA-BR-6453 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-6454       TCGA-BR-6455       TCGA-BR-6456       TCGA-BR-6457 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-6458       TCGA-BR-6563       TCGA-BR-6564       TCGA-BR-6565 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-6566       TCGA-BR-6705       TCGA-BR-6706       TCGA-BR-6707 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-6710       TCGA-BR-6801       TCGA-BR-6802       TCGA-BR-6803 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-6852       TCGA-BR-7196       TCGA-BR-7197       TCGA-BR-7703 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-7707       TCGA-BR-7715       TCGA-BR-7716       TCGA-BR-7717 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-7722       TCGA-BR-7723       TCGA-BR-7851       TCGA-BR-7901 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-7957       TCGA-BR-7958       TCGA-BR-7959       TCGA-BR-8058 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-8059       TCGA-BR-8077       TCGA-BR-8078       TCGA-BR-8080 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-8081       TCGA-BR-8284       TCGA-BR-8286       TCGA-BR-8289 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-8291       TCGA-BR-8295       TCGA-BR-8296       TCGA-BR-8297 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-8360       TCGA-BR-8361       TCGA-BR-8363       TCGA-BR-8364 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-8365       TCGA-BR-8366       TCGA-BR-8367       TCGA-BR-8368 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-8369       TCGA-BR-8370       TCGA-BR-8371       TCGA-BR-8372 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-8373       TCGA-BR-8380       TCGA-BR-8381       TCGA-BR-8382 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-8384       TCGA-BR-8483       TCGA-BR-8484       TCGA-BR-8485 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-8486       TCGA-BR-8487       TCGA-BR-8588       TCGA-BR-8589 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-8590       TCGA-BR-8591       TCGA-BR-8592       TCGA-BR-8676 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-8677       TCGA-BR-8678       TCGA-BR-8679       TCGA-BR-8680 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-8682       TCGA-BR-8683       TCGA-BR-8686       TCGA-BR-8687 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-8690       TCGA-BR-A44T       TCGA-BR-A44U       TCGA-BR-A452 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-A453       TCGA-BR-A4CQ       TCGA-BR-A4CR       TCGA-BR-A4CS 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-A4IU       TCGA-BR-A4IV       TCGA-BR-A4IY       TCGA-BR-A4IZ 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-A4J1       TCGA-BR-A4J2       TCGA-BR-A4J4       TCGA-BR-A4J6 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-A4J7       TCGA-BR-A4J8       TCGA-BR-A4PD       TCGA-BR-A4PE 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-BR-A4PF       TCGA-BR-A4QI       TCGA-BR-A4QL       TCGA-BR-A4QM 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-CD-5798       TCGA-CD-5799       TCGA-CD-5800       TCGA-CD-5801 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-CD-5802       TCGA-CD-5803       TCGA-CD-5804       TCGA-CD-5813 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-CD-8524       TCGA-CD-8525       TCGA-CD-8526       TCGA-CD-8527 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-CD-8528       TCGA-CD-8529       TCGA-CD-8530       TCGA-CD-8531 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-CD-8532       TCGA-CD-8534       TCGA-CD-8535       TCGA-CD-8536 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-CD-A486       TCGA-CD-A487       TCGA-CD-A489       TCGA-CD-A48A 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-CD-A48C       TCGA-CD-A4MG       TCGA-CD-A4MH       TCGA-CD-A4MI 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-CD-A4MJ       TCGA-D7-5577       TCGA-D7-5578       TCGA-D7-5579 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-D7-6518       TCGA-D7-6519       TCGA-D7-6520       TCGA-D7-6521 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-D7-6522       TCGA-D7-6524       TCGA-D7-6525       TCGA-D7-6526 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-D7-6527       TCGA-D7-6528       TCGA-D7-6815       TCGA-D7-6817 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-D7-6818       TCGA-D7-6820       TCGA-D7-6822       TCGA-D7-8570 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-D7-8572       TCGA-D7-8573       TCGA-D7-8574       TCGA-D7-8575 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-D7-8576       TCGA-D7-8578       TCGA-D7-8579       TCGA-D7-A4YT 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-D7-A4YU       TCGA-D7-A4YV       TCGA-D7-A4YX       TCGA-D7-A4YY 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-D7-A4Z0       TCGA-EQ-5647       TCGA-EQ-8122       TCGA-EQ-A4SO 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-F1-6177       TCGA-F1-6874       TCGA-F1-6875       TCGA-F1-A448 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-FP-7735       TCGA-FP-7829       TCGA-FP-7916       TCGA-FP-7998 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-FP-8099       TCGA-FP-8209       TCGA-FP-8210       TCGA-FP-8211 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-FP-8631       TCGA-FP-A4BE       TCGA-FP-A4BF       TCGA-HJ-7597 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-HU-8243       TCGA-HU-8245       TCGA-HU-8249       TCGA-HU-8602 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-HU-8604       TCGA-HU-8608       TCGA-HU-8610       TCGA-HU-A4G2 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-HU-A4G3       TCGA-HU-A4G6       TCGA-HU-A4G8       TCGA-HU-A4G9 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-HU-A4GC       TCGA-HU-A4GD       TCGA-HU-A4GF       TCGA-HU-A4GH 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-HU-A4GP       TCGA-HU-A4GQ       TCGA-HU-A4GT       TCGA-HU-A4GU 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-HU-A4GX       TCGA-HU-A4GY       TCGA-HU-A4H0       TCGA-HU-A4H2 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-HU-A4H3       TCGA-HU-A4H4       TCGA-HU-A4H5       TCGA-HU-A4H6 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-HU-A4H8       TCGA-HU-A4HD       TCGA-IN-7806       TCGA-IN-7808 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-IN-8462       TCGA-IN-8663       TCGA-IP-7968 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 

Clustering(560) Variable = TAS2R10 MUTATION ANALYSIS
D560V1, survival
                   sevent
clus2                 0   1
  TAS2R10 MUTATED     2   0
  TAS2R10 WILD-TYPE 179  80
  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
                2               259 
  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
                0                80 
$`TAS2R10 MUTATED`
TCGA-HU-A4G8 TCGA-HU-A4GU 
       11.84         6.25 

$`TAS2R10 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
             6.25              0.00 
  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
            11.84            105.07 
  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
            9.045            12.660 
[1] "6.2 - 11.8 (9.0)"   "0.0 - 105.1 (12.7)"
[1] "Remove cluster labels:" "TAS2R10 MUTATED"       
D560V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TAS2R10 MUTATED         1        0        0        0         0         2
  TAS2R10 WILD-TYPE       0        9       27       26        31        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TAS2R10 MUTATED           0          0          0          0        0
  TAS2R10 WILD-TYPE         3         49         36         24       24
D560V3, multiclass
            clus
vv           TAS2R10 MUTATED TAS2R10 WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                 0                 9
  STAGE IB                 0                27
  STAGE II                 0                26
  STAGE IIA                0                31
  STAGE IIB                2                42
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               0                36
  STAGE IIIC               0                24
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TAS2R10 MUTATED     1   0   2   0
  TAS2R10 WILD-TYPE  10  72 120  75
D560V4, multiclass
    clus
vv   TAS2R10 MUTATED TAS2R10 WILD-TYPE
  T1               1                10
  T2               0                72
  T3               2               120
  T4               0                75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  TAS2R10 MUTATED    0  3  0  0
  TAS2R10 WILD-TYPE 93 78 50 53
D560V5, multiclass
    clus
vv   TAS2R10 MUTATED TAS2R10 WILD-TYPE
  N0               0                93
  N1               3                78
  N2               0                50
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D560V6, binary
                   cls
clus                  0   1
  TAS2R10 MUTATED     2   0
  TAS2R10 WILD-TYPE 255  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R10 MUTATED      2    0
  TAS2R10 WILD-TYPE  255   18
   clus
vv  TAS2R10 MUTATED TAS2R10 WILD-TYPE
  0               2               255
  1               0                18
[1] 2 2
[1] FALSE
D560V7, binary
                   cls
clus                  0   1
  TAS2R10 MUTATED     1   2
  TAS2R10 WILD-TYPE 109 177
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R10 MUTATED      1    2
  TAS2R10 WILD-TYPE  109  177
        clus
vv       TAS2R10 MUTATED TAS2R10 WILD-TYPE
  FEMALE               1               109
  MALE                 2               177
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TAS2R10 MUTATED                                       2
  TAS2R10 WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TAS2R10 MUTATED                                                        1
  TAS2R10 WILD-TYPE                                                    134
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TAS2R10 MUTATED                                                                   0
  TAS2R10 WILD-TYPE                                                                40
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TAS2R10 MUTATED                                                  0
  TAS2R10 WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TAS2R10 MUTATED                                                          0
  TAS2R10 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TAS2R10 MUTATED                                                           0
  TAS2R10 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TAS2R10 MUTATED                                          0
  TAS2R10 WILD-TYPE                                        3
D560V8, multiclass
                                                                   clus
vv                                                                  TAS2R10 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          1
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  TAS2R10 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D560V9, binary
                   cls
clus                  0   1
  TAS2R10 MUTATED     0   3
  TAS2R10 WILD-TYPE   5 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R10 MUTATED      0    3
  TAS2R10 WILD-TYPE    5  281
     clus
vv    TAS2R10 MUTATED TAS2R10 WILD-TYPE
  NO                0                 5
  YES               3               281
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TAS2R10 MUTATED     2   0   0   0
  TAS2R10 WILD-TYPE 225  10  10  24
D560V10, multiclass
[1] "Remove cluster labels:" "TAS2R10 MUTATED"       
clus
  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
                2               269 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-4187        TCGA-BR-4188        TCGA-BR-4191        TCGA-BR-4201 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-4294        TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-4363        TCGA-BR-4366        TCGA-BR-4368        TCGA-BR-4369 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-4370        TCGA-BR-4371        TCGA-BR-6452        TCGA-BR-6453 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-6710        TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-6852        TCGA-BR-7196        TCGA-BR-7197        TCGA-BR-7703 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-7707        TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-7722        TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-7957        TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8058 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-8059        TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-8081        TCGA-BR-8284        TCGA-BR-8286        TCGA-BR-8289 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-8360        TCGA-BR-8361        TCGA-BR-8363        TCGA-BR-8364 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-8365        TCGA-BR-8366        TCGA-BR-8367        TCGA-BR-8368 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-8369        TCGA-BR-8370        TCGA-BR-8371        TCGA-BR-8372 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-8373        TCGA-BR-8380        TCGA-BR-8381        TCGA-BR-8382 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-8384        TCGA-BR-8483        TCGA-BR-8484        TCGA-BR-8485 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-8486        TCGA-BR-8487        TCGA-BR-8588        TCGA-BR-8589 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-8590        TCGA-BR-8591        TCGA-BR-8592        TCGA-BR-8676 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-8677        TCGA-BR-8678        TCGA-BR-8679        TCGA-BR-8680 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-8682        TCGA-BR-8683        TCGA-BR-8686        TCGA-BR-8687 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-8690        TCGA-BR-A44T        TCGA-BR-A44U        TCGA-BR-A452 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-A453        TCGA-BR-A4CQ        TCGA-BR-A4CR        TCGA-BR-A4CS 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY        TCGA-BR-A4IZ 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4        TCGA-BR-A4J6 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-A4J7        TCGA-BR-A4J8        TCGA-BR-A4PD        TCGA-BR-A4PE 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-BR-A4QM 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5804        TCGA-CD-8524 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-CD-8525        TCGA-CD-8526        TCGA-CD-8527        TCGA-CD-8528 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-CD-8529        TCGA-CD-8530        TCGA-CD-8531        TCGA-CD-8532 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-CD-8534        TCGA-CD-8535        TCGA-CD-8536        TCGA-CD-A487 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4462 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4474 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-CG-4475        TCGA-CG-4476        TCGA-CG-4477        TCGA-CG-5717 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5726 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-D7-8570        TCGA-D7-8572        TCGA-D7-8573        TCGA-D7-8574 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-D7-8575        TCGA-D7-8576        TCGA-D7-8578        TCGA-D7-8579 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-D7-A4YT        TCGA-D7-A4YU        TCGA-D7-A4YV        TCGA-D7-A4YX 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-D7-A4YY        TCGA-D7-A4Z0        TCGA-EQ-5647        TCGA-EQ-A4SO 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-F1-A448        TCGA-FP-7735 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-FP-8211        TCGA-FP-8631        TCGA-FP-A4BE        TCGA-FP-A4BF 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-HF-7132        TCGA-HF-7133        TCGA-HF-7136        TCGA-HJ-7597 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-HU-8243        TCGA-HU-8245        TCGA-HU-8249        TCGA-HU-8602 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-HU-8604        TCGA-HU-8608        TCGA-HU-8610        TCGA-HU-A4G2 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-HU-A4G3        TCGA-HU-A4G6        TCGA-HU-A4G9        TCGA-HU-A4GC 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-HU-A4GD        TCGA-HU-A4GF        TCGA-HU-A4GH        TCGA-HU-A4GN 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-HU-A4GP        TCGA-HU-A4GQ        TCGA-HU-A4GT        TCGA-HU-A4GX 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-HU-A4GY        TCGA-HU-A4H0        TCGA-HU-A4H2        TCGA-HU-A4H3 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-HU-A4H4        TCGA-HU-A4H5        TCGA-HU-A4H6        TCGA-HU-A4H8 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-HU-A4HD        TCGA-IN-7806        TCGA-IN-8462        TCGA-IN-8663 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-IP-7968 
"TAS2R10 WILD-TYPE" 
D560V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TAS2R10 MUTATED       2                         1     0
  TAS2R10 WILD-TYPE    74                         3   168
D560V12, multiclass
                           clus
vv                          TAS2R10 MUTATED TAS2R10 WILD-TYPE
  ASIAN                                   2                74
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   0               168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(561) Variable = TNKS1BP1 MUTATION ANALYSIS
D561V1, survival
                    sevent
clus2                  0   1
  TNKS1BP1 MUTATED    13   5
  TNKS1BP1 WILD-TYPE 168  75
  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
                18                243 
  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
                 5                 75 
$`TNKS1BP1 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7851 TCGA-BR-8370 TCGA-BR-8372 
        6.97        30.90        34.68        12.43         3.32        19.17 
TCGA-BR-8382 TCGA-BR-A452 TCGA-BR-A4QL TCGA-CD-8529 TCGA-CD-A4MG TCGA-CG-4306 
       15.85         7.53        11.57         0.13         6.58         1.02 
TCGA-CG-4437 TCGA-CG-5721 TCGA-CG-5723 TCGA-FP-A4BE TCGA-HU-A4G8 TCGA-HU-A4G9 
        8.05         6.02       105.07        11.08        11.84        24.20 

$`TNKS1BP1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       15.42        28.01        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       14.04        11.80        14.79         0.26         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56        13.87         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.07         0.10         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       15.95         7.99        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99         0.99        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
        5.03        13.58         0.56         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.30         5.59        12.30         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
              0.13               0.00 
  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
            105.07              79.07 
  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
            11.325             12.790 
[1] "0.1 - 105.1 (11.3)" "0.0 - 79.1 (12.8)" 
[1] "hr=" "1.3"
D561V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TNKS1BP1 MUTATED         0        1        0        2         3         2
  TNKS1BP1 WILD-TYPE       1        8       27       24        28        42
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNKS1BP1 MUTATED           0          3          2          2        3
  TNKS1BP1 WILD-TYPE         3         46         34         22       21
D561V3, multiclass
            clus
vv           TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  1                  8
  STAGE IB                  0                 27
  STAGE II                  2                 24
  STAGE IIA                 3                 28
  STAGE IIB                 2                 42
  STAGE III                 0                  3
  STAGE IIIA                3                 46
  STAGE IIIB                2                 34
  STAGE IIIC                2                 22
  STAGE IV                  3                 21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  TNKS1BP1 MUTATED     1   3   8   7
  TNKS1BP1 WILD-TYPE  10  69 114  68
D561V4, multiclass
    clus
vv   TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  T1                1                 10
  T2                3                 69
  T3                8                114
  T4                7                 68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  TNKS1BP1 MUTATED    7  6  1  4
  TNKS1BP1 WILD-TYPE 86 75 49 49
D561V5, multiclass
    clus
vv   TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  N0                7                 86
  N1                6                 75
  N2                1                 49
  N3                4                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D561V6, binary
                    cls
clus                   0   1
  TNKS1BP1 MUTATED    16   2
  TNKS1BP1 WILD-TYPE 241  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TNKS1BP1 MUTATED     16    2
  TNKS1BP1 WILD-TYPE  241   16
   clus
vv  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  0               16                241
  1                2                 16
[1] 2 2
[1] FALSE
D561V7, binary
                    cls
clus                   0   1
  TNKS1BP1 MUTATED     7  12
  TNKS1BP1 WILD-TYPE 103 167
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TNKS1BP1 MUTATED      7   12
  TNKS1BP1 WILD-TYPE  103  167
        clus
vv       TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  FEMALE                7                103
  MALE                 12                167
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TNKS1BP1 MUTATED                                       3
  TNKS1BP1 WILD-TYPE                                    47
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TNKS1BP1 MUTATED                                                       10
  TNKS1BP1 WILD-TYPE                                                    125
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TNKS1BP1 MUTATED                                                                   3
  TNKS1BP1 WILD-TYPE                                                                37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TNKS1BP1 MUTATED                                                  2
  TNKS1BP1 WILD-TYPE                                               36
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TNKS1BP1 MUTATED                                                          1
  TNKS1BP1 WILD-TYPE                                                       15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TNKS1BP1 MUTATED                                                           0
  TNKS1BP1 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TNKS1BP1 MUTATED                                          0
  TNKS1BP1 WILD-TYPE                                        3
D561V8, multiclass
                                                                   clus
vv                                                                  TNKS1BP1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  TNKS1BP1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D561V9, binary
                    cls
clus                   0   1
  TNKS1BP1 MUTATED     0  19
  TNKS1BP1 WILD-TYPE   5 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TNKS1BP1 MUTATED      0   19
  TNKS1BP1 WILD-TYPE    5  265
     clus
vv    TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  NO                 0                  5
  YES               19                265
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  TNKS1BP1 MUTATED    13   0   1   3
  TNKS1BP1 WILD-TYPE 214  10   9  21
D561V10, multiclass
    clus
vv   TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  R0               13                214
  R1                0                 10
  R2                1                  9
  RX                3                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D561V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TNKS1BP1 MUTATED       5                         1     9
  TNKS1BP1 WILD-TYPE    71                         3   159
D561V12, multiclass
                           clus
vv                          TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  ASIAN                                    5                 71
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                    9                159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(562) Variable = KIRREL2 MUTATION ANALYSIS
D562V1, survival
                   sevent
clus2                 0   1
  KIRREL2 MUTATED     8   2
  KIRREL2 WILD-TYPE 173  78
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
               10               251 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
                2                78 
$`KIRREL2 MUTATED`
TCGA-BR-6566 TCGA-BR-8487 TCGA-BR-8686 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-5721 
       32.78         1.12        15.68        11.57         6.58         6.02 
TCGA-F1-6874 TCGA-FP-7735 TCGA-HU-A4GN TCGA-HU-A4GT 
       14.47         3.48        29.98         6.51 

$`KIRREL2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         9.86         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23        21.27        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       24.20         3.25        22.75        25.81        11.77         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
             1.12              0.00 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
            32.78            105.07 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
            9.075            12.660 
[1] "1.1 - 32.8 (9.1)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.5"
D562V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIRREL2 MUTATED         0        0        3        1         5         0
  KIRREL2 WILD-TYPE       1        9       24       25        26        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIRREL2 MUTATED           0          0          2          0        1
  KIRREL2 WILD-TYPE         3         49         34         24       23
D562V3, multiclass
            clus
vv           KIRREL2 MUTATED KIRREL2 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 3                24
  STAGE II                 1                25
  STAGE IIA                5                26
  STAGE IIB                0                44
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               2                34
  STAGE IIIC               0                24
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  KIRREL2 MUTATED     0   5   5   2
  KIRREL2 WILD-TYPE  11  67 117  73
D562V4, multiclass
    clus
vv   KIRREL2 MUTATED KIRREL2 WILD-TYPE
  T1               0                11
  T2               5                67
  T3               5               117
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  KIRREL2 MUTATED    7  4  0  1
  KIRREL2 WILD-TYPE 86 77 50 52
D562V5, multiclass
    clus
vv   KIRREL2 MUTATED KIRREL2 WILD-TYPE
  N0               7                86
  N1               4                77
  N2               0                50
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D562V6, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED    11   0
  KIRREL2 WILD-TYPE 246  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED     11    0
  KIRREL2 WILD-TYPE  246   18
   clus
vv  KIRREL2 MUTATED KIRREL2 WILD-TYPE
  0              11               246
  1               0                18
[1] 2 2
[1] FALSE
D562V7, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED     4   8
  KIRREL2 WILD-TYPE 106 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED      4    8
  KIRREL2 WILD-TYPE  106  171
        clus
vv       KIRREL2 MUTATED KIRREL2 WILD-TYPE
  FEMALE               4               106
  MALE                 8               171
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KIRREL2 MUTATED                                       1
  KIRREL2 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIRREL2 MUTATED                                                        4
  KIRREL2 WILD-TYPE                                                    131
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIRREL2 MUTATED                                                                   3
  KIRREL2 WILD-TYPE                                                                37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KIRREL2 MUTATED                                                  3
  KIRREL2 WILD-TYPE                                               35
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KIRREL2 MUTATED                                                          1
  KIRREL2 WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KIRREL2 MUTATED                                                           0
  KIRREL2 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KIRREL2 MUTATED                                          0
  KIRREL2 WILD-TYPE                                        3
D562V8, multiclass
                                                                   clus
vv                                                                  KIRREL2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  KIRREL2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D562V9, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED     1  11
  KIRREL2 WILD-TYPE   4 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED      1   11
  KIRREL2 WILD-TYPE    4  273
     clus
vv    KIRREL2 MUTATED KIRREL2 WILD-TYPE
  NO                1                 4
  YES              11               273
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  KIRREL2 MUTATED    11   0   0   0
  KIRREL2 WILD-TYPE 216  10  10  24
D562V10, multiclass
    clus
vv   KIRREL2 MUTATED KIRREL2 WILD-TYPE
  R0              11               216
  R1               0                10
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D562V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIRREL2 MUTATED       4                         1     4
  KIRREL2 WILD-TYPE    72                         3   164
D562V12, multiclass
                           clus
vv                          KIRREL2 MUTATED KIRREL2 WILD-TYPE
  ASIAN                                   4                72
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   4               164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(563) Variable = NID2 MUTATION ANALYSIS
D563V1, survival
                sevent
clus2              0   1
  NID2 MUTATED     9   4
  NID2 WILD-TYPE 172  76
  NID2 MUTATED NID2 WILD-TYPE 
            13            248 
  NID2 MUTATED NID2 WILD-TYPE 
             4             76 
$`NID2 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8368 TCGA-CD-A4MI 
        6.97        30.90        34.68        19.50         4.31         0.10 
TCGA-CD-A4MJ TCGA-CG-5721 TCGA-CG-5733 TCGA-D7-6524 TCGA-HJ-7597 TCGA-HU-A4GN 
       12.62         6.02        21.07        17.85        26.47        29.98 
TCGA-HU-A4GX 
       10.19 

$`NID2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.20        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56        11.08         5.52         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77         8.98         0.10         6.51         6.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  NID2 MUTATED NID2 WILD-TYPE 
           0.1            0.0 
  NID2 MUTATED NID2 WILD-TYPE 
         34.68         105.07 
  NID2 MUTATED NID2 WILD-TYPE 
        17.850         12.575 
[1] "0.1 - 34.7 (17.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D563V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NID2 MUTATED         0        0        3        2         2         0
  NID2 WILD-TYPE       1        9       24       24        29        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NID2 MUTATED           0          2          1          2        1
  NID2 WILD-TYPE         3         47         35         22       23
D563V3, multiclass
            clus
vv           NID2 MUTATED NID2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              3             24
  STAGE II              2             24
  STAGE IIA             2             29
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            1             35
  STAGE IIIC            2             22
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NID2 MUTATED     1   8   3   3
  NID2 WILD-TYPE  10  64 119  72
D563V4, multiclass
    clus
vv   NID2 MUTATED NID2 WILD-TYPE
  T1            1             10
  T2            8             64
  T3            3            119
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  NID2 MUTATED    4  8  3  0
  NID2 WILD-TYPE 89 73 47 53
D563V5, multiclass
    clus
vv   NID2 MUTATED NID2 WILD-TYPE
  N0            4             89
  N1            8             73
  N2            3             47
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D563V6, binary
                cls
clus               0   1
  NID2 MUTATED    15   0
  NID2 WILD-TYPE 242  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  NID2 MUTATED     15    0
  NID2 WILD-TYPE  242   18
   clus
vv  NID2 MUTATED NID2 WILD-TYPE
  0           15            242
  1            0             18
[1] 2 2
[1] FALSE
D563V7, binary
                cls
clus               0   1
  NID2 MUTATED     9   8
  NID2 WILD-TYPE 101 171
[1] "tbl2"
                cls
clus             [,1] [,2]
  NID2 MUTATED      9    8
  NID2 WILD-TYPE  101  171
        clus
vv       NID2 MUTATED NID2 WILD-TYPE
  FEMALE            9            101
  MALE              8            171
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NID2 MUTATED                                       2
  NID2 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NID2 MUTATED                                                       10
  NID2 WILD-TYPE                                                    125
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NID2 MUTATED                                                                   2
  NID2 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NID2 MUTATED                                                  1
  NID2 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NID2 MUTATED                                                          1
  NID2 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NID2 MUTATED                                                           0
  NID2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NID2 MUTATED                                          1
  NID2 WILD-TYPE                                        2
D563V8, multiclass
                                                                   clus
vv                                                                  NID2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  NID2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D563V9, binary
                cls
clus               0   1
  NID2 MUTATED     1  16
  NID2 WILD-TYPE   4 268
[1] "tbl2"
                cls
clus             [,1] [,2]
  NID2 MUTATED      1   16
  NID2 WILD-TYPE    4  268
     clus
vv    NID2 MUTATED NID2 WILD-TYPE
  NO             1              4
  YES           16            268
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NID2 MUTATED     9   1   0   5
  NID2 WILD-TYPE 218   9  10  19
D563V10, multiclass
    clus
vv   NID2 MUTATED NID2 WILD-TYPE
  R0            9            218
  R1            1              9
  R2            0             10
  RX            5             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D563V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NID2 MUTATED       4                         0    10
  NID2 WILD-TYPE    72                         4   158
D563V12, multiclass
                           clus
vv                          NID2 MUTATED NID2 WILD-TYPE
  ASIAN                                4             72
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               10            158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(564) Variable = FOXQ1 MUTATION ANALYSIS
D564V1, survival
                 sevent
clus2               0   1
  FOXQ1 MUTATED     2   1
  FOXQ1 WILD-TYPE 179  79
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              3             258 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              1              79 
$`FOXQ1 MUTATED`
TCGA-BR-7707 TCGA-BR-8078 TCGA-CG-4306 
       23.93        12.26         1.02 

$`FOXQ1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
           1.02            0.00 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
          23.93          105.07 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
          12.26           12.64 
[1] "1.0 - 23.9 (12.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D564V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FOXQ1 MUTATED         0        0        1        0         0         1
  FOXQ1 WILD-TYPE       1        9       26       26        31        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FOXQ1 MUTATED           0          0          0          0        1
  FOXQ1 WILD-TYPE         3         49         36         24       23
D564V3, multiclass
            clus
vv           FOXQ1 MUTATED FOXQ1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              0              31
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FOXQ1 MUTATED     0   1   1   1
  FOXQ1 WILD-TYPE  11  71 121  74
D564V4, multiclass
    clus
vv   FOXQ1 MUTATED FOXQ1 WILD-TYPE
  T1             0              11
  T2             1              71
  T3             1             121
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  FOXQ1 MUTATED    2  0  1  0
  FOXQ1 WILD-TYPE 91 81 49 53
D564V5, multiclass
    clus
vv   FOXQ1 MUTATED FOXQ1 WILD-TYPE
  N0             2              91
  N1             0              81
  N2             1              49
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D564V6, binary
                 cls
clus                0   1
  FOXQ1 MUTATED     2   1
  FOXQ1 WILD-TYPE 255  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED      2    1
  FOXQ1 WILD-TYPE  255   17
   clus
vv  FOXQ1 MUTATED FOXQ1 WILD-TYPE
  0             2             255
  1             1              17
[1] 2 2
[1] FALSE
D564V7, binary
                 cls
clus                0   1
  FOXQ1 MUTATED     2   1
  FOXQ1 WILD-TYPE 108 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED      2    1
  FOXQ1 WILD-TYPE  108  178
        clus
vv       FOXQ1 MUTATED FOXQ1 WILD-TYPE
  FEMALE             2             108
  MALE               1             178
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FOXQ1 MUTATED                                       0
  FOXQ1 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FOXQ1 MUTATED                                                        3
  FOXQ1 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FOXQ1 MUTATED                                                                   0
  FOXQ1 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FOXQ1 MUTATED                                                  0
  FOXQ1 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FOXQ1 MUTATED                                                          0
  FOXQ1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FOXQ1 MUTATED                                                           0
  FOXQ1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FOXQ1 MUTATED                                          0
  FOXQ1 WILD-TYPE                                        3
D564V8, multiclass
                                                                   clus
vv                                                                  FOXQ1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  FOXQ1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D564V9, binary
                 cls
clus                0   1
  FOXQ1 MUTATED     0   3
  FOXQ1 WILD-TYPE   5 281
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED      0    3
  FOXQ1 WILD-TYPE    5  281
     clus
vv    FOXQ1 MUTATED FOXQ1 WILD-TYPE
  NO              0               5
  YES             3             281
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FOXQ1 MUTATED     2   0   1   0
  FOXQ1 WILD-TYPE 225  10   9  24
D564V10, multiclass
    clus
vv   FOXQ1 MUTATED FOXQ1 WILD-TYPE
  R0             2             225
  R1             0              10
  R2             1               9
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D564V11, continuous
[1] "Remove cluster labels:" "FOXQ1 MUTATED"         
clus
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              2             249 
     TCGA-B7-5816      TCGA-BR-4183      TCGA-BR-4184      TCGA-BR-4188 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4191      TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4361 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4362      TCGA-BR-4368      TCGA-BR-6452      TCGA-BR-6453 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6852      TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-7715      TCGA-BR-7716      TCGA-BR-7717      TCGA-BR-7722 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-7723      TCGA-BR-7851      TCGA-BR-7901      TCGA-BR-7957 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-7958      TCGA-BR-7959      TCGA-BR-8058      TCGA-BR-8059 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8077      TCGA-BR-8080      TCGA-BR-8081      TCGA-BR-8284 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8286      TCGA-BR-8289      TCGA-BR-8291      TCGA-BR-8295 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8296      TCGA-BR-8297      TCGA-BR-8360      TCGA-BR-8361 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8363      TCGA-BR-8364      TCGA-BR-8365      TCGA-BR-8366 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8367      TCGA-BR-8368      TCGA-BR-8369      TCGA-BR-8370 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8371      TCGA-BR-8372      TCGA-BR-8373      TCGA-BR-8380 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8381      TCGA-BR-8382      TCGA-BR-8384      TCGA-BR-8483 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8484      TCGA-BR-8485      TCGA-BR-8486      TCGA-BR-8487 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8588      TCGA-BR-8589      TCGA-BR-8590      TCGA-BR-8591 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8592      TCGA-BR-8676      TCGA-BR-8677      TCGA-BR-8678 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8679      TCGA-BR-8680      TCGA-BR-8682      TCGA-BR-8683 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8686      TCGA-BR-8687      TCGA-BR-8690      TCGA-BR-A44T 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A44U      TCGA-BR-A452      TCGA-BR-A453      TCGA-BR-A4CQ 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4CR      TCGA-BR-A4CS      TCGA-BR-A4IU      TCGA-BR-A4IV 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4IY      TCGA-BR-A4IZ      TCGA-BR-A4J1      TCGA-BR-A4J2 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4J4      TCGA-BR-A4J6      TCGA-BR-A4J8      TCGA-BR-A4PD 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4PE      TCGA-BR-A4PF      TCGA-BR-A4QI      TCGA-BR-A4QL 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4QM      TCGA-CD-5804      TCGA-CD-8525      TCGA-CD-8526 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-8531      TCGA-CD-8535      TCGA-CD-A487      TCGA-CG-4301 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CG-4304      TCGA-CG-4305      TCGA-CG-4436      TCGA-CG-4437 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CG-4438      TCGA-CG-4440      TCGA-CG-4441      TCGA-CG-4442 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CG-4443      TCGA-CG-4444      TCGA-CG-4449      TCGA-CG-4455 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CG-4462      TCGA-CG-4465      TCGA-CG-4466      TCGA-CG-4469 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CG-4474      TCGA-CG-4475      TCGA-CG-4476      TCGA-CG-4477 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CG-5717      TCGA-CG-5718      TCGA-CG-5719      TCGA-CG-5720 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CG-5721      TCGA-CG-5722      TCGA-CG-5723      TCGA-CG-5724 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CG-5726      TCGA-CG-5727      TCGA-CG-5728      TCGA-CG-5730 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CG-5732      TCGA-CG-5733      TCGA-CG-5734      TCGA-D7-5577 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-5578      TCGA-D7-5579      TCGA-D7-6518      TCGA-D7-6519 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-6520      TCGA-D7-6521      TCGA-D7-6522      TCGA-D7-6524 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-6525      TCGA-D7-6526      TCGA-D7-6527      TCGA-D7-6528 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-6815      TCGA-D7-6817      TCGA-D7-6818      TCGA-D7-6820 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-6822      TCGA-D7-8570      TCGA-D7-8572      TCGA-D7-8573 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-8574      TCGA-D7-8575      TCGA-D7-8576      TCGA-D7-8578 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-8579      TCGA-D7-A4YT      TCGA-D7-A4YU      TCGA-D7-A4YV 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-A4YX      TCGA-D7-A4YY      TCGA-D7-A4Z0      TCGA-EQ-5647 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-EQ-8122      TCGA-EQ-A4SO      TCGA-F1-6177      TCGA-F1-6874 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-F1-6875      TCGA-F1-A448      TCGA-FP-7735      TCGA-FP-7829 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FP-7916      TCGA-FP-7998      TCGA-FP-8099      TCGA-FP-8209 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FP-8210      TCGA-FP-8211      TCGA-FP-8631      TCGA-FP-A4BE 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FP-A4BF      TCGA-HF-7132      TCGA-HF-7133      TCGA-HF-7136 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HJ-7597      TCGA-HU-8243      TCGA-HU-8245      TCGA-HU-8249 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-8602      TCGA-HU-8604      TCGA-HU-8608      TCGA-HU-8610 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4G2      TCGA-HU-A4G3      TCGA-HU-A4G6      TCGA-HU-A4G8 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD      TCGA-HU-A4GF 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4GH      TCGA-HU-A4GN      TCGA-HU-A4GP      TCGA-HU-A4GQ 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX      TCGA-HU-A4GY 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3      TCGA-HU-A4H4 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8      TCGA-HU-A4HD 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-IN-7806      TCGA-IN-7808      TCGA-IN-8462      TCGA-IN-8663 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-IP-7968 
"FOXQ1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FOXQ1 MUTATED       0                         0     2
  FOXQ1 WILD-TYPE    76                         4   166
D564V12, multiclass
[1] "Remove cluster labels:" "FOXQ1 MUTATED"         
clus
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              2             246 
     TCGA-B7-5816      TCGA-B7-5818      TCGA-BR-4183      TCGA-BR-4184 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4187      TCGA-BR-4188      TCGA-BR-4191      TCGA-BR-4201 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256      TCGA-BR-4257 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4292 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4294      TCGA-BR-4357      TCGA-BR-4361      TCGA-BR-4362 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4363      TCGA-BR-4366      TCGA-BR-4368      TCGA-BR-4369 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4370      TCGA-BR-4371      TCGA-BR-6452      TCGA-BR-6453 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6852      TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-7715      TCGA-BR-7716      TCGA-BR-7717      TCGA-BR-7722 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-7723      TCGA-BR-7851      TCGA-BR-7901      TCGA-BR-7957 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-7958      TCGA-BR-7959      TCGA-BR-8058      TCGA-BR-8059 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8077      TCGA-BR-8080      TCGA-BR-8081      TCGA-BR-8284 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8286      TCGA-BR-8289      TCGA-BR-8291      TCGA-BR-8295 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8296      TCGA-BR-8297      TCGA-BR-8360      TCGA-BR-8361 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8363      TCGA-BR-8364      TCGA-BR-8365      TCGA-BR-8366 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8367      TCGA-BR-8368      TCGA-BR-8369      TCGA-BR-8370 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8371      TCGA-BR-8372      TCGA-BR-8373      TCGA-BR-8380 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8381      TCGA-BR-8382      TCGA-BR-8384      TCGA-BR-8483 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8484      TCGA-BR-8485      TCGA-BR-8486      TCGA-BR-8487 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8588      TCGA-BR-8589      TCGA-BR-8590      TCGA-BR-8591 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8592      TCGA-BR-8676      TCGA-BR-8677      TCGA-BR-8678 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8679      TCGA-BR-8680      TCGA-BR-8682      TCGA-BR-8683 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8686      TCGA-BR-8687      TCGA-BR-8690      TCGA-BR-A44T 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A44U      TCGA-BR-A452      TCGA-BR-A453      TCGA-BR-A4CQ 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4CR      TCGA-BR-A4CS      TCGA-BR-A4IU      TCGA-BR-A4IV 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4IY      TCGA-BR-A4IZ      TCGA-BR-A4J1      TCGA-BR-A4J2 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4J4      TCGA-BR-A4J6      TCGA-BR-A4J7      TCGA-BR-A4J8 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4PD      TCGA-BR-A4PE      TCGA-BR-A4PF      TCGA-BR-A4QI 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4QL      TCGA-BR-A4QM      TCGA-CD-5798      TCGA-CD-5799 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-5800      TCGA-CD-5801      TCGA-CD-5802      TCGA-CD-5803 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-5804      TCGA-CD-5813      TCGA-CD-8524      TCGA-CD-8525 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-8526      TCGA-CD-8527      TCGA-CD-8528      TCGA-CD-8529 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-8530      TCGA-CD-8531      TCGA-CD-8532      TCGA-CD-8534 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-8535      TCGA-CD-8536      TCGA-CD-A486      TCGA-CD-A487 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-A489      TCGA-CD-A48A      TCGA-CD-A48C      TCGA-CD-A4MG 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-A4MH      TCGA-CD-A4MI      TCGA-CD-A4MJ      TCGA-D7-5577 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-5578      TCGA-D7-5579      TCGA-D7-6518      TCGA-D7-6519 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-6520      TCGA-D7-6521      TCGA-D7-6522      TCGA-D7-6524 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-6525      TCGA-D7-6526      TCGA-D7-6527      TCGA-D7-6528 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-6815      TCGA-D7-6817      TCGA-D7-6818      TCGA-D7-6820 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-6822      TCGA-D7-8570      TCGA-D7-8572      TCGA-D7-8573 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-8574      TCGA-D7-8575      TCGA-D7-8576      TCGA-D7-8578 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-8579      TCGA-D7-A4YT      TCGA-D7-A4YU      TCGA-D7-A4YV 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-A4YX      TCGA-D7-A4YY      TCGA-D7-A4Z0      TCGA-EQ-5647 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-EQ-8122      TCGA-EQ-A4SO      TCGA-F1-6177      TCGA-F1-6874 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-F1-6875      TCGA-F1-A448      TCGA-FP-7735      TCGA-FP-7829 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FP-7916      TCGA-FP-7998      TCGA-FP-8099      TCGA-FP-8209 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FP-8210      TCGA-FP-8211      TCGA-FP-8631      TCGA-FP-A4BE 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FP-A4BF      TCGA-HJ-7597      TCGA-HU-8243      TCGA-HU-8245 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-8249      TCGA-HU-8602      TCGA-HU-8604      TCGA-HU-8608 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-8610      TCGA-HU-A4G2      TCGA-HU-A4G3      TCGA-HU-A4G6 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4G8      TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4GF      TCGA-HU-A4GH      TCGA-HU-A4GN      TCGA-HU-A4GP 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4GQ      TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4GY      TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4H4      TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4HD      TCGA-IN-7806      TCGA-IN-7808      TCGA-IN-8462 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-IN-8663      TCGA-IP-7968 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 

Clustering(565) Variable = SMAD2 MUTATION ANALYSIS
D565V1, survival
                 sevent
clus2               0   1
  SMAD2 MUTATED     7   1
  SMAD2 WILD-TYPE 174  79
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              8             253 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              1              79 
$`SMAD2 MUTATED`
TCGA-BR-6452 TCGA-BR-7851 TCGA-BR-A4QL TCGA-CG-4444 TCGA-CG-4462 TCGA-F1-A448 
       34.68        12.43        11.57        47.05         0.00        21.27 
TCGA-HU-8604 TCGA-HU-A4H3 
       12.10        19.36 

$`SMAD2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       16.24        14.47        72.23         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       11.41        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  SMAD2 MUTATED SMAD2 WILD-TYPE 
           0.00            0.07 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
          47.05          105.07 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
         15.895          12.620 
[1] "0.0 - 47.0 (15.9)"  "0.1 - 105.1 (12.6)"
[1] "hr=" "3.6"
D565V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMAD2 MUTATED         0        0        0        0         2         1
  SMAD2 WILD-TYPE       1        9       27       26        29        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMAD2 MUTATED           0          1          2          1        1
  SMAD2 WILD-TYPE         3         48         34         23       23
D565V3, multiclass
            clus
vv           SMAD2 MUTATED SMAD2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             2              34
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SMAD2 MUTATED     0   2   5   2
  SMAD2 WILD-TYPE  11  70 117  73
D565V4, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  T1             0              11
  T2             2              70
  T3             5             117
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  SMAD2 MUTATED    3  0  1  4
  SMAD2 WILD-TYPE 90 81 49 49
D565V5, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  N0             3              90
  N1             0              81
  N2             1              49
  N3             4              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D565V6, binary
                 cls
clus                0   1
  SMAD2 MUTATED     8   1
  SMAD2 WILD-TYPE 249  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      8    1
  SMAD2 WILD-TYPE  249   17
   clus
vv  SMAD2 MUTATED SMAD2 WILD-TYPE
  0             8             249
  1             1              17
[1] 2 2
[1] FALSE
D565V7, binary
                 cls
clus                0   1
  SMAD2 MUTATED     6   3
  SMAD2 WILD-TYPE 104 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      6    3
  SMAD2 WILD-TYPE  104  176
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  FEMALE             6             104
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SMAD2 MUTATED                                       3
  SMAD2 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SMAD2 MUTATED                                                        3
  SMAD2 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SMAD2 MUTATED                                                                   1
  SMAD2 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SMAD2 MUTATED                                                  1
  SMAD2 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SMAD2 MUTATED                                                          1
  SMAD2 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SMAD2 MUTATED                                                           0
  SMAD2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SMAD2 MUTATED                                          0
  SMAD2 WILD-TYPE                                        3
D565V8, multiclass
                                                                   clus
vv                                                                  SMAD2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  SMAD2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D565V9, binary
                 cls
clus                0   1
  SMAD2 MUTATED     0   9
  SMAD2 WILD-TYPE   5 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      0    9
  SMAD2 WILD-TYPE    5  275
     clus
vv    SMAD2 MUTATED SMAD2 WILD-TYPE
  NO              0               5
  YES             9             275
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SMAD2 MUTATED     7   0   1   1
  SMAD2 WILD-TYPE 220  10   9  23
D565V10, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             1               9
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D565V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMAD2 MUTATED       2                         0     5
  SMAD2 WILD-TYPE    74                         4   163
D565V12, multiclass
                           clus
vv                          SMAD2 MUTATED SMAD2 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(566) Variable = LARP1 MUTATION ANALYSIS
D566V1, survival
                 sevent
clus2               0   1
  LARP1 MUTATED     4   2
  LARP1 WILD-TYPE 177  78
  LARP1 MUTATED LARP1 WILD-TYPE 
              6             255 
  LARP1 MUTATED LARP1 WILD-TYPE 
              2              78 
$`LARP1 MUTATED`
TCGA-BR-6452 TCGA-BR-6707 TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-5726 
       34.68        19.89        12.26         1.12        15.81        28.96 

$`LARP1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-6801 
        9.17        32.78        25.61        18.05         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  LARP1 MUTATED LARP1 WILD-TYPE 
           1.12            0.00 
  LARP1 MUTATED LARP1 WILD-TYPE 
          34.68          105.07 
  LARP1 MUTATED LARP1 WILD-TYPE 
          17.85           12.59 
[1] "1.1 - 34.7 (17.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D566V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LARP1 MUTATED         0        1        0        1         3         1
  LARP1 WILD-TYPE       1        8       27       25        28        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LARP1 MUTATED           0          0          0          0        1
  LARP1 WILD-TYPE         3         49         36         24       23
D566V3, multiclass
            clus
vv           LARP1 MUTATED LARP1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              3              28
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LARP1 MUTATED     1   1   3   2
  LARP1 WILD-TYPE  10  71 119  73
D566V4, multiclass
    clus
vv   LARP1 MUTATED LARP1 WILD-TYPE
  T1             1              10
  T2             1              71
  T3             3             119
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  LARP1 MUTATED    5  2  1  0
  LARP1 WILD-TYPE 88 79 49 53
D566V5, multiclass
    clus
vv   LARP1 MUTATED LARP1 WILD-TYPE
  N0             5              88
  N1             2              79
  N2             1              49
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D566V6, binary
                 cls
clus                0   1
  LARP1 MUTATED     9   1
  LARP1 WILD-TYPE 248  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP1 MUTATED      9    1
  LARP1 WILD-TYPE  248   17
   clus
vv  LARP1 MUTATED LARP1 WILD-TYPE
  0             9             248
  1             1              17
[1] 2 2
[1] FALSE
D566V7, binary
                 cls
clus                0   1
  LARP1 MUTATED     5   5
  LARP1 WILD-TYPE 105 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP1 MUTATED      5    5
  LARP1 WILD-TYPE  105  174
        clus
vv       LARP1 MUTATED LARP1 WILD-TYPE
  FEMALE             5             105
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  LARP1 MUTATED                                       0
  LARP1 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LARP1 MUTATED                                                        7
  LARP1 WILD-TYPE                                                    128
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LARP1 MUTATED                                                                   1
  LARP1 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  LARP1 MUTATED                                                  1
  LARP1 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  LARP1 MUTATED                                                          1
  LARP1 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  LARP1 MUTATED                                                           0
  LARP1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  LARP1 MUTATED                                          0
  LARP1 WILD-TYPE                                        3
D566V8, multiclass
                                                                   clus
vv                                                                  LARP1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  LARP1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D566V9, binary
                 cls
clus                0   1
  LARP1 MUTATED     1   9
  LARP1 WILD-TYPE   4 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP1 MUTATED      1    9
  LARP1 WILD-TYPE    4  275
     clus
vv    LARP1 MUTATED LARP1 WILD-TYPE
  NO              1               4
  YES             9             275
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LARP1 MUTATED     7   0   0   3
  LARP1 WILD-TYPE 220  10  10  21
D566V10, multiclass
    clus
vv   LARP1 MUTATED LARP1 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D566V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LARP1 MUTATED       1                         0     7
  LARP1 WILD-TYPE    75                         4   161
D566V12, multiclass
                           clus
vv                          LARP1 MUTATED LARP1 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 7             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(567) Variable = FAM186B MUTATION ANALYSIS
D567V1, survival
                   sevent
clus2                 0   1
  FAM186B MUTATED     5   4
  FAM186B WILD-TYPE 176  76
  FAM186B MUTATED FAM186B WILD-TYPE 
                9               252 
  FAM186B MUTATED FAM186B WILD-TYPE 
                4                76 
$`FAM186B MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6852 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CG-4462 
        6.97        30.90        32.94         1.12         6.58         0.00 
TCGA-F1-6874 TCGA-HU-8602 TCGA-HU-A4GT 
       14.47        11.41         6.51 

$`FAM186B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 
       14.01        29.98        47.05        19.07        12.03         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        5.52        26.47         5.92        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  FAM186B MUTATED FAM186B WILD-TYPE 
             0.00              0.07 
  FAM186B MUTATED FAM186B WILD-TYPE 
            32.94            105.07 
  FAM186B MUTATED FAM186B WILD-TYPE 
             6.97             12.71 
[1] "0.0 - 32.9 (7.0)"   "0.1 - 105.1 (12.7)"
[1] "hr=" "1.6"
D567V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM186B MUTATED         0        0        1        0         4         1
  FAM186B WILD-TYPE       1        9       26       26        27        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM186B MUTATED           0          1          0          0        1
  FAM186B WILD-TYPE         3         48         36         24       23
D567V3, multiclass
            clus
vv           FAM186B MUTATED FAM186B WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 0                26
  STAGE IIA                4                27
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               0                36
  STAGE IIIC               0                24
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM186B MUTATED     0   2   7   1
  FAM186B WILD-TYPE  11  70 115  74
D567V4, multiclass
    clus
vv   FAM186B MUTATED FAM186B WILD-TYPE
  T1               0                11
  T2               2                70
  T3               7               115
  T4               1                74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  FAM186B MUTATED    6  1  0  1
  FAM186B WILD-TYPE 87 80 50 52
D567V5, multiclass
    clus
vv   FAM186B MUTATED FAM186B WILD-TYPE
  N0               6                87
  N1               1                80
  N2               0                50
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D567V6, binary
                   cls
clus                  0   1
  FAM186B MUTATED     7   1
  FAM186B WILD-TYPE 250  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM186B MUTATED      7    1
  FAM186B WILD-TYPE  250   17
   clus
vv  FAM186B MUTATED FAM186B WILD-TYPE
  0               7               250
  1               1                17
[1] 2 2
[1] FALSE
D567V7, binary
                   cls
clus                  0   1
  FAM186B MUTATED     7   3
  FAM186B WILD-TYPE 103 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM186B MUTATED      7    3
  FAM186B WILD-TYPE  103  176
        clus
vv       FAM186B MUTATED FAM186B WILD-TYPE
  FEMALE               7               103
  MALE                 3               176
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FAM186B MUTATED                                       3
  FAM186B WILD-TYPE                                    47
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAM186B MUTATED                                                        5
  FAM186B WILD-TYPE                                                    130
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAM186B MUTATED                                                                   1
  FAM186B WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FAM186B MUTATED                                                  1
  FAM186B WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FAM186B MUTATED                                                          0
  FAM186B WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FAM186B MUTATED                                                           0
  FAM186B WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FAM186B MUTATED                                          0
  FAM186B WILD-TYPE                                        3
D567V8, multiclass
                                                                   clus
vv                                                                  FAM186B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  FAM186B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D567V9, binary
                   cls
clus                  0   1
  FAM186B MUTATED     0  10
  FAM186B WILD-TYPE   5 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM186B MUTATED      0   10
  FAM186B WILD-TYPE    5  274
     clus
vv    FAM186B MUTATED FAM186B WILD-TYPE
  NO                0                 5
  YES              10               274
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM186B MUTATED     5   0   1   3
  FAM186B WILD-TYPE 222  10   9  21
D567V10, multiclass
    clus
vv   FAM186B MUTATED FAM186B WILD-TYPE
  R0               5               222
  R1               0                10
  R2               1                 9
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D567V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM186B MUTATED       3                         0     6
  FAM186B WILD-TYPE    73                         4   162
D567V12, multiclass
                           clus
vv                          FAM186B MUTATED FAM186B WILD-TYPE
  ASIAN                                   3                73
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   6               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(568) Variable = TBC1D23 MUTATION ANALYSIS
D568V1, survival
                   sevent
clus2                 0   1
  TBC1D23 MUTATED     2   1
  TBC1D23 WILD-TYPE 179  79
  TBC1D23 MUTATED TBC1D23 WILD-TYPE 
                3               258 
  TBC1D23 MUTATED TBC1D23 WILD-TYPE 
                1                79 
$`TBC1D23 MUTATED`
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
        0.10         6.51        10.19 

$`TBC1D23 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
       11.77        29.98         8.98         6.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  TBC1D23 MUTATED TBC1D23 WILD-TYPE 
              0.1               0.0 
  TBC1D23 MUTATED TBC1D23 WILD-TYPE 
            10.19            105.07 
  TBC1D23 MUTATED TBC1D23 WILD-TYPE 
             6.51             12.71 
[1] "0.1 - 10.2 (6.5)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "3.1"
D568V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TBC1D23 MUTATED         0        0        0        0         1         0
  TBC1D23 WILD-TYPE       1        9       27       26        30        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBC1D23 MUTATED           0          0          0          2        0
  TBC1D23 WILD-TYPE         3         49         36         22       24
D568V3, multiclass
            clus
vv           TBC1D23 MUTATED TBC1D23 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 0                27
  STAGE II                 0                26
  STAGE IIA                1                30
  STAGE IIB                0                44
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               0                36
  STAGE IIIC               2                22
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TBC1D23 MUTATED     0   0   1   2
  TBC1D23 WILD-TYPE  11  72 121  73
D568V4, multiclass
    clus
vv   TBC1D23 MUTATED TBC1D23 WILD-TYPE
  T1               0                11
  T2               0                72
  T3               1               121
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  TBC1D23 MUTATED    1  0  2  0
  TBC1D23 WILD-TYPE 92 81 48 53
D568V5, multiclass
    clus
vv   TBC1D23 MUTATED TBC1D23 WILD-TYPE
  N0               1                92
  N1               0                81
  N2               2                48
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D568V6, binary
                   cls
clus                  0   1
  TBC1D23 MUTATED     4   0
  TBC1D23 WILD-TYPE 253  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D23 MUTATED      4    0
  TBC1D23 WILD-TYPE  253   18
   clus
vv  TBC1D23 MUTATED TBC1D23 WILD-TYPE
  0               4               253
  1               0                18
[1] 2 2
[1] FALSE
D568V7, binary
                   cls
clus                  0   1
  TBC1D23 MUTATED     3   1
  TBC1D23 WILD-TYPE 107 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D23 MUTATED      3    1
  TBC1D23 WILD-TYPE  107  178
        clus
vv       TBC1D23 MUTATED TBC1D23 WILD-TYPE
  FEMALE               3               107
  MALE                 1               178
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TBC1D23 MUTATED                                       1
  TBC1D23 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TBC1D23 MUTATED                                                        1
  TBC1D23 WILD-TYPE                                                    134
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TBC1D23 MUTATED                                                                   0
  TBC1D23 WILD-TYPE                                                                40
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TBC1D23 MUTATED                                                  2
  TBC1D23 WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TBC1D23 MUTATED                                                          0
  TBC1D23 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TBC1D23 MUTATED                                                           0
  TBC1D23 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TBC1D23 MUTATED                                          0
  TBC1D23 WILD-TYPE                                        3
D568V8, multiclass
                                                                   clus
vv                                                                  TBC1D23 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          1
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  TBC1D23 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D568V9, binary
                   cls
clus                  0   1
  TBC1D23 MUTATED     0   4
  TBC1D23 WILD-TYPE   5 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D23 MUTATED      0    4
  TBC1D23 WILD-TYPE    5  280
     clus
vv    TBC1D23 MUTATED TBC1D23 WILD-TYPE
  NO                0                 5
  YES               4               280
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TBC1D23 MUTATED     3   0   0   1
  TBC1D23 WILD-TYPE 224  10  10  23
D568V10, multiclass
    clus
vv   TBC1D23 MUTATED TBC1D23 WILD-TYPE
  R0               3               224
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D568V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TBC1D23 MUTATED       3                         0     1
  TBC1D23 WILD-TYPE    73                         4   167
D568V12, multiclass
                           clus
vv                          TBC1D23 MUTATED TBC1D23 WILD-TYPE
  ASIAN                                   3                73
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   1               167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(569) Variable = UGP2 MUTATION ANALYSIS
D569V1, survival
                sevent
clus2              0   1
  UGP2 MUTATED     6   0
  UGP2 WILD-TYPE 175  80
  UGP2 MUTATED UGP2 WILD-TYPE 
             6            255 
  UGP2 MUTATED UGP2 WILD-TYPE 
             0             80 
$`UGP2 MUTATED`
TCGA-BR-7707 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CG-5723 TCGA-CG-5728 
       23.93        13.45        11.57         0.10       105.07        65.10 

$`UGP2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        79.07         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  UGP2 MUTATED UGP2 WILD-TYPE 
           0.1            0.0 
  UGP2 MUTATED UGP2 WILD-TYPE 
        105.07          79.07 
  UGP2 MUTATED UGP2 WILD-TYPE 
         18.69          12.59 
[1] "0.1 - 105.1 (18.7)" "0.0 - 79.1 (12.6)" 
[1] "hr="   "3e+07"
D569V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UGP2 MUTATED         0        0        2        2         0         0
  UGP2 WILD-TYPE       1        9       25       24        31        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UGP2 MUTATED           0          0          1          1        0
  UGP2 WILD-TYPE         3         49         35         23       24
D569V3, multiclass
            clus
vv           UGP2 MUTATED UGP2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              2             24
  STAGE IIA             0             31
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            1             35
  STAGE IIIC            1             23
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  UGP2 MUTATED     0   3   2   1
  UGP2 WILD-TYPE  11  69 120  74
D569V4, multiclass
    clus
vv   UGP2 MUTATED UGP2 WILD-TYPE
  T1            0             11
  T2            3             69
  T3            2            120
  T4            1             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  UGP2 MUTATED    3  2  0  2
  UGP2 WILD-TYPE 90 79 50 51
D569V5, multiclass
    clus
vv   UGP2 MUTATED UGP2 WILD-TYPE
  N0            3             90
  N1            2             79
  N2            0             50
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D569V6, binary
                cls
clus               0   1
  UGP2 MUTATED     7   0
  UGP2 WILD-TYPE 250  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGP2 MUTATED      7    0
  UGP2 WILD-TYPE  250   18
   clus
vv  UGP2 MUTATED UGP2 WILD-TYPE
  0            7            250
  1            0             18
[1] 2 2
[1] FALSE
D569V7, binary
                cls
clus               0   1
  UGP2 MUTATED     4   3
  UGP2 WILD-TYPE 106 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGP2 MUTATED      4    3
  UGP2 WILD-TYPE  106  176
        clus
vv       UGP2 MUTATED UGP2 WILD-TYPE
  FEMALE            4            106
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  UGP2 MUTATED                                       0
  UGP2 WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  UGP2 MUTATED                                                        6
  UGP2 WILD-TYPE                                                    129
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  UGP2 MUTATED                                                                   1
  UGP2 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  UGP2 MUTATED                                                  0
  UGP2 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  UGP2 MUTATED                                                          0
  UGP2 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  UGP2 MUTATED                                                           0
  UGP2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  UGP2 MUTATED                                          0
  UGP2 WILD-TYPE                                        3
D569V8, multiclass
                                                                   clus
vv                                                                  UGP2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  UGP2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D569V9, binary
                cls
clus               0   1
  UGP2 MUTATED     0   7
  UGP2 WILD-TYPE   5 277
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGP2 MUTATED      0    7
  UGP2 WILD-TYPE    5  277
     clus
vv    UGP2 MUTATED UGP2 WILD-TYPE
  NO             0              5
  YES            7            277
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  UGP2 MUTATED     6   0   0   1
  UGP2 WILD-TYPE 221  10  10  23
D569V10, multiclass
    clus
vv   UGP2 MUTATED UGP2 WILD-TYPE
  R0            6            221
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D569V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UGP2 MUTATED       1                         0     4
  UGP2 WILD-TYPE    75                         4   164
D569V12, multiclass
                           clus
vv                          UGP2 MUTATED UGP2 WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                4            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(570) Variable = FBN3 MUTATION ANALYSIS
D570V1, survival
                sevent
clus2              0   1
  FBN3 MUTATED    17   8
  FBN3 WILD-TYPE 164  72
  FBN3 MUTATED FBN3 WILD-TYPE 
            25            236 
  FBN3 MUTATED FBN3 WILD-TYPE 
             8             72 
$`FBN3 MUTATED`
TCGA-BR-4183 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6801 
        6.61         6.61        34.68         9.17        32.78        21.11 
TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8372 
       23.93        12.43        12.26         4.31        11.80        19.17 
TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4CS TCGA-CD-5801 TCGA-CD-A4MG 
       15.85         1.12        15.81         1.48        13.18         6.58 
TCGA-CG-4305 TCGA-CG-4469 TCGA-CG-5721 TCGA-HU-A4G9 TCGA-HU-A4GT TCGA-HU-A4GU 
       15.95         7.07         6.02        24.20         6.51         6.25 
TCGA-HU-A4H5 
       12.30 

$`FBN3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       30.90         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 
       13.68        19.33        39.12        26.10        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       19.89         8.98        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       14.04         3.32        14.79         0.26         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08        22.26        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.15         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
        0.10        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        11.84         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  FBN3 MUTATED FBN3 WILD-TYPE 
          1.12           0.00 
  FBN3 MUTATED FBN3 WILD-TYPE 
         34.68         105.07 
  FBN3 MUTATED FBN3 WILD-TYPE 
        12.260         12.775 
[1] "1.1 - 34.7 (12.3)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.2"
D570V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FBN3 MUTATED         0        1        4        1         6         4
  FBN3 WILD-TYPE       1        8       23       25        25        40
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBN3 MUTATED           1          3          1          3        3
  FBN3 WILD-TYPE         2         46         35         21       21
D570V3, multiclass
            clus
vv           FBN3 MUTATED FBN3 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              4             23
  STAGE II              1             25
  STAGE IIA             6             25
  STAGE IIB             4             40
  STAGE III             1              2
  STAGE IIIA            3             46
  STAGE IIIB            1             35
  STAGE IIIC            3             21
  STAGE IV              3             21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FBN3 MUTATED     1   6  11   9
  FBN3 WILD-TYPE  10  66 111  66
D570V4, multiclass
    clus
vv   FBN3 MUTATED FBN3 WILD-TYPE
  T1            1             10
  T2            6             66
  T3           11            111
  T4            9             66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  FBN3 MUTATED   15  7  1  5
  FBN3 WILD-TYPE 78 74 49 48
D570V5, multiclass
    clus
vv   FBN3 MUTATED FBN3 WILD-TYPE
  N0           15             78
  N1            7             74
  N2            1             49
  N3            5             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D570V6, binary
                cls
clus               0   1
  FBN3 MUTATED    27   1
  FBN3 WILD-TYPE 230  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN3 MUTATED     27    1
  FBN3 WILD-TYPE  230   17
   clus
vv  FBN3 MUTATED FBN3 WILD-TYPE
  0           27            230
  1            1             17
[1] 2 2
[1] FALSE
D570V7, binary
                cls
clus               0   1
  FBN3 MUTATED    13  15
  FBN3 WILD-TYPE  97 164
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN3 MUTATED     13   15
  FBN3 WILD-TYPE   97  164
        clus
vv       FBN3 MUTATED FBN3 WILD-TYPE
  FEMALE           13             97
  MALE             15            164
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FBN3 MUTATED                                       2
  FBN3 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FBN3 MUTATED                                                       18
  FBN3 WILD-TYPE                                                    117
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FBN3 MUTATED                                                                   4
  FBN3 WILD-TYPE                                                                36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FBN3 MUTATED                                                  3
  FBN3 WILD-TYPE                                               35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FBN3 MUTATED                                                          0
  FBN3 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FBN3 MUTATED                                                           1
  FBN3 WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FBN3 MUTATED                                          0
  FBN3 WILD-TYPE                                        3
D570V8, multiclass
                                                                   clus
vv                                                                  FBN3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      18
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  FBN3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       117
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D570V9, binary
                cls
clus               0   1
  FBN3 MUTATED     0  28
  FBN3 WILD-TYPE   5 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN3 MUTATED      0   28
  FBN3 WILD-TYPE    5  256
     clus
vv    FBN3 MUTATED FBN3 WILD-TYPE
  NO             0              5
  YES           28            256
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FBN3 MUTATED    22   1   0   4
  FBN3 WILD-TYPE 205   9  10  20
D570V10, multiclass
    clus
vv   FBN3 MUTATED FBN3 WILD-TYPE
  R0           22            205
  R1            1              9
  R2            0             10
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D570V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FBN3 MUTATED       7                         0    17
  FBN3 WILD-TYPE    69                         4   151
D570V12, multiclass
                           clus
vv                          FBN3 MUTATED FBN3 WILD-TYPE
  ASIAN                                7             69
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               17            151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(571) Variable = IK MUTATION ANALYSIS
D571V1, survival
              sevent
clus2            0   1
  IK MUTATED     3   2
  IK WILD-TYPE 178  78
  IK MUTATED IK WILD-TYPE 
           5          256 
  IK MUTATED IK WILD-TYPE 
           2           78 
$`IK MUTATED`
TCGA-BR-4280 TCGA-BR-6452 TCGA-CD-8529 TCGA-D7-A4YV TCGA-HU-A4HD 
        6.61        34.68         0.13         5.92        27.42 

$`IK WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
       18.35        30.90         6.18         9.57        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.10         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       14.27        16.44        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-IN-7806 
       19.36        23.84        12.30         9.67         8.88        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  IK MUTATED IK WILD-TYPE 
        0.13         0.00 
  IK MUTATED IK WILD-TYPE 
       34.68       105.07 
  IK MUTATED IK WILD-TYPE 
        6.61        12.64 
[1] "0.1 - 34.7 (6.6)"   "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D571V2, continuous
              vv
clus           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  IK MUTATED         0        0        1        0         1         1         1
  IK WILD-TYPE       1        9       26       26        30        43         2
              vv
clus           STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IK MUTATED            1          0          0        1
  IK WILD-TYPE         48         36         24       23
D571V3, multiclass
            clus
vv           IK MUTATED IK WILD-TYPE
  STAGE I             0            1
  STAGE IA            0            9
  STAGE IB            1           26
  STAGE II            0           26
  STAGE IIA           1           30
  STAGE IIB           1           43
  STAGE III           1            2
  STAGE IIIA          1           48
  STAGE IIIB          0           36
  STAGE IIIC          0           24
  STAGE IV            1           23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            T1  T2  T3  T4
  IK MUTATED     0   2   3   1
  IK WILD-TYPE  11  70 119  74
D571V4, multiclass
    clus
vv   IK MUTATED IK WILD-TYPE
  T1          0           11
  T2          2           70
  T3          3          119
  T4          1           74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           N0 N1 N2 N3
  IK MUTATED    3  2  1  0
  IK WILD-TYPE 90 79 49 53
D571V5, multiclass
    clus
vv   IK MUTATED IK WILD-TYPE
  N0          3           90
  N1          2           79
  N2          1           49
  N3          0           53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D571V6, binary
              cls
clus             0   1
  IK MUTATED     5   1
  IK WILD-TYPE 252  17
[1] "tbl2"
              cls
clus           [,1] [,2]
  IK MUTATED      5    1
  IK WILD-TYPE  252   17
   clus
vv  IK MUTATED IK WILD-TYPE
  0          5          252
  1          1           17
[1] 2 2
[1] FALSE
D571V7, binary
              cls
clus             0   1
  IK MUTATED     3   3
  IK WILD-TYPE 107 176
[1] "tbl2"
              cls
clus           [,1] [,2]
  IK MUTATED      3    3
  IK WILD-TYPE  107  176
        clus
vv       IK MUTATED IK WILD-TYPE
  FEMALE          3          107
  MALE            3          176
[1] 2 2
[1] FALSE
              vv
clus           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  IK MUTATED                                       0
  IK WILD-TYPE                                    50
              vv
clus           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IK MUTATED                                                        2
  IK WILD-TYPE                                                    133
              vv
clus           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IK MUTATED                                                                   1
  IK WILD-TYPE                                                                39
              vv
clus           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  IK MUTATED                                                  2
  IK WILD-TYPE                                               36
              vv
clus           STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  IK MUTATED                                                          1
  IK WILD-TYPE                                                       15
              vv
clus           STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  IK MUTATED                                                           0
  IK WILD-TYPE                                                         6
              vv
clus           STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  IK MUTATED                                          0
  IK WILD-TYPE                                        3
D571V8, multiclass
                                                                   clus
vv                                                                  IK MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                      0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                     2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)          1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                           2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                   1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                  0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                   0
                                                                   clus
vv                                                                  IK WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                     133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D571V9, binary
              cls
clus             0   1
  IK MUTATED     0   6
  IK WILD-TYPE   5 278
[1] "tbl2"
              cls
clus           [,1] [,2]
  IK MUTATED      0    6
  IK WILD-TYPE    5  278
     clus
vv    IK MUTATED IK WILD-TYPE
  NO           0            5
  YES          6          278
[1] 2 2
[1] FALSE
              vv
clus            R0  R1  R2  RX
  IK MUTATED     5   0   0   1
  IK WILD-TYPE 222  10  10  23
D571V10, multiclass
    clus
vv   IK MUTATED IK WILD-TYPE
  R0          5          222
  R1          0           10
  R2          0           10
  RX          1           23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D571V11, continuous
              vv
clus           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IK MUTATED       2                         0     3
  IK WILD-TYPE    74                         4   165
D571V12, multiclass
                           clus
vv                          IK MUTATED IK WILD-TYPE
  ASIAN                              2           74
  BLACK OR AFRICAN AMERICAN          0            4
  WHITE                              3          165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(572) Variable = FAHD2B MUTATION ANALYSIS
D572V1, survival
                  sevent
clus2                0   1
  FAHD2B MUTATED     3   2
  FAHD2B WILD-TYPE 178  78
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               5              256 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               2               78 
$`FAHD2B MUTATED`
TCGA-BR-4201 TCGA-BR-8680 TCGA-CD-8536 TCGA-CD-A4MJ TCGA-CG-4306 
       30.90        15.81         0.10        12.62         1.02 

$`FAHD2B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  FAHD2B MUTATED FAHD2B WILD-TYPE 
             0.1              0.0 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
           30.90           105.07 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
          12.620           12.625 
[1] "0.1 - 30.9 (12.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D572V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAHD2B MUTATED         0        0        1        1         0         0
  FAHD2B WILD-TYPE       1        9       26       25        31        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAHD2B MUTATED           0          0          0          0        2
  FAHD2B WILD-TYPE         3         49         36         24       22
D572V3, multiclass
            clus
vv           FAHD2B MUTATED FAHD2B WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                1               25
  STAGE IIA               0               31
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAHD2B MUTATED     0   2   2   1
  FAHD2B WILD-TYPE  11  70 120  74
D572V4, multiclass
    clus
vv   FAHD2B MUTATED FAHD2B WILD-TYPE
  T1              0               11
  T2              2               70
  T3              2              120
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  FAHD2B MUTATED    2  0  2  0
  FAHD2B WILD-TYPE 91 81 48 53
D572V5, multiclass
    clus
vv   FAHD2B MUTATED FAHD2B WILD-TYPE
  N0              2               91
  N1              0               81
  N2              2               48
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D572V6, binary
                  cls
clus                 0   1
  FAHD2B MUTATED     3   2
  FAHD2B WILD-TYPE 254  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2B MUTATED      3    2
  FAHD2B WILD-TYPE  254   16
   clus
vv  FAHD2B MUTATED FAHD2B WILD-TYPE
  0              3              254
  1              2               16
[1] 2 2
[1] FALSE
D572V7, binary
                  cls
clus                 0   1
  FAHD2B MUTATED     1   4
  FAHD2B WILD-TYPE 109 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2B MUTATED      1    4
  FAHD2B WILD-TYPE  109  175
        clus
vv       FAHD2B MUTATED FAHD2B WILD-TYPE
  FEMALE              1              109
  MALE                4              175
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FAHD2B MUTATED                                       0
  FAHD2B WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAHD2B MUTATED                                                        4
  FAHD2B WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAHD2B MUTATED                                                                   0
  FAHD2B WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FAHD2B MUTATED                                                  1
  FAHD2B WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FAHD2B MUTATED                                                          0
  FAHD2B WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FAHD2B MUTATED                                                           0
  FAHD2B WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FAHD2B MUTATED                                          0
  FAHD2B WILD-TYPE                                        3
D572V8, multiclass
                                                                   clus
vv                                                                  FAHD2B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  FAHD2B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D572V9, binary
                  cls
clus                 0   1
  FAHD2B MUTATED     0   5
  FAHD2B WILD-TYPE   5 279
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2B MUTATED      0    5
  FAHD2B WILD-TYPE    5  279
     clus
vv    FAHD2B MUTATED FAHD2B WILD-TYPE
  NO               0                5
  YES              5              279
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FAHD2B MUTATED     2   0   1   1
  FAHD2B WILD-TYPE 225  10   9  23
D572V10, multiclass
    clus
vv   FAHD2B MUTATED FAHD2B WILD-TYPE
  R0              2              225
  R1              0               10
  R2              1                9
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D572V11, continuous
[1] "Remove cluster labels:" "FAHD2B MUTATED"        
clus
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               1              250 
      TCGA-B7-5816       TCGA-BR-4183       TCGA-BR-4184       TCGA-BR-4188 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-4191       TCGA-BR-4253       TCGA-BR-4255       TCGA-BR-4256 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-4267       TCGA-BR-4279       TCGA-BR-4280       TCGA-BR-4361 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-4362       TCGA-BR-4368       TCGA-BR-6452       TCGA-BR-6453 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-6454       TCGA-BR-6455       TCGA-BR-6456       TCGA-BR-6457 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-6458       TCGA-BR-6563       TCGA-BR-6564       TCGA-BR-6565 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-6566       TCGA-BR-6705       TCGA-BR-6706       TCGA-BR-6707 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-6710       TCGA-BR-6801       TCGA-BR-6802       TCGA-BR-6803 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-6852       TCGA-BR-7196       TCGA-BR-7197       TCGA-BR-7703 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-7707       TCGA-BR-7715       TCGA-BR-7716       TCGA-BR-7717 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-7722       TCGA-BR-7723       TCGA-BR-7851       TCGA-BR-7901 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-7957       TCGA-BR-7958       TCGA-BR-7959       TCGA-BR-8058 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-8059       TCGA-BR-8077       TCGA-BR-8078       TCGA-BR-8080 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-8081       TCGA-BR-8284       TCGA-BR-8286       TCGA-BR-8289 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-8291       TCGA-BR-8295       TCGA-BR-8296       TCGA-BR-8297 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-8360       TCGA-BR-8361       TCGA-BR-8363       TCGA-BR-8364 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-8365       TCGA-BR-8366       TCGA-BR-8367       TCGA-BR-8368 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-8369       TCGA-BR-8370       TCGA-BR-8371       TCGA-BR-8372 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-8373       TCGA-BR-8380       TCGA-BR-8381       TCGA-BR-8382 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-8384       TCGA-BR-8483       TCGA-BR-8484       TCGA-BR-8485 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-8486       TCGA-BR-8487       TCGA-BR-8588       TCGA-BR-8589 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-8590       TCGA-BR-8591       TCGA-BR-8592       TCGA-BR-8676 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-8677       TCGA-BR-8678       TCGA-BR-8679       TCGA-BR-8682 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-8683       TCGA-BR-8686       TCGA-BR-8687       TCGA-BR-8690 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-A44T       TCGA-BR-A44U       TCGA-BR-A452       TCGA-BR-A453 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-A4CQ       TCGA-BR-A4CR       TCGA-BR-A4CS       TCGA-BR-A4IU 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-A4IV       TCGA-BR-A4IY       TCGA-BR-A4IZ       TCGA-BR-A4J1 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-A4J2       TCGA-BR-A4J4       TCGA-BR-A4J6       TCGA-BR-A4J8 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-A4PD       TCGA-BR-A4PE       TCGA-BR-A4PF       TCGA-BR-A4QI 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-BR-A4QL       TCGA-BR-A4QM       TCGA-CD-5804       TCGA-CD-8525 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-CD-8526       TCGA-CD-8531       TCGA-CD-8535       TCGA-CD-A487 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-CG-4301       TCGA-CG-4304       TCGA-CG-4305       TCGA-CG-4436 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-CG-4437       TCGA-CG-4438       TCGA-CG-4440       TCGA-CG-4441 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-CG-4442       TCGA-CG-4443       TCGA-CG-4444       TCGA-CG-4449 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-CG-4455       TCGA-CG-4462       TCGA-CG-4465       TCGA-CG-4466 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-CG-4469       TCGA-CG-4474       TCGA-CG-4475       TCGA-CG-4476 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-CG-4477       TCGA-CG-5717       TCGA-CG-5718       TCGA-CG-5719 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-CG-5720       TCGA-CG-5721       TCGA-CG-5722       TCGA-CG-5723 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-CG-5724       TCGA-CG-5726       TCGA-CG-5727       TCGA-CG-5728 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-CG-5730       TCGA-CG-5732       TCGA-CG-5733       TCGA-CG-5734 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-D7-5577       TCGA-D7-5578       TCGA-D7-5579       TCGA-D7-6518 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-D7-6519       TCGA-D7-6520       TCGA-D7-6521       TCGA-D7-6522 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-D7-6524       TCGA-D7-6525       TCGA-D7-6526       TCGA-D7-6527 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-D7-6528       TCGA-D7-6815       TCGA-D7-6817       TCGA-D7-6818 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-D7-6820       TCGA-D7-6822       TCGA-D7-8570       TCGA-D7-8572 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-D7-8573       TCGA-D7-8574       TCGA-D7-8575       TCGA-D7-8576 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-D7-8578       TCGA-D7-8579       TCGA-D7-A4YT       TCGA-D7-A4YU 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-D7-A4YV       TCGA-D7-A4YX       TCGA-D7-A4YY       TCGA-D7-A4Z0 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-EQ-5647       TCGA-EQ-8122       TCGA-EQ-A4SO       TCGA-F1-6177 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-F1-6874       TCGA-F1-6875       TCGA-F1-A448       TCGA-FP-7735 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-FP-7829       TCGA-FP-7916       TCGA-FP-7998       TCGA-FP-8099 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-FP-8209       TCGA-FP-8210       TCGA-FP-8211       TCGA-FP-8631 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-FP-A4BE       TCGA-FP-A4BF       TCGA-HF-7132       TCGA-HF-7133 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-HF-7136       TCGA-HJ-7597       TCGA-HU-8243       TCGA-HU-8245 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-HU-8249       TCGA-HU-8602       TCGA-HU-8604       TCGA-HU-8608 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-HU-8610       TCGA-HU-A4G2       TCGA-HU-A4G3       TCGA-HU-A4G6 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-HU-A4G8       TCGA-HU-A4G9       TCGA-HU-A4GC       TCGA-HU-A4GD 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-HU-A4GF       TCGA-HU-A4GH       TCGA-HU-A4GN       TCGA-HU-A4GP 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-HU-A4GQ       TCGA-HU-A4GT       TCGA-HU-A4GU       TCGA-HU-A4GX 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-HU-A4GY       TCGA-HU-A4H0       TCGA-HU-A4H2       TCGA-HU-A4H3 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-HU-A4H4       TCGA-HU-A4H5       TCGA-HU-A4H6       TCGA-HU-A4H8 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-HU-A4HD       TCGA-IN-7806       TCGA-IN-7808       TCGA-IN-8462 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-IN-8663       TCGA-IP-7968 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAHD2B MUTATED       3                         0     1
  FAHD2B WILD-TYPE    73                         4   167
D572V12, multiclass
                           clus
vv                          FAHD2B MUTATED FAHD2B WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  1              167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(573) Variable = GPC4 MUTATION ANALYSIS
D573V1, survival
                sevent
clus2              0   1
  GPC4 MUTATED     8   0
  GPC4 WILD-TYPE 173  80
  GPC4 MUTATED GPC4 WILD-TYPE 
             8            253 
  GPC4 MUTATED GPC4 WILD-TYPE 
             0             80 
$`GPC4 MUTATED`
TCGA-BR-7703 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8486 TCGA-CG-4437 
       24.76        12.26        19.50         4.31        20.22         8.05 
TCGA-F1-A448 TCGA-FP-A4BE 
       21.27        11.08 

$`GPC4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 
       15.85         3.72         5.39        25.18         9.21         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         7.99        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        72.23         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  GPC4 MUTATED GPC4 WILD-TYPE 
          4.31           0.00 
  GPC4 MUTATED GPC4 WILD-TYPE 
         24.76         105.07 
  GPC4 MUTATED GPC4 WILD-TYPE 
         15.88          12.62 
[1] "4.3 - 24.8 (15.9)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "2.6e+07"
D573V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPC4 MUTATED         0        2        1        1         1         1
  GPC4 WILD-TYPE       1        7       26       25        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPC4 MUTATED           0          0          1          1        0
  GPC4 WILD-TYPE         3         49         35         23       24
D573V3, multiclass
            clus
vv           GPC4 MUTATED GPC4 WILD-TYPE
  STAGE I               0              1
  STAGE IA              2              7
  STAGE IB              1             26
  STAGE II              1             25
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            1             35
  STAGE IIIC            1             23
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GPC4 MUTATED     3   2   2   2
  GPC4 WILD-TYPE   8  70 120  73
D573V4, multiclass
    clus
vv   GPC4 MUTATED GPC4 WILD-TYPE
  T1            3              8
  T2            2             70
  T3            2            120
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  GPC4 MUTATED    5  1  1  1
  GPC4 WILD-TYPE 88 80 49 52
D573V5, multiclass
    clus
vv   GPC4 MUTATED GPC4 WILD-TYPE
  N0            5             88
  N1            1             80
  N2            1             49
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D573V6, binary
                cls
clus               0   1
  GPC4 MUTATED     9   0
  GPC4 WILD-TYPE 248  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPC4 MUTATED      9    0
  GPC4 WILD-TYPE  248   18
   clus
vv  GPC4 MUTATED GPC4 WILD-TYPE
  0            9            248
  1            0             18
[1] 2 2
[1] FALSE
D573V7, binary
                cls
clus               0   1
  GPC4 MUTATED     5   4
  GPC4 WILD-TYPE 105 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPC4 MUTATED      5    4
  GPC4 WILD-TYPE  105  175
        clus
vv       GPC4 MUTATED GPC4 WILD-TYPE
  FEMALE            5            105
  MALE              4            175
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GPC4 MUTATED                                       0
  GPC4 WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPC4 MUTATED                                                        6
  GPC4 WILD-TYPE                                                    129
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPC4 MUTATED                                                                   1
  GPC4 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GPC4 MUTATED                                                  0
  GPC4 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GPC4 MUTATED                                                          1
  GPC4 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GPC4 MUTATED                                                           1
  GPC4 WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GPC4 MUTATED                                          0
  GPC4 WILD-TYPE                                        3
D573V8, multiclass
                                                                   clus
vv                                                                  GPC4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  GPC4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D573V9, binary
                cls
clus               0   1
  GPC4 MUTATED     0   9
  GPC4 WILD-TYPE   5 275
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPC4 MUTATED      0    9
  GPC4 WILD-TYPE    5  275
     clus
vv    GPC4 MUTATED GPC4 WILD-TYPE
  NO             0              5
  YES            9            275
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GPC4 MUTATED     8   0   0   1
  GPC4 WILD-TYPE 219  10  10  23
D573V10, multiclass
    clus
vv   GPC4 MUTATED GPC4 WILD-TYPE
  R0            8            219
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D573V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPC4 MUTATED       0                         1     7
  GPC4 WILD-TYPE    76                         3   161
D573V12, multiclass
                           clus
vv                          GPC4 MUTATED GPC4 WILD-TYPE
  ASIAN                                0             76
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                                7            161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(574) Variable = CLGN MUTATION ANALYSIS
D574V1, survival
                sevent
clus2              0   1
  CLGN MUTATED     5   1
  CLGN WILD-TYPE 176  79
  CLGN MUTATED CLGN WILD-TYPE 
             6            255 
  CLGN MUTATED CLGN WILD-TYPE 
             1             79 
$`CLGN MUTATED`
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8361 TCGA-CD-A4MI TCGA-CG-5721 
        6.61        34.68         6.18        19.50         0.10         6.02 

$`CLGN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
       18.35        30.90         6.18         9.57        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  CLGN MUTATED CLGN WILD-TYPE 
           0.1            0.0 
  CLGN MUTATED CLGN WILD-TYPE 
         34.68         105.07 
  CLGN MUTATED CLGN WILD-TYPE 
         6.395         12.660 
[1] "0.1 - 34.7 (6.4)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.6"
D574V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CLGN MUTATED         0        0        0        0         2         0
  CLGN WILD-TYPE       1        9       27       26        29        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLGN MUTATED           1          1          1          1        1
  CLGN WILD-TYPE         2         48         35         23       23
D574V3, multiclass
            clus
vv           CLGN MUTATED CLGN WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              0             26
  STAGE IIA             2             29
  STAGE IIB             0             44
  STAGE III             1              2
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            1             23
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CLGN MUTATED     0   1   3   3
  CLGN WILD-TYPE  11  71 119  72
D574V4, multiclass
    clus
vv   CLGN MUTATED CLGN WILD-TYPE
  T1            0             11
  T2            1             71
  T3            3            119
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  CLGN MUTATED    3  3  1  0
  CLGN WILD-TYPE 90 78 49 53
D574V5, multiclass
    clus
vv   CLGN MUTATED CLGN WILD-TYPE
  N0            3             90
  N1            3             78
  N2            1             49
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D574V6, binary
                cls
clus               0   1
  CLGN MUTATED     8   0
  CLGN WILD-TYPE 249  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLGN MUTATED      8    0
  CLGN WILD-TYPE  249   18
   clus
vv  CLGN MUTATED CLGN WILD-TYPE
  0            8            249
  1            0             18
[1] 2 2
[1] FALSE
D574V7, binary
                cls
clus               0   1
  CLGN MUTATED     5   3
  CLGN WILD-TYPE 105 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLGN MUTATED      5    3
  CLGN WILD-TYPE  105  176
        clus
vv       CLGN MUTATED CLGN WILD-TYPE
  FEMALE            5            105
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CLGN MUTATED                                       0
  CLGN WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CLGN MUTATED                                                        6
  CLGN WILD-TYPE                                                    129
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CLGN MUTATED                                                                   2
  CLGN WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CLGN MUTATED                                                  0
  CLGN WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CLGN MUTATED                                                          0
  CLGN WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CLGN MUTATED                                                           0
  CLGN WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CLGN MUTATED                                          0
  CLGN WILD-TYPE                                        3
D574V8, multiclass
                                                                   clus
vv                                                                  CLGN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  CLGN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D574V9, binary
                cls
clus               0   1
  CLGN MUTATED     0   8
  CLGN WILD-TYPE   5 276
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLGN MUTATED      0    8
  CLGN WILD-TYPE    5  276
     clus
vv    CLGN MUTATED CLGN WILD-TYPE
  NO             0              5
  YES            8            276
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CLGN MUTATED     4   0   0   3
  CLGN WILD-TYPE 223  10  10  21
D574V10, multiclass
    clus
vv   CLGN MUTATED CLGN WILD-TYPE
  R0            4            223
  R1            0             10
  R2            0             10
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D574V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CLGN MUTATED       1                         0     6
  CLGN WILD-TYPE    75                         4   162
D574V12, multiclass
                           clus
vv                          CLGN MUTATED CLGN WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                6            162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(575) Variable = NF1 MUTATION ANALYSIS
D575V1, survival
               sevent
clus2             0   1
  NF1 MUTATED    10   6
  NF1 WILD-TYPE 171  74
  NF1 MUTATED NF1 WILD-TYPE 
           16           245 
  NF1 MUTATED NF1 WILD-TYPE 
            6            74 
$`NF1 MUTATED`
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8680 
       20.55         8.05         0.26        19.17        15.85        15.81 
TCGA-BR-A44U TCGA-CD-A4MG TCGA-CG-4440 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5728 
       13.87         6.58         4.01         6.02         0.99        65.10 
TCGA-FP-8211 TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H3 
       13.58         0.10         6.51        19.36 

$`NF1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        19.50        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       10.68        12.56         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        8.05        54.08        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5723 
       30.97         6.97        36.00         1.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        79.07         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BE 
       22.29        17.06        59.54         5.03         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       12.95        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  NF1 MUTATED NF1 WILD-TYPE 
          0.1           0.0 
  NF1 MUTATED NF1 WILD-TYPE 
        65.10        105.07 
  NF1 MUTATED NF1 WILD-TYPE 
       10.815        12.620 
[1] "0.1 - 65.1 (10.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D575V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NF1 MUTATED         1        0        3        0         2         2
  NF1 WILD-TYPE       0        9       24       26        29        42
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NF1 MUTATED           0          1          1          5        4
  NF1 WILD-TYPE         3         48         35         19       20
D575V3, multiclass
            clus
vv           NF1 MUTATED NF1 WILD-TYPE
  STAGE I              1             0
  STAGE IA             0             9
  STAGE IB             3            24
  STAGE II             0            26
  STAGE IIA            2            29
  STAGE IIB            2            42
  STAGE III            0             3
  STAGE IIIA           1            48
  STAGE IIIB           1            35
  STAGE IIIC           5            19
  STAGE IV             4            20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NF1 MUTATED     2   4   7   9
  NF1 WILD-TYPE   9  68 115  66
D575V4, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  T1           2             9
  T2           4            68
  T3           7           115
  T4           9            66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  NF1 MUTATED    7  5  3  6
  NF1 WILD-TYPE 86 76 47 47
D575V5, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  N0           7            86
  N1           5            76
  N2           3            47
  N3           6            47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D575V6, binary
               cls
clus              0   1
  NF1 MUTATED    19   3
  NF1 WILD-TYPE 238  15
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     19    3
  NF1 WILD-TYPE  238   15
   clus
vv  NF1 MUTATED NF1 WILD-TYPE
  0          19           238
  1           3            15
[1] 2 2
[1] FALSE
D575V7, binary
               cls
clus              0   1
  NF1 MUTATED    14  11
  NF1 WILD-TYPE  96 168
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     14   11
  NF1 WILD-TYPE   96  168
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE          14            96
  MALE            11           168
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NF1 MUTATED                                       2
  NF1 WILD-TYPE                                    48
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NF1 MUTATED                                                       14
  NF1 WILD-TYPE                                                    121
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NF1 MUTATED                                                                   6
  NF1 WILD-TYPE                                                                34
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NF1 MUTATED                                                  3
  NF1 WILD-TYPE                                               35
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NF1 MUTATED                                                          0
  NF1 WILD-TYPE                                                       16
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NF1 MUTATED                                                           0
  NF1 WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NF1 MUTATED                                          0
  NF1 WILD-TYPE                                        3
D575V8, multiclass
                                                                   clus
vv                                                                  NF1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                     14
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  NF1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      121
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D575V9, binary
               cls
clus              0   1
  NF1 MUTATED     0  25
  NF1 WILD-TYPE   5 259
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      0   25
  NF1 WILD-TYPE    5  259
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO            0             5
  YES          25           259
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  NF1 MUTATED    14   1   2   7
  NF1 WILD-TYPE 213   9   8  17
D575V10, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  R0          14           213
  R1           1             9
  R2           2             8
  RX           7            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D575V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NF1 MUTATED       5                         1    14
  NF1 WILD-TYPE    71                         3   154
D575V12, multiclass
                           clus
vv                          NF1 MUTATED NF1 WILD-TYPE
  ASIAN                               5            71
  BLACK OR AFRICAN AMERICAN           1             3
  WHITE                              14           154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(576) Variable = LCE1A MUTATION ANALYSIS
D576V1, survival
                 sevent
clus2               0   1
  LCE1A MUTATED     2   1
  LCE1A WILD-TYPE 179  79
  LCE1A MUTATED LCE1A WILD-TYPE 
              3             258 
  LCE1A MUTATED LCE1A WILD-TYPE 
              1              79 
$`LCE1A MUTATED`
TCGA-BR-8297 TCGA-BR-A452 TCGA-BR-A4PD 
        7.40         7.53        20.65 

$`LCE1A WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56        13.87         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        19.36        13.51        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  LCE1A MUTATED LCE1A WILD-TYPE 
            7.4             0.0 
  LCE1A MUTATED LCE1A WILD-TYPE 
          20.65          105.07 
  LCE1A MUTATED LCE1A WILD-TYPE 
           7.53           12.64 
[1] "7.4 - 20.6 (7.5)"   "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D576V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LCE1A MUTATED         0        0        0        0         0         1
  LCE1A WILD-TYPE       1        9       27       26        31        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LCE1A MUTATED           0          1          0          1        0
  LCE1A WILD-TYPE         3         48         36         23       24
D576V3, multiclass
            clus
vv           LCE1A MUTATED LCE1A WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              0              31
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LCE1A MUTATED     0   0   0   3
  LCE1A WILD-TYPE  11  72 122  72
D576V4, multiclass
    clus
vv   LCE1A MUTATED LCE1A WILD-TYPE
  T1             0              11
  T2             0              72
  T3             0             122
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  LCE1A MUTATED    1  1  0  1
  LCE1A WILD-TYPE 92 80 50 52
D576V5, multiclass
    clus
vv   LCE1A MUTATED LCE1A WILD-TYPE
  N0             1              92
  N1             1              80
  N2             0              50
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D576V6, binary
                 cls
clus                0   1
  LCE1A MUTATED     3   0
  LCE1A WILD-TYPE 254  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE1A MUTATED      3    0
  LCE1A WILD-TYPE  254   18
   clus
vv  LCE1A MUTATED LCE1A WILD-TYPE
  0             3             254
  1             0              18
[1] 2 2
[1] FALSE
D576V7, binary
                 cls
clus                0   1
  LCE1A MUTATED     1   2
  LCE1A WILD-TYPE 109 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE1A MUTATED      1    2
  LCE1A WILD-TYPE  109  177
        clus
vv       LCE1A MUTATED LCE1A WILD-TYPE
  FEMALE             1             109
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  LCE1A MUTATED                                       1
  LCE1A WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LCE1A MUTATED                                                        1
  LCE1A WILD-TYPE                                                    134
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LCE1A MUTATED                                                                   0
  LCE1A WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  LCE1A MUTATED                                                  1
  LCE1A WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  LCE1A MUTATED                                                          0
  LCE1A WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  LCE1A MUTATED                                                           0
  LCE1A WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  LCE1A MUTATED                                          0
  LCE1A WILD-TYPE                                        3
D576V8, multiclass
                                                                   clus
vv                                                                  LCE1A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        1
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  LCE1A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D576V9, binary
                 cls
clus                0   1
  LCE1A MUTATED     0   3
  LCE1A WILD-TYPE   5 281
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE1A MUTATED      0    3
  LCE1A WILD-TYPE    5  281
     clus
vv    LCE1A MUTATED LCE1A WILD-TYPE
  NO              0               5
  YES             3             281
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LCE1A MUTATED     3   0   0   0
  LCE1A WILD-TYPE 224  10  10  24
D576V10, multiclass
    clus
vv   LCE1A MUTATED LCE1A WILD-TYPE
  R0             3             224
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D576V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LCE1A MUTATED       1                         0     2
  LCE1A WILD-TYPE    75                         4   166
D576V12, multiclass
                           clus
vv                          LCE1A MUTATED LCE1A WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 2             166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(577) Variable = NBN MUTATION ANALYSIS
D577V1, survival
               sevent
clus2             0   1
  NBN MUTATED     6   3
  NBN WILD-TYPE 175  77
  NBN MUTATED NBN WILD-TYPE 
            9           252 
  NBN MUTATED NBN WILD-TYPE 
            3            77 
$`NBN MUTATED`
TCGA-BR-6801 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48C TCGA-CG-4306 TCGA-HU-A4G8 
       21.11         0.10         3.42        11.61         1.02        11.84 
TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H8 
        0.10        10.19         8.88 

$`NBN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.10         0.13         9.34        11.31        12.43 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       11.77        29.98         8.98         6.51         6.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  NBN MUTATED NBN WILD-TYPE 
          0.1           0.0 
  NBN MUTATED NBN WILD-TYPE 
        21.11        105.07 
  NBN MUTATED NBN WILD-TYPE 
         8.88         12.79 
[1] "0.1 - 21.1 (8.9)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "2.1"
D577V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NBN MUTATED         0        0        1        2         2         2
  NBN WILD-TYPE       1        9       26       24        29        42
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NBN MUTATED           0          1          0          2        1
  NBN WILD-TYPE         3         48         36         22       23
D577V3, multiclass
            clus
vv           NBN MUTATED NBN WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             9
  STAGE IB             1            26
  STAGE II             2            24
  STAGE IIA            2            29
  STAGE IIB            2            42
  STAGE III            0             3
  STAGE IIIA           1            48
  STAGE IIIB           0            36
  STAGE IIIC           2            22
  STAGE IV             1            23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NBN MUTATED     1   1   6   3
  NBN WILD-TYPE  10  71 116  72
D577V4, multiclass
    clus
vv   NBN MUTATED NBN WILD-TYPE
  T1           1            10
  T2           1            71
  T3           6           116
  T4           3            72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  NBN MUTATED    4  5  3  0
  NBN WILD-TYPE 89 76 47 53
D577V5, multiclass
    clus
vv   NBN MUTATED NBN WILD-TYPE
  N0           4            89
  N1           5            76
  N2           3            47
  N3           0            53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D577V6, binary
               cls
clus              0   1
  NBN MUTATED    12   1
  NBN WILD-TYPE 245  17
[1] "tbl2"
               cls
clus            [,1] [,2]
  NBN MUTATED     12    1
  NBN WILD-TYPE  245   17
   clus
vv  NBN MUTATED NBN WILD-TYPE
  0          12           245
  1           1            17
[1] 2 2
[1] FALSE
D577V7, binary
               cls
clus              0   1
  NBN MUTATED     5   8
  NBN WILD-TYPE 105 171
[1] "tbl2"
               cls
clus            [,1] [,2]
  NBN MUTATED      5    8
  NBN WILD-TYPE  105  171
        clus
vv       NBN MUTATED NBN WILD-TYPE
  FEMALE           5           105
  MALE             8           171
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NBN MUTATED                                       2
  NBN WILD-TYPE                                    48
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NBN MUTATED                                                        8
  NBN WILD-TYPE                                                    127
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NBN MUTATED                                                                   0
  NBN WILD-TYPE                                                                40
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NBN MUTATED                                                  2
  NBN WILD-TYPE                                               36
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NBN MUTATED                                                          1
  NBN WILD-TYPE                                                       15
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NBN MUTATED                                                           0
  NBN WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NBN MUTATED                                          0
  NBN WILD-TYPE                                        3
D577V8, multiclass
                                                                   clus
vv                                                                  NBN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  NBN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D577V9, binary
               cls
clus              0   1
  NBN MUTATED     1  12
  NBN WILD-TYPE   4 272
[1] "tbl2"
               cls
clus            [,1] [,2]
  NBN MUTATED      1   12
  NBN WILD-TYPE    4  272
     clus
vv    NBN MUTATED NBN WILD-TYPE
  NO            1             4
  YES          12           272
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  NBN MUTATED     6   0   1   3
  NBN WILD-TYPE 221  10   9  21
D577V10, multiclass
    clus
vv   NBN MUTATED NBN WILD-TYPE
  R0           6           221
  R1           0            10
  R2           1             9
  RX           3            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D577V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NBN MUTATED       7                         0     4
  NBN WILD-TYPE    69                         4   164
D577V12, multiclass
                           clus
vv                          NBN MUTATED NBN WILD-TYPE
  ASIAN                               7            69
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                               4           164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(578) Variable = PRKAR1B MUTATION ANALYSIS
D578V1, survival
                   sevent
clus2                 0   1
  PRKAR1B MUTATED     3   0
  PRKAR1B WILD-TYPE 178  80
  PRKAR1B MUTATED PRKAR1B WILD-TYPE 
                3               258 
  PRKAR1B MUTATED PRKAR1B WILD-TYPE 
                0                80 
$`PRKAR1B MUTATED`
TCGA-BR-8081 TCGA-BR-8381 TCGA-BR-8487 
       20.55         0.26         1.12 

$`PRKAR1B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       19.17        14.79        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  PRKAR1B MUTATED PRKAR1B WILD-TYPE 
             0.26              0.00 
  PRKAR1B MUTATED PRKAR1B WILD-TYPE 
            20.55            105.07 
  PRKAR1B MUTATED PRKAR1B WILD-TYPE 
             1.12             12.64 
[1] "0.3 - 20.6 (1.1)"   "0.0 - 105.1 (12.6)"
[1] "hr="     "3300000"
D578V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRKAR1B MUTATED         0        0        1        1         1         2
  PRKAR1B WILD-TYPE       1        9       26       25        30        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRKAR1B MUTATED           0          0          0          0        0
  PRKAR1B WILD-TYPE         3         49         36         24       24
D578V3, multiclass
            clus
vv           PRKAR1B MUTATED PRKAR1B WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 1                25
  STAGE IIA                1                30
  STAGE IIB                2                42
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               0                36
  STAGE IIIC               0                24
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PRKAR1B MUTATED     0   2   2   1
  PRKAR1B WILD-TYPE  11  70 120  74
D578V4, multiclass
    clus
vv   PRKAR1B MUTATED PRKAR1B WILD-TYPE
  T1               0                11
  T2               2                70
  T3               2               120
  T4               1                74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  PRKAR1B MUTATED    3  2  0  0
  PRKAR1B WILD-TYPE 90 79 50 53
D578V5, multiclass
    clus
vv   PRKAR1B MUTATED PRKAR1B WILD-TYPE
  N0               3                90
  N1               2                79
  N2               0                50
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D578V6, binary
                   cls
clus                  0   1
  PRKAR1B MUTATED     5   0
  PRKAR1B WILD-TYPE 252  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRKAR1B MUTATED      5    0
  PRKAR1B WILD-TYPE  252   18
   clus
vv  PRKAR1B MUTATED PRKAR1B WILD-TYPE
  0               5               252
  1               0                18
[1] 2 2
[1] FALSE
D578V7, binary
                   cls
clus                  0   1
  PRKAR1B MUTATED     2   3
  PRKAR1B WILD-TYPE 108 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRKAR1B MUTATED      2    3
  PRKAR1B WILD-TYPE  108  176
        clus
vv       PRKAR1B MUTATED PRKAR1B WILD-TYPE
  FEMALE               2               108
  MALE                 3               176
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PRKAR1B MUTATED                                       0
  PRKAR1B WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PRKAR1B MUTATED                                                        3
  PRKAR1B WILD-TYPE                                                    132
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PRKAR1B MUTATED                                                                   1
  PRKAR1B WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PRKAR1B MUTATED                                                  0
  PRKAR1B WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PRKAR1B MUTATED                                                          1
  PRKAR1B WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PRKAR1B MUTATED                                                           0
  PRKAR1B WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PRKAR1B MUTATED                                          0
  PRKAR1B WILD-TYPE                                        3
D578V8, multiclass
                                                                   clus
vv                                                                  PRKAR1B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  PRKAR1B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D578V9, binary
                   cls
clus                  0   1
  PRKAR1B MUTATED     1   4
  PRKAR1B WILD-TYPE   4 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRKAR1B MUTATED      1    4
  PRKAR1B WILD-TYPE    4  280
     clus
vv    PRKAR1B MUTATED PRKAR1B WILD-TYPE
  NO                1                 4
  YES               4               280
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PRKAR1B MUTATED     5   0   0   0
  PRKAR1B WILD-TYPE 222  10  10  24
D578V10, multiclass
    clus
vv   PRKAR1B MUTATED PRKAR1B WILD-TYPE
  R0               5               222
  R1               0                10
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D578V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRKAR1B MUTATED       0                         0     3
  PRKAR1B WILD-TYPE    76                         4   165
D578V12, multiclass
                           clus
vv                          PRKAR1B MUTATED PRKAR1B WILD-TYPE
  ASIAN                                   0                76
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   3               165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(579) Variable = PPP1R13B MUTATION ANALYSIS
D579V1, survival
                    sevent
clus2                  0   1
  PPP1R13B MUTATED     5   3
  PPP1R13B WILD-TYPE 176  77
  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
                 8                253 
  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
                 3                 77 
$`PPP1R13B MUTATED`
TCGA-BR-8059 TCGA-BR-8081 TCGA-CG-4304 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-5721 
       14.43        20.55        27.02         0.00        18.97         6.02 
TCGA-CG-5723 TCGA-CG-5726 
      105.07        28.96 

$`PPP1R13B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       18.71        17.49         0.69        12.26         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
       12.03         9.01         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 
       36.00         1.02         0.99         0.99        12.03        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
              0.00               0.07 
  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
            105.07              79.07 
  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
             19.76              12.56 
[1] "0.0 - 105.1 (19.8)" "0.1 - 79.1 (12.6)" 
[1] "hr=" "1.5"
D579V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPP1R13B MUTATED         0        1        2        2         0         1
  PPP1R13B WILD-TYPE       1        8       25       24        31        43
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP1R13B MUTATED           1          0          0          0        2
  PPP1R13B WILD-TYPE         2         49         36         24       22
D579V3, multiclass
            clus
vv           PPP1R13B MUTATED PPP1R13B WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  1                  8
  STAGE IB                  2                 25
  STAGE II                  2                 24
  STAGE IIA                 0                 31
  STAGE IIB                 1                 43
  STAGE III                 1                  2
  STAGE IIIA                0                 49
  STAGE IIIB                0                 36
  STAGE IIIC                0                 24
  STAGE IV                  2                 22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  PPP1R13B MUTATED     1   4   1   3
  PPP1R13B WILD-TYPE  10  68 121  72
D579V4, multiclass
    clus
vv   PPP1R13B MUTATED PPP1R13B WILD-TYPE
  T1                1                 10
  T2                4                 68
  T3                1                121
  T4                3                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  PPP1R13B MUTATED    4  4  0  1
  PPP1R13B WILD-TYPE 89 77 50 52
D579V5, multiclass
    clus
vv   PPP1R13B MUTATED PPP1R13B WILD-TYPE
  N0                4                 89
  N1                4                 77
  N2                0                 50
  N3                1                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D579V6, binary
                    cls
clus                   0   1
  PPP1R13B MUTATED     9   1
  PPP1R13B WILD-TYPE 248  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R13B MUTATED      9    1
  PPP1R13B WILD-TYPE  248   17
   clus
vv  PPP1R13B MUTATED PPP1R13B WILD-TYPE
  0                9                248
  1                1                 17
[1] 2 2
[1] FALSE
D579V7, binary
                    cls
clus                   0   1
  PPP1R13B MUTATED     4   6
  PPP1R13B WILD-TYPE 106 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R13B MUTATED      4    6
  PPP1R13B WILD-TYPE  106  173
        clus
vv       PPP1R13B MUTATED PPP1R13B WILD-TYPE
  FEMALE                4                106
  MALE                  6                173
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PPP1R13B MUTATED                                       1
  PPP1R13B WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PPP1R13B MUTATED                                                        4
  PPP1R13B WILD-TYPE                                                    131
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PPP1R13B MUTATED                                                                   4
  PPP1R13B WILD-TYPE                                                                36
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PPP1R13B MUTATED                                                  0
  PPP1R13B WILD-TYPE                                               38
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PPP1R13B MUTATED                                                          1
  PPP1R13B WILD-TYPE                                                       15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PPP1R13B MUTATED                                                           0
  PPP1R13B WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PPP1R13B MUTATED                                          0
  PPP1R13B WILD-TYPE                                        3
D579V8, multiclass
                                                                   clus
vv                                                                  PPP1R13B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  PPP1R13B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D579V9, binary
                    cls
clus                   0   1
  PPP1R13B MUTATED     1   9
  PPP1R13B WILD-TYPE   4 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R13B MUTATED      1    9
  PPP1R13B WILD-TYPE    4  275
     clus
vv    PPP1R13B MUTATED PPP1R13B WILD-TYPE
  NO                 1                  4
  YES                9                275
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  PPP1R13B MUTATED     8   0   1   1
  PPP1R13B WILD-TYPE 219  10   9  23
D579V10, multiclass
    clus
vv   PPP1R13B MUTATED PPP1R13B WILD-TYPE
  R0                8                219
  R1                0                 10
  R2                1                  9
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D579V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPP1R13B MUTATED       0                         0     3
  PPP1R13B WILD-TYPE    76                         4   165
D579V12, multiclass
                           clus
vv                          PPP1R13B MUTATED PPP1R13B WILD-TYPE
  ASIAN                                    0                 76
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    3                165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(580) Variable = PHACTR1 MUTATION ANALYSIS
D580V1, survival
                   sevent
clus2                 0   1
  PHACTR1 MUTATED     3   3
  PHACTR1 WILD-TYPE 178  77
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
                6               255 
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
                3                77 
$`PHACTR1 MUTATED`
TCGA-BR-4280 TCGA-BR-8059 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CG-4305 TCGA-HU-A4GQ 
        6.61        14.43        13.45        11.57        15.95         0.10 

$`PHACTR1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
              0.1               0.0 
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
            15.95            105.07 
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
            12.51             12.62 
[1] "0.1 - 15.9 (12.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.4"
D580V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PHACTR1 MUTATED         1        0        0        1         0         0
  PHACTR1 WILD-TYPE       0        9       27       25        31        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PHACTR1 MUTATED           2          1          1          2        0
  PHACTR1 WILD-TYPE         1         48         35         22       24
D580V3, multiclass
            clus
vv           PHACTR1 MUTATED PHACTR1 WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                 0                 9
  STAGE IB                 0                27
  STAGE II                 1                25
  STAGE IIA                0                31
  STAGE IIB                0                44
  STAGE III                2                 1
  STAGE IIIA               1                48
  STAGE IIIB               1                35
  STAGE IIIC               2                22
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PHACTR1 MUTATED     1   2   1   4
  PHACTR1 WILD-TYPE  10  70 121  71
D580V4, multiclass
    clus
vv   PHACTR1 MUTATED PHACTR1 WILD-TYPE
  T1               1                10
  T2               2                70
  T3               1               121
  T4               4                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  PHACTR1 MUTATED    1  4  1  2
  PHACTR1 WILD-TYPE 92 77 49 51
D580V5, multiclass
    clus
vv   PHACTR1 MUTATED PHACTR1 WILD-TYPE
  N0               1                92
  N1               4                77
  N2               1                49
  N3               2                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D580V6, binary
                   cls
clus                  0   1
  PHACTR1 MUTATED     8   0
  PHACTR1 WILD-TYPE 249  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR1 MUTATED      8    0
  PHACTR1 WILD-TYPE  249   18
   clus
vv  PHACTR1 MUTATED PHACTR1 WILD-TYPE
  0               8               249
  1               0                18
[1] 2 2
[1] FALSE
D580V7, binary
                   cls
clus                  0   1
  PHACTR1 MUTATED     4   5
  PHACTR1 WILD-TYPE 106 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR1 MUTATED      4    5
  PHACTR1 WILD-TYPE  106  174
        clus
vv       PHACTR1 MUTATED PHACTR1 WILD-TYPE
  FEMALE               4               106
  MALE                 5               174
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PHACTR1 MUTATED                                       0
  PHACTR1 WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PHACTR1 MUTATED                                                        7
  PHACTR1 WILD-TYPE                                                    128
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PHACTR1 MUTATED                                                                   1
  PHACTR1 WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PHACTR1 MUTATED                                                  1
  PHACTR1 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PHACTR1 MUTATED                                                          0
  PHACTR1 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PHACTR1 MUTATED                                                           0
  PHACTR1 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PHACTR1 MUTATED                                          0
  PHACTR1 WILD-TYPE                                        3
D580V8, multiclass
                                                                   clus
vv                                                                  PHACTR1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  PHACTR1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D580V9, binary
                   cls
clus                  0   1
  PHACTR1 MUTATED     0   9
  PHACTR1 WILD-TYPE   5 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR1 MUTATED      0    9
  PHACTR1 WILD-TYPE    5  275
     clus
vv    PHACTR1 MUTATED PHACTR1 WILD-TYPE
  NO                0                 5
  YES               9               275
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PHACTR1 MUTATED     6   0   0   3
  PHACTR1 WILD-TYPE 221  10  10  21
D580V10, multiclass
    clus
vv   PHACTR1 MUTATED PHACTR1 WILD-TYPE
  R0               6               221
  R1               0                10
  R2               0                10
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D580V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHACTR1 MUTATED       1                         1     6
  PHACTR1 WILD-TYPE    75                         3   162
D580V12, multiclass
                           clus
vv                          PHACTR1 MUTATED PHACTR1 WILD-TYPE
  ASIAN                                   1                75
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   6               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(581) Variable = DHRS9 MUTATION ANALYSIS
D581V1, survival
                 sevent
clus2               0   1
  DHRS9 MUTATED     6   1
  DHRS9 WILD-TYPE 175  79
  DHRS9 MUTATED DHRS9 WILD-TYPE 
              7             254 
  DHRS9 MUTATED DHRS9 WILD-TYPE 
              1              79 
$`DHRS9 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8382 TCGA-BR-8591 TCGA-CG-4444 TCGA-D7-6528 
       30.90        34.68        15.85        13.45        47.05        15.22 
TCGA-HU-A4H0 
        2.10 

$`DHRS9 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       18.35         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  DHRS9 MUTATED DHRS9 WILD-TYPE 
            2.1             0.0 
  DHRS9 MUTATED DHRS9 WILD-TYPE 
          47.05          105.07 
  DHRS9 MUTATED DHRS9 WILD-TYPE 
         15.850          12.495 
[1] "2.1 - 47.0 (15.8)"  "0.0 - 105.1 (12.5)"
[1] "hr=" "3.8"
D581V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DHRS9 MUTATED         0        0        1        0         1         0
  DHRS9 WILD-TYPE       1        9       26       26        30        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DHRS9 MUTATED           0          2          0          3        0
  DHRS9 WILD-TYPE         3         47         36         21       24
D581V3, multiclass
            clus
vv           DHRS9 MUTATED DHRS9 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             0              36
  STAGE IIIC             3              21
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DHRS9 MUTATED     0   3   1   4
  DHRS9 WILD-TYPE  11  69 121  71
D581V4, multiclass
    clus
vv   DHRS9 MUTATED DHRS9 WILD-TYPE
  T1             0              11
  T2             3              69
  T3             1             121
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  DHRS9 MUTATED    3  0  1  3
  DHRS9 WILD-TYPE 90 81 49 50
D581V5, multiclass
    clus
vv   DHRS9 MUTATED DHRS9 WILD-TYPE
  N0             3              90
  N1             0              81
  N2             1              49
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D581V6, binary
                 cls
clus                0   1
  DHRS9 MUTATED     9   0
  DHRS9 WILD-TYPE 248  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS9 MUTATED      9    0
  DHRS9 WILD-TYPE  248   18
   clus
vv  DHRS9 MUTATED DHRS9 WILD-TYPE
  0             9             248
  1             0              18
[1] 2 2
[1] FALSE
D581V7, binary
                 cls
clus                0   1
  DHRS9 MUTATED     6   3
  DHRS9 WILD-TYPE 104 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS9 MUTATED      6    3
  DHRS9 WILD-TYPE  104  176
        clus
vv       DHRS9 MUTATED DHRS9 WILD-TYPE
  FEMALE             6             104
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DHRS9 MUTATED                                       2
  DHRS9 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DHRS9 MUTATED                                                        6
  DHRS9 WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DHRS9 MUTATED                                                                   0
  DHRS9 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DHRS9 MUTATED                                                  1
  DHRS9 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DHRS9 MUTATED                                                          0
  DHRS9 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DHRS9 MUTATED                                                           0
  DHRS9 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DHRS9 MUTATED                                          0
  DHRS9 WILD-TYPE                                        3
D581V8, multiclass
                                                                   clus
vv                                                                  DHRS9 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  DHRS9 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D581V9, binary
                 cls
clus                0   1
  DHRS9 MUTATED     0   9
  DHRS9 WILD-TYPE   5 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS9 MUTATED      0    9
  DHRS9 WILD-TYPE    5  275
     clus
vv    DHRS9 MUTATED DHRS9 WILD-TYPE
  NO              0               5
  YES             9             275
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DHRS9 MUTATED     6   0   0   3
  DHRS9 WILD-TYPE 221  10  10  21
D581V10, multiclass
    clus
vv   DHRS9 MUTATED DHRS9 WILD-TYPE
  R0             6             221
  R1             0              10
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D581V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DHRS9 MUTATED       1                         0     7
  DHRS9 WILD-TYPE    75                         4   161
D581V12, multiclass
                           clus
vv                          DHRS9 MUTATED DHRS9 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 7             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(582) Variable = PRICKLE4 MUTATION ANALYSIS
D582V1, survival
                    sevent
clus2                  0   1
  PRICKLE4 MUTATED     3   1
  PRICKLE4 WILD-TYPE 178  79
  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
                 4                257 
  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
                 1                 79 
$`PRICKLE4 MUTATED`
TCGA-CG-4305 TCGA-CG-5723 TCGA-CG-5726 TCGA-HU-A4GX 
       15.95       105.07        28.96        10.19 

$`PRICKLE4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
        0.10        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 
        0.99         6.02         0.99        12.03        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
             10.19               0.00 
  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
            105.07              79.07 
  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
            22.455             12.590 
[1] "10.2 - 105.1 (22.5)" "0.0 - 79.1 (12.6)"  
[1] "hr=" "3.3"
D582V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRICKLE4 MUTATED         0        1        0        2         0         0
  PRICKLE4 WILD-TYPE       1        8       27       24        31        44
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRICKLE4 MUTATED           0          0          0          1        0
  PRICKLE4 WILD-TYPE         3         49         36         23       24
D582V3, multiclass
            clus
vv           PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  1                  8
  STAGE IB                  0                 27
  STAGE II                  2                 24
  STAGE IIA                 0                 31
  STAGE IIB                 0                 44
  STAGE III                 0                  3
  STAGE IIIA                0                 49
  STAGE IIIB                0                 36
  STAGE IIIC                1                 23
  STAGE IV                  0                 24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  PRICKLE4 MUTATED     1   2   1   1
  PRICKLE4 WILD-TYPE  10  70 121  74
D582V4, multiclass
    clus
vv   PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  T1                1                 10
  T2                2                 70
  T3                1                121
  T4                1                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  PRICKLE4 MUTATED    1  2  1  0
  PRICKLE4 WILD-TYPE 92 79 49 53
D582V5, multiclass
    clus
vv   PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  N0                1                 92
  N1                2                 79
  N2                1                 49
  N3                0                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D582V6, binary
                    cls
clus                   0   1
  PRICKLE4 MUTATED     5   0
  PRICKLE4 WILD-TYPE 252  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRICKLE4 MUTATED      5    0
  PRICKLE4 WILD-TYPE  252   18
   clus
vv  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  0                5                252
  1                0                 18
[1] 2 2
[1] FALSE
D582V7, binary
                    cls
clus                   0   1
  PRICKLE4 MUTATED     3   3
  PRICKLE4 WILD-TYPE 107 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRICKLE4 MUTATED      3    3
  PRICKLE4 WILD-TYPE  107  176
        clus
vv       PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  FEMALE                3                107
  MALE                  3                176
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PRICKLE4 MUTATED                                       1
  PRICKLE4 WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PRICKLE4 MUTATED                                                        4
  PRICKLE4 WILD-TYPE                                                    131
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PRICKLE4 MUTATED                                                                   1
  PRICKLE4 WILD-TYPE                                                                39
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PRICKLE4 MUTATED                                                  0
  PRICKLE4 WILD-TYPE                                               38
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PRICKLE4 MUTATED                                                          0
  PRICKLE4 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PRICKLE4 MUTATED                                                           0
  PRICKLE4 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PRICKLE4 MUTATED                                          0
  PRICKLE4 WILD-TYPE                                        3
D582V8, multiclass
                                                                   clus
vv                                                                  PRICKLE4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  PRICKLE4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D582V9, binary
                    cls
clus                   0   1
  PRICKLE4 MUTATED     0   6
  PRICKLE4 WILD-TYPE   5 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRICKLE4 MUTATED      0    6
  PRICKLE4 WILD-TYPE    5  278
     clus
vv    PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  NO                 0                  5
  YES                6                278
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  PRICKLE4 MUTATED     4   0   0   2
  PRICKLE4 WILD-TYPE 223  10  10  22
D582V10, multiclass
    clus
vv   PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  R0                4                223
  R1                0                 10
  R2                0                 10
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D582V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRICKLE4 MUTATED       1                         0     2
  PRICKLE4 WILD-TYPE    75                         4   166
D582V12, multiclass
                           clus
vv                          PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  ASIAN                                    1                 75
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    2                166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(583) Variable = TRIM46 MUTATION ANALYSIS
D583V1, survival
                  sevent
clus2                0   1
  TRIM46 MUTATED     8   2
  TRIM46 WILD-TYPE 173  78
  TRIM46 MUTATED TRIM46 WILD-TYPE 
              10              251 
  TRIM46 MUTATED TRIM46 WILD-TYPE 
               2               78 
$`TRIM46 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-8487 TCGA-BR-8591 
       34.68        32.94        23.93        12.43         1.12        13.45 
TCGA-CD-A4MG TCGA-CG-4300 TCGA-CG-4305 TCGA-HU-A4GT 
        6.58        20.02        15.95         6.51 

$`TRIM46 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       15.42        28.01        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        15.81         9.34         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       12.62         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  TRIM46 MUTATED TRIM46 WILD-TYPE 
            1.12             0.00 
  TRIM46 MUTATED TRIM46 WILD-TYPE 
           34.68           105.07 
  TRIM46 MUTATED TRIM46 WILD-TYPE 
           14.70            12.59 
[1] "1.1 - 34.7 (14.7)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.9"
D583V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRIM46 MUTATED         0        0        1        1         5         1
  TRIM46 WILD-TYPE       1        9       26       25        26        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM46 MUTATED           0          0          1          1        1
  TRIM46 WILD-TYPE         3         49         35         23       23
D583V3, multiclass
            clus
vv           TRIM46 MUTATED TRIM46 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                1               25
  STAGE IIA               5               26
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              1               35
  STAGE IIIC              1               23
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM46 MUTATED     0   2   6   3
  TRIM46 WILD-TYPE  11  70 116  72
D583V4, multiclass
    clus
vv   TRIM46 MUTATED TRIM46 WILD-TYPE
  T1              0               11
  T2              2               70
  T3              6              116
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  TRIM46 MUTATED    7  2  2  1
  TRIM46 WILD-TYPE 86 79 48 52
D583V5, multiclass
    clus
vv   TRIM46 MUTATED TRIM46 WILD-TYPE
  N0              7               86
  N1              2               79
  N2              2               48
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D583V6, binary
                  cls
clus                 0   1
  TRIM46 MUTATED    12   0
  TRIM46 WILD-TYPE 245  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM46 MUTATED     12    0
  TRIM46 WILD-TYPE  245   18
   clus
vv  TRIM46 MUTATED TRIM46 WILD-TYPE
  0             12              245
  1              0               18
[1] 2 2
[1] FALSE
D583V7, binary
                  cls
clus                 0   1
  TRIM46 MUTATED     7   5
  TRIM46 WILD-TYPE 103 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM46 MUTATED      7    5
  TRIM46 WILD-TYPE  103  174
        clus
vv       TRIM46 MUTATED TRIM46 WILD-TYPE
  FEMALE              7              103
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TRIM46 MUTATED                                       1
  TRIM46 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TRIM46 MUTATED                                                        9
  TRIM46 WILD-TYPE                                                    126
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TRIM46 MUTATED                                                                   1
  TRIM46 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TRIM46 MUTATED                                                  1
  TRIM46 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TRIM46 MUTATED                                                          0
  TRIM46 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TRIM46 MUTATED                                                           0
  TRIM46 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TRIM46 MUTATED                                          0
  TRIM46 WILD-TYPE                                        3
D583V8, multiclass
                                                                   clus
vv                                                                  TRIM46 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  TRIM46 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D583V9, binary
                  cls
clus                 0   1
  TRIM46 MUTATED     0  12
  TRIM46 WILD-TYPE   5 272
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM46 MUTATED      0   12
  TRIM46 WILD-TYPE    5  272
     clus
vv    TRIM46 MUTATED TRIM46 WILD-TYPE
  NO               0                5
  YES             12              272
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRIM46 MUTATED     9   0   0   2
  TRIM46 WILD-TYPE 218  10  10  22
D583V10, multiclass
    clus
vv   TRIM46 MUTATED TRIM46 WILD-TYPE
  R0              9              218
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D583V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TRIM46 MUTATED       2                         0     8
  TRIM46 WILD-TYPE    74                         4   160
D583V12, multiclass
                           clus
vv                          TRIM46 MUTATED TRIM46 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  8              160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(584) Variable = FOXJ1 MUTATION ANALYSIS
D584V1, survival
                 sevent
clus2               0   1
  FOXJ1 MUTATED     3   0
  FOXJ1 WILD-TYPE 178  80
  FOXJ1 MUTATED FOXJ1 WILD-TYPE 
              3             258 
  FOXJ1 MUTATED FOXJ1 WILD-TYPE 
              0              80 
$`FOXJ1 MUTATED`
TCGA-BR-8078 TCGA-BR-8487 TCGA-F1-6874 
       12.26         1.12        14.47 

$`FOXJ1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 
       14.76         0.62         7.99        16.24        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  FOXJ1 MUTATED FOXJ1 WILD-TYPE 
           1.12            0.00 
  FOXJ1 MUTATED FOXJ1 WILD-TYPE 
          14.47          105.07 
  FOXJ1 MUTATED FOXJ1 WILD-TYPE 
          12.26           12.64 
[1] "1.1 - 14.5 (12.3)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "3300000"
D584V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FOXJ1 MUTATED         1        0        1        0         1         1
  FOXJ1 WILD-TYPE       0        9       26       26        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FOXJ1 MUTATED           0          0          0          0        0
  FOXJ1 WILD-TYPE         3         49         36         24       24
D584V3, multiclass
            clus
vv           FOXJ1 MUTATED FOXJ1 WILD-TYPE
  STAGE I                1               0
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FOXJ1 MUTATED     1   1   1   1
  FOXJ1 WILD-TYPE  10  71 121  74
D584V4, multiclass
    clus
vv   FOXJ1 MUTATED FOXJ1 WILD-TYPE
  T1             1              10
  T2             1              71
  T3             1             121
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  FOXJ1 MUTATED    3  2  0  0
  FOXJ1 WILD-TYPE 90 79 50 53
D584V5, multiclass
    clus
vv   FOXJ1 MUTATED FOXJ1 WILD-TYPE
  N0             3              90
  N1             2              79
  N2             0              50
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D584V6, binary
                 cls
clus                0   1
  FOXJ1 MUTATED     4   0
  FOXJ1 WILD-TYPE 253  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXJ1 MUTATED      4    0
  FOXJ1 WILD-TYPE  253   18
   clus
vv  FOXJ1 MUTATED FOXJ1 WILD-TYPE
  0             4             253
  1             0              18
[1] 2 2
[1] FALSE
D584V7, binary
                 cls
clus                0   1
  FOXJ1 MUTATED     3   2
  FOXJ1 WILD-TYPE 107 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXJ1 MUTATED      3    2
  FOXJ1 WILD-TYPE  107  177
        clus
vv       FOXJ1 MUTATED FOXJ1 WILD-TYPE
  FEMALE             3             107
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FOXJ1 MUTATED                                       0
  FOXJ1 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FOXJ1 MUTATED                                                        4
  FOXJ1 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FOXJ1 MUTATED                                                                   1
  FOXJ1 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FOXJ1 MUTATED                                                  0
  FOXJ1 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FOXJ1 MUTATED                                                          0
  FOXJ1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FOXJ1 MUTATED                                                           0
  FOXJ1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FOXJ1 MUTATED                                          0
  FOXJ1 WILD-TYPE                                        3
D584V8, multiclass
                                                                   clus
vv                                                                  FOXJ1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  FOXJ1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D584V9, binary
                 cls
clus                0   1
  FOXJ1 MUTATED     0   5
  FOXJ1 WILD-TYPE   5 279
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXJ1 MUTATED      0    5
  FOXJ1 WILD-TYPE    5  279
     clus
vv    FOXJ1 MUTATED FOXJ1 WILD-TYPE
  NO              0               5
  YES             5             279
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FOXJ1 MUTATED     4   0   0   1
  FOXJ1 WILD-TYPE 223  10  10  23
D584V10, multiclass
    clus
vv   FOXJ1 MUTATED FOXJ1 WILD-TYPE
  R0             4             223
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D584V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FOXJ1 MUTATED       0                         1     4
  FOXJ1 WILD-TYPE    76                         3   164
D584V12, multiclass
                           clus
vv                          FOXJ1 MUTATED FOXJ1 WILD-TYPE
  ASIAN                                 0              76
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(585) Variable = DCHS1 MUTATION ANALYSIS
D585V1, survival
                 sevent
clus2               0   1
  DCHS1 MUTATED    19   7
  DCHS1 WILD-TYPE 162  73
  DCHS1 MUTATED DCHS1 WILD-TYPE 
             26             235 
  DCHS1 MUTATED DCHS1 WILD-TYPE 
              7              73 
$`DCHS1 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7851 
       26.70         6.97        30.90        34.68        32.78        12.43 
TCGA-BR-7959 TCGA-BR-8361 TCGA-BR-A4PF TCGA-BR-A4QL TCGA-CD-A4MJ TCGA-CG-5721 
       18.71        19.50         1.15        11.57        12.62         6.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-6527 TCGA-D7-A4YV TCGA-F1-6874 TCGA-HJ-7597 
       28.96        65.10        10.26         5.92        14.47        26.47 
TCGA-HU-8602 TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H2 
       11.41        24.20        11.77         0.10         6.51        12.95 
TCGA-HU-A4H4 TCGA-HU-A4HD 
       23.84        27.42 

$`DCHS1 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 
       11.70         6.61         4.64         7.43        18.35         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10         9.17        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       12.82         9.21        24.76        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI 
        0.66        19.36        13.51        20.65        20.42        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       14.27        16.44        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.99        16.24        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56        11.08         5.52         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP 
       11.84         3.25        22.75        25.81        29.98         8.98 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H5 
        6.25        10.19         0.26         2.10        19.36        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        9.67         8.88        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  DCHS1 MUTATED DCHS1 WILD-TYPE 
            0.1             0.0 
  DCHS1 MUTATED DCHS1 WILD-TYPE 
          65.10          105.07 
  DCHS1 MUTATED DCHS1 WILD-TYPE 
          13.71           12.56 
[1] "0.1 - 65.1 (13.7)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.6"
D585V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DCHS1 MUTATED         1        3        4        1         3         5
  DCHS1 WILD-TYPE       0        6       23       25        28        39
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DCHS1 MUTATED           0          4          3          2        1
  DCHS1 WILD-TYPE         3         45         33         22       23
D585V3, multiclass
            clus
vv           DCHS1 MUTATED DCHS1 WILD-TYPE
  STAGE I                1               0
  STAGE IA               3               6
  STAGE IB               4              23
  STAGE II               1              25
  STAGE IIA              3              28
  STAGE IIB              5              39
  STAGE III              0               3
  STAGE IIIA             4              45
  STAGE IIIB             3              33
  STAGE IIIC             2              22
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DCHS1 MUTATED     4   7   8   9
  DCHS1 WILD-TYPE   7  65 114  66
D585V4, multiclass
    clus
vv   DCHS1 MUTATED DCHS1 WILD-TYPE
  T1             4               7
  T2             7              65
  T3             8             114
  T4             9              66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  DCHS1 MUTATED   14  7  5  2
  DCHS1 WILD-TYPE 79 74 45 51
D585V5, multiclass
    clus
vv   DCHS1 MUTATED DCHS1 WILD-TYPE
  N0            14              79
  N1             7              74
  N2             5              45
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D585V6, binary
                 cls
clus                0   1
  DCHS1 MUTATED    26   0
  DCHS1 WILD-TYPE 231  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCHS1 MUTATED     26    0
  DCHS1 WILD-TYPE  231   18
   clus
vv  DCHS1 MUTATED DCHS1 WILD-TYPE
  0            26             231
  1             0              18
[1] 2 2
[1] FALSE
D585V7, binary
                 cls
clus                0   1
  DCHS1 MUTATED    16  13
  DCHS1 WILD-TYPE  94 166
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCHS1 MUTATED     16   13
  DCHS1 WILD-TYPE   94  166
        clus
vv       DCHS1 MUTATED DCHS1 WILD-TYPE
  FEMALE            16              94
  MALE              13             166
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DCHS1 MUTATED                                       2
  DCHS1 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DCHS1 MUTATED                                                       11
  DCHS1 WILD-TYPE                                                    124
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DCHS1 MUTATED                                                                   5
  DCHS1 WILD-TYPE                                                                35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DCHS1 MUTATED                                                  8
  DCHS1 WILD-TYPE                                               30
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DCHS1 MUTATED                                                          1
  DCHS1 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DCHS1 MUTATED                                                           1
  DCHS1 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DCHS1 MUTATED                                          1
  DCHS1 WILD-TYPE                                        2
D585V8, multiclass
                                                                   clus
vv                                                                  DCHS1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  DCHS1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               30
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D585V9, binary
                 cls
clus                0   1
  DCHS1 MUTATED     0  29
  DCHS1 WILD-TYPE   5 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCHS1 MUTATED      0   29
  DCHS1 WILD-TYPE    5  255
     clus
vv    DCHS1 MUTATED DCHS1 WILD-TYPE
  NO              0               5
  YES            29             255
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DCHS1 MUTATED    24   0   0   4
  DCHS1 WILD-TYPE 203  10  10  20
D585V10, multiclass
    clus
vv   DCHS1 MUTATED DCHS1 WILD-TYPE
  R0            24             203
  R1             0              10
  R2             0              10
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D585V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DCHS1 MUTATED       9                         1    16
  DCHS1 WILD-TYPE    67                         3   152
D585V12, multiclass
                           clus
vv                          DCHS1 MUTATED DCHS1 WILD-TYPE
  ASIAN                                 9              67
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                16             152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(586) Variable = HLA-F MUTATION ANALYSIS
D586V1, survival
                 sevent
clus2               0   1
  HLA-F MUTATED     8   1
  HLA-F WILD-TYPE 173  79
  HLA-F MUTATED HLA-F WILD-TYPE 
              9             252 
  HLA-F MUTATED HLA-F WILD-TYPE 
              1              79 
$`HLA-F MUTATED`
TCGA-BR-7851 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8487 TCGA-CG-5718 TCGA-CG-5721 
       12.43        12.26         6.18         1.12        36.00         6.02 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H8 
        6.51        10.19         8.88 

$`HLA-F WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        6.97         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY 
       11.77        29.98         8.98         0.10         6.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  HLA-F MUTATED HLA-F WILD-TYPE 
           1.12            0.00 
  HLA-F MUTATED HLA-F WILD-TYPE 
          36.00          105.07 
  HLA-F MUTATED HLA-F WILD-TYPE 
           8.88           12.79 
[1] "1.1 - 36.0 (8.9)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "2.2"
D586V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HLA-F MUTATED         0        0        1        1         3         2
  HLA-F WILD-TYPE       1        9       26       25        28        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HLA-F MUTATED           0          1          0          1        1
  HLA-F WILD-TYPE         3         48         36         23       23
D586V3, multiclass
            clus
vv           HLA-F MUTATED HLA-F WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              3              28
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HLA-F MUTATED     1   1   3   5
  HLA-F WILD-TYPE  10  71 119  70
D586V4, multiclass
    clus
vv   HLA-F MUTATED HLA-F WILD-TYPE
  T1             1              10
  T2             1              71
  T3             3             119
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  HLA-F MUTATED    6  3  1  0
  HLA-F WILD-TYPE 87 78 49 53
D586V5, multiclass
    clus
vv   HLA-F MUTATED HLA-F WILD-TYPE
  N0             6              87
  N1             3              78
  N2             1              49
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D586V6, binary
                 cls
clus                0   1
  HLA-F MUTATED    11   0
  HLA-F WILD-TYPE 246  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-F MUTATED     11    0
  HLA-F WILD-TYPE  246   18
   clus
vv  HLA-F MUTATED HLA-F WILD-TYPE
  0            11             246
  1             0              18
[1] 2 2
[1] FALSE
D586V7, binary
                 cls
clus                0   1
  HLA-F MUTATED     7   4
  HLA-F WILD-TYPE 103 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-F MUTATED      7    4
  HLA-F WILD-TYPE  103  175
        clus
vv       HLA-F MUTATED HLA-F WILD-TYPE
  FEMALE             7             103
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  HLA-F MUTATED                                       1
  HLA-F WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HLA-F MUTATED                                                        4
  HLA-F WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HLA-F MUTATED                                                                   4
  HLA-F WILD-TYPE                                                                36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  HLA-F MUTATED                                                  2
  HLA-F WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  HLA-F MUTATED                                                          0
  HLA-F WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  HLA-F MUTATED                                                           0
  HLA-F WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  HLA-F MUTATED                                          0
  HLA-F WILD-TYPE                                        3
D586V8, multiclass
                                                                   clus
vv                                                                  HLA-F MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  HLA-F WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D586V9, binary
                 cls
clus                0   1
  HLA-F MUTATED     0  11
  HLA-F WILD-TYPE   5 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-F MUTATED      0   11
  HLA-F WILD-TYPE    5  273
     clus
vv    HLA-F MUTATED HLA-F WILD-TYPE
  NO              0               5
  YES            11             273
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HLA-F MUTATED     9   0   0   2
  HLA-F WILD-TYPE 218  10  10  22
D586V10, multiclass
    clus
vv   HLA-F MUTATED HLA-F WILD-TYPE
  R0             9             218
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D586V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HLA-F MUTATED       3                         0     6
  HLA-F WILD-TYPE    73                         4   162
D586V12, multiclass
                           clus
vv                          HLA-F MUTATED HLA-F WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(587) Variable = WNT9A MUTATION ANALYSIS
D587V1, survival
                 sevent
clus2               0   1
  WNT9A MUTATED     6   2
  WNT9A WILD-TYPE 175  78
  WNT9A MUTATED WNT9A WILD-TYPE 
              8             253 
  WNT9A MUTATED WNT9A WILD-TYPE 
              2              78 
$`WNT9A MUTATED`
TCGA-BR-7197 TCGA-BR-8078 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4465 TCGA-D7-8573 
        9.21        12.26         6.58         0.10         9.01        19.50 
TCGA-F1-6874 TCGA-HU-A4G8 
       14.47        11.84 

$`WNT9A WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       12.43        11.61        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        24.72        16.80        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  WNT9A MUTATED WNT9A WILD-TYPE 
            0.1             0.0 
  WNT9A MUTATED WNT9A WILD-TYPE 
          19.50          105.07 
  WNT9A MUTATED WNT9A WILD-TYPE 
         10.525          12.760 
[1] "0.1 - 19.5 (10.5)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.2"
D587V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WNT9A MUTATED         0        0        1        1         2         2
  WNT9A WILD-TYPE       1        9       26       25        29        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WNT9A MUTATED           0          0          1          0        1
  WNT9A WILD-TYPE         3         49         35         24       23
D587V3, multiclass
            clus
vv           WNT9A MUTATED WNT9A WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              2              29
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WNT9A MUTATED     0   1   5   2
  WNT9A WILD-TYPE  11  71 117  73
D587V4, multiclass
    clus
vv   WNT9A MUTATED WNT9A WILD-TYPE
  T1             0              11
  T2             1              71
  T3             5             117
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  WNT9A MUTATED    5  2  0  1
  WNT9A WILD-TYPE 88 79 50 52
D587V5, multiclass
    clus
vv   WNT9A MUTATED WNT9A WILD-TYPE
  N0             5              88
  N1             2              79
  N2             0              50
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D587V6, binary
                 cls
clus                0   1
  WNT9A MUTATED     7   1
  WNT9A WILD-TYPE 250  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT9A MUTATED      7    1
  WNT9A WILD-TYPE  250   17
   clus
vv  WNT9A MUTATED WNT9A WILD-TYPE
  0             7             250
  1             1              17
[1] 2 2
[1] FALSE
D587V7, binary
                 cls
clus                0   1
  WNT9A MUTATED     3   5
  WNT9A WILD-TYPE 107 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT9A MUTATED      3    5
  WNT9A WILD-TYPE  107  174
        clus
vv       WNT9A MUTATED WNT9A WILD-TYPE
  FEMALE             3             107
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  WNT9A MUTATED                                       3
  WNT9A WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WNT9A MUTATED                                                        3
  WNT9A WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WNT9A MUTATED                                                                   1
  WNT9A WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  WNT9A MUTATED                                                  1
  WNT9A WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  WNT9A MUTATED                                                          0
  WNT9A WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  WNT9A MUTATED                                                           0
  WNT9A WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  WNT9A MUTATED                                          0
  WNT9A WILD-TYPE                                        3
D587V8, multiclass
                                                                   clus
vv                                                                  WNT9A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  WNT9A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D587V9, binary
                 cls
clus                0   1
  WNT9A MUTATED     0   8
  WNT9A WILD-TYPE   5 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT9A MUTATED      0    8
  WNT9A WILD-TYPE    5  276
     clus
vv    WNT9A MUTATED WNT9A WILD-TYPE
  NO              0               5
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  WNT9A MUTATED     4   0   1   0
  WNT9A WILD-TYPE 223  10   9  24
D587V10, multiclass
    clus
vv   WNT9A MUTATED WNT9A WILD-TYPE
  R0             4             223
  R1             0              10
  R2             1               9
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D587V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WNT9A MUTATED       3                         0     4
  WNT9A WILD-TYPE    73                         4   164
D587V12, multiclass
                           clus
vv                          WNT9A MUTATED WNT9A WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(588) Variable = PPL MUTATION ANALYSIS
D588V1, survival
               sevent
clus2             0   1
  PPL MUTATED    11   3
  PPL WILD-TYPE 170  77
  PPL MUTATED PPL WILD-TYPE 
           14           247 
  PPL MUTATED PPL WILD-TYPE 
            3            77 
$`PPL MUTATED`
TCGA-B7-5816 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-8372 TCGA-BR-8589 TCGA-CD-A4MG 
       26.70        32.78        32.94        19.17        15.81         6.58 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5732 TCGA-FP-A4BE TCGA-HU-A4GT 
        6.02       105.07        28.96        69.04        11.08         6.51 
TCGA-HU-A4H4 TCGA-HU-A4H8 
       23.84         8.88 

$`PPL WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 
        1.02         0.99         0.99        12.03        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         0.10         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        19.36        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        9.67        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  PPL MUTATED PPL WILD-TYPE 
         6.02          0.00 
  PPL MUTATED PPL WILD-TYPE 
       105.07         79.07 
  PPL MUTATED PPL WILD-TYPE 
       21.505        12.560 
[1] "6.0 - 105.1 (21.5)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "3.1"
D588V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPL MUTATED         0        1        1        1         5         2
  PPL WILD-TYPE       1        8       26       25        26        42
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPL MUTATED           0          1          1          1        2
  PPL WILD-TYPE         3         48         35         23       22
D588V3, multiclass
            clus
vv           PPL MUTATED PPL WILD-TYPE
  STAGE I              0             1
  STAGE IA             1             8
  STAGE IB             1            26
  STAGE II             1            25
  STAGE IIA            5            26
  STAGE IIB            2            42
  STAGE III            0             3
  STAGE IIIA           1            48
  STAGE IIIB           1            35
  STAGE IIIC           1            23
  STAGE IV             2            22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  PPL MUTATED     3   3   5   5
  PPL WILD-TYPE   8  69 117  70
D588V4, multiclass
    clus
vv   PPL MUTATED PPL WILD-TYPE
  T1           3             8
  T2           3            69
  T3           5           117
  T4           5            70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  PPL MUTATED    8  4  1  2
  PPL WILD-TYPE 85 77 49 51
D588V5, multiclass
    clus
vv   PPL MUTATED PPL WILD-TYPE
  N0           8            85
  N1           4            77
  N2           1            49
  N3           2            51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D588V6, binary
               cls
clus              0   1
  PPL MUTATED    16   0
  PPL WILD-TYPE 241  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  PPL MUTATED     16    0
  PPL WILD-TYPE  241   18
   clus
vv  PPL MUTATED PPL WILD-TYPE
  0          16           241
  1           0            18
[1] 2 2
[1] FALSE
D588V7, binary
               cls
clus              0   1
  PPL MUTATED     7   9
  PPL WILD-TYPE 103 170
[1] "tbl2"
               cls
clus            [,1] [,2]
  PPL MUTATED      7    9
  PPL WILD-TYPE  103  170
        clus
vv       PPL MUTATED PPL WILD-TYPE
  FEMALE           7           103
  MALE             9           170
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PPL MUTATED                                       2
  PPL WILD-TYPE                                    48
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PPL MUTATED                                                        8
  PPL WILD-TYPE                                                    127
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PPL MUTATED                                                                   3
  PPL WILD-TYPE                                                                37
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PPL MUTATED                                                  3
  PPL WILD-TYPE                                               35
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PPL MUTATED                                                          0
  PPL WILD-TYPE                                                       16
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PPL MUTATED                                                           0
  PPL WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PPL MUTATED                                          0
  PPL WILD-TYPE                                        3
D588V8, multiclass
                                                                   clus
vv                                                                  PPL MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  PPL WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D588V9, binary
               cls
clus              0   1
  PPL MUTATED     0  16
  PPL WILD-TYPE   5 268
[1] "tbl2"
               cls
clus            [,1] [,2]
  PPL MUTATED      0   16
  PPL WILD-TYPE    5  268
     clus
vv    PPL MUTATED PPL WILD-TYPE
  NO            0             5
  YES          16           268
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  PPL MUTATED    13   0   0   2
  PPL WILD-TYPE 214  10  10  22
D588V10, multiclass
    clus
vv   PPL MUTATED PPL WILD-TYPE
  R0          13           214
  R1           0            10
  R2           0            10
  RX           2            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D588V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPL MUTATED       4                         1     7
  PPL WILD-TYPE    72                         3   161
D588V12, multiclass
                           clus
vv                          PPL MUTATED PPL WILD-TYPE
  ASIAN                               4            72
  BLACK OR AFRICAN AMERICAN           1             3
  WHITE                               7           161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(589) Variable = PTOV1 MUTATION ANALYSIS
D589V1, survival
                 sevent
clus2               0   1
  PTOV1 MUTATED     7   2
  PTOV1 WILD-TYPE 174  78
  PTOV1 MUTATED PTOV1 WILD-TYPE 
              9             252 
  PTOV1 MUTATED PTOV1 WILD-TYPE 
              2              78 
$`PTOV1 MUTATED`
TCGA-BR-4280 TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-8080 TCGA-BR-8368 TCGA-BR-8372 
        6.61        32.78        30.90         9.60         4.31        19.17 
TCGA-CD-A4MJ TCGA-HU-A4GT TCGA-HU-A4H3 
       12.62         6.51        19.36 

$`PTOV1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69        12.26        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  PTOV1 MUTATED PTOV1 WILD-TYPE 
           4.31            0.00 
  PTOV1 MUTATED PTOV1 WILD-TYPE 
          32.78          105.07 
  PTOV1 MUTATED PTOV1 WILD-TYPE 
         12.620          12.625 
[1] "4.3 - 32.8 (12.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.7"
D589V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTOV1 MUTATED         0        0        2        0         2         0
  PTOV1 WILD-TYPE       1        9       25       26        29        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTOV1 MUTATED           1          1          0          3        0
  PTOV1 WILD-TYPE         2         48         36         21       24
D589V3, multiclass
            clus
vv           PTOV1 MUTATED PTOV1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              0              44
  STAGE III              1               2
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             3              21
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTOV1 MUTATED     0   3   3   3
  PTOV1 WILD-TYPE  11  69 119  72
D589V4, multiclass
    clus
vv   PTOV1 MUTATED PTOV1 WILD-TYPE
  T1             0              11
  T2             3              69
  T3             3             119
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PTOV1 MUTATED    4  1  1  3
  PTOV1 WILD-TYPE 89 80 49 50
D589V5, multiclass
    clus
vv   PTOV1 MUTATED PTOV1 WILD-TYPE
  N0             4              89
  N1             1              80
  N2             1              49
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D589V6, binary
                 cls
clus                0   1
  PTOV1 MUTATED     9   0
  PTOV1 WILD-TYPE 248  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTOV1 MUTATED      9    0
  PTOV1 WILD-TYPE  248   18
   clus
vv  PTOV1 MUTATED PTOV1 WILD-TYPE
  0             9             248
  1             0              18
[1] 2 2
[1] FALSE
D589V7, binary
                 cls
clus                0   1
  PTOV1 MUTATED     6   3
  PTOV1 WILD-TYPE 104 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTOV1 MUTATED      6    3
  PTOV1 WILD-TYPE  104  176
        clus
vv       PTOV1 MUTATED PTOV1 WILD-TYPE
  FEMALE             6             104
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PTOV1 MUTATED                                       1
  PTOV1 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PTOV1 MUTATED                                                        6
  PTOV1 WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PTOV1 MUTATED                                                                   0
  PTOV1 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PTOV1 MUTATED                                                  1
  PTOV1 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PTOV1 MUTATED                                                          1
  PTOV1 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PTOV1 MUTATED                                                           0
  PTOV1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PTOV1 MUTATED                                          0
  PTOV1 WILD-TYPE                                        3
D589V8, multiclass
                                                                   clus
vv                                                                  PTOV1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  PTOV1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D589V9, binary
                 cls
clus                0   1
  PTOV1 MUTATED     0   9
  PTOV1 WILD-TYPE   5 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTOV1 MUTATED      0    9
  PTOV1 WILD-TYPE    5  275
     clus
vv    PTOV1 MUTATED PTOV1 WILD-TYPE
  NO              0               5
  YES             9             275
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PTOV1 MUTATED     7   0   0   1
  PTOV1 WILD-TYPE 220  10  10  23
D589V10, multiclass
    clus
vv   PTOV1 MUTATED PTOV1 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D589V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTOV1 MUTATED       3                         0     6
  PTOV1 WILD-TYPE    73                         4   162
D589V12, multiclass
                           clus
vv                          PTOV1 MUTATED PTOV1 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(590) Variable = PCCA MUTATION ANALYSIS
D590V1, survival
                sevent
clus2              0   1
  PCCA MUTATED     4   3
  PCCA WILD-TYPE 177  77
  PCCA MUTATED PCCA WILD-TYPE 
             7            254 
  PCCA MUTATED PCCA WILD-TYPE 
             3             77 
$`PCCA MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8368 TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5733 
        6.97        34.68         4.31         6.02        28.96        21.07 
TCGA-HU-A4H4 
       23.84 

$`PCCA WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        79.07        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        19.36        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  PCCA MUTATED PCCA WILD-TYPE 
          4.31           0.00 
  PCCA MUTATED PCCA WILD-TYPE 
         34.68         105.07 
  PCCA MUTATED PCCA WILD-TYPE 
        21.070         12.605 
[1] "4.3 - 34.7 (21.1)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1"  
D590V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PCCA MUTATED         0        1        1        0         1         1
  PCCA WILD-TYPE       1        8       26       26        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCCA MUTATED           0          3          0          0        1
  PCCA WILD-TYPE         3         46         36         24       23
D590V3, multiclass
            clus
vv           PCCA MUTATED PCCA WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            3             46
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PCCA MUTATED     1   3   2   2
  PCCA WILD-TYPE  10  69 120  73
D590V4, multiclass
    clus
vv   PCCA MUTATED PCCA WILD-TYPE
  T1            1             10
  T2            3             69
  T3            2            120
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  PCCA MUTATED    4  2  2  0
  PCCA WILD-TYPE 89 79 48 53
D590V5, multiclass
    clus
vv   PCCA MUTATED PCCA WILD-TYPE
  N0            4             89
  N1            2             79
  N2            2             48
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D590V6, binary
                cls
clus               0   1
  PCCA MUTATED     7   0
  PCCA WILD-TYPE 250  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCCA MUTATED      7    0
  PCCA WILD-TYPE  250   18
   clus
vv  PCCA MUTATED PCCA WILD-TYPE
  0            7            250
  1            0             18
[1] 2 2
[1] FALSE
D590V7, binary
                cls
clus               0   1
  PCCA MUTATED     5   3
  PCCA WILD-TYPE 105 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCCA MUTATED      5    3
  PCCA WILD-TYPE  105  176
        clus
vv       PCCA MUTATED PCCA WILD-TYPE
  FEMALE            5            105
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PCCA MUTATED                                       0
  PCCA WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PCCA MUTATED                                                        4
  PCCA WILD-TYPE                                                    131
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PCCA MUTATED                                                                   3
  PCCA WILD-TYPE                                                                37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PCCA MUTATED                                                  1
  PCCA WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PCCA MUTATED                                                          0
  PCCA WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PCCA MUTATED                                                           0
  PCCA WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PCCA MUTATED                                          0
  PCCA WILD-TYPE                                        3
D590V8, multiclass
                                                                   clus
vv                                                                  PCCA MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  PCCA WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D590V9, binary
                cls
clus               0   1
  PCCA MUTATED     0   8
  PCCA WILD-TYPE   5 276
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCCA MUTATED      0    8
  PCCA WILD-TYPE    5  276
     clus
vv    PCCA MUTATED PCCA WILD-TYPE
  NO             0              5
  YES            8            276
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PCCA MUTATED     6   0   0   2
  PCCA WILD-TYPE 221  10  10  22
D590V10, multiclass
    clus
vv   PCCA MUTATED PCCA WILD-TYPE
  R0            6            221
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D590V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PCCA MUTATED       1                         0     4
  PCCA WILD-TYPE    75                         4   164
D590V12, multiclass
                           clus
vv                          PCCA MUTATED PCCA WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                4            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(591) Variable = TAF6 MUTATION ANALYSIS
D591V1, survival
                sevent
clus2              0   1
  TAF6 MUTATED     7   3
  TAF6 WILD-TYPE 174  77
  TAF6 MUTATED TAF6 WILD-TYPE 
            10            251 
  TAF6 MUTATED TAF6 WILD-TYPE 
             3             77 
$`TAF6 MUTATED`
TCGA-B7-5816 TCGA-BR-7851 TCGA-BR-8683 TCGA-BR-A4J1 TCGA-CD-8536 TCGA-CG-5721 
       26.70        12.43         9.86         0.72         0.10         6.02 
TCGA-D7-A4YV TCGA-D7-A4YY TCGA-HU-8602 TCGA-HU-A4G9 
        5.92        13.78        11.41        24.20 

$`TAF6 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       16.44        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
       12.89         8.98        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        15.16 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       26.47         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        11.84         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  TAF6 MUTATED TAF6 WILD-TYPE 
           0.1            0.0 
  TAF6 MUTATED TAF6 WILD-TYPE 
         26.70         105.07 
  TAF6 MUTATED TAF6 WILD-TYPE 
        10.635         12.760 
[1] "0.1 - 26.7 (10.6)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.3"
D591V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TAF6 MUTATED         0        1        0        1         0         4
  TAF6 WILD-TYPE       1        8       27       25        31        40
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TAF6 MUTATED           0          2          2          0        1
  TAF6 WILD-TYPE         3         47         34         24       23
D591V3, multiclass
            clus
vv           TAF6 MUTATED TAF6 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              0             27
  STAGE II              1             25
  STAGE IIA             0             31
  STAGE IIB             4             40
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            2             34
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TAF6 MUTATED     1   0   3   7
  TAF6 WILD-TYPE  10  72 119  68
D591V4, multiclass
    clus
vv   TAF6 MUTATED TAF6 WILD-TYPE
  T1            1             10
  T2            0             72
  T3            3            119
  T4            7             68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  TAF6 MUTATED    6  4  1  1
  TAF6 WILD-TYPE 87 77 49 52
D591V5, multiclass
    clus
vv   TAF6 MUTATED TAF6 WILD-TYPE
  N0            6             87
  N1            4             77
  N2            1             49
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D591V6, binary
                cls
clus               0   1
  TAF6 MUTATED    12   0
  TAF6 WILD-TYPE 245  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED     12    0
  TAF6 WILD-TYPE  245   18
   clus
vv  TAF6 MUTATED TAF6 WILD-TYPE
  0           12            245
  1            0             18
[1] 2 2
[1] FALSE
D591V7, binary
                cls
clus               0   1
  TAF6 MUTATED     6   6
  TAF6 WILD-TYPE 104 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED      6    6
  TAF6 WILD-TYPE  104  173
        clus
vv       TAF6 MUTATED TAF6 WILD-TYPE
  FEMALE            6            104
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TAF6 MUTATED                                       2
  TAF6 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TAF6 MUTATED                                                        5
  TAF6 WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TAF6 MUTATED                                                                   2
  TAF6 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TAF6 MUTATED                                                  3
  TAF6 WILD-TYPE                                               35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TAF6 MUTATED                                                          0
  TAF6 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TAF6 MUTATED                                                           0
  TAF6 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TAF6 MUTATED                                          0
  TAF6 WILD-TYPE                                        3
D591V8, multiclass
                                                                   clus
vv                                                                  TAF6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  TAF6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D591V9, binary
                cls
clus               0   1
  TAF6 MUTATED     0  12
  TAF6 WILD-TYPE   5 272
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED      0   12
  TAF6 WILD-TYPE    5  272
     clus
vv    TAF6 MUTATED TAF6 WILD-TYPE
  NO             0              5
  YES           12            272
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TAF6 MUTATED    10   0   0   2
  TAF6 WILD-TYPE 217  10  10  22
D591V10, multiclass
    clus
vv   TAF6 MUTATED TAF6 WILD-TYPE
  R0           10            217
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D591V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TAF6 MUTATED       5                         0     6
  TAF6 WILD-TYPE    71                         4   162
D591V12, multiclass
                           clus
vv                          TAF6 MUTATED TAF6 WILD-TYPE
  ASIAN                                5             71
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                6            162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(592) Variable = ITGA7 MUTATION ANALYSIS
D592V1, survival
                 sevent
clus2               0   1
  ITGA7 MUTATED     8   3
  ITGA7 WILD-TYPE 173  77
  ITGA7 MUTATED ITGA7 WILD-TYPE 
             11             250 
  ITGA7 MUTATED ITGA7 WILD-TYPE 
              3              77 
$`ITGA7 MUTATED`
TCGA-BR-6852 TCGA-BR-7851 TCGA-BR-8363 TCGA-BR-8382 TCGA-BR-8591 TCGA-CD-A4MG 
       32.94        12.43         0.26        15.85        13.45         6.58 
TCGA-CG-4465 TCGA-CG-5721 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GT 
        9.01         6.02        11.41        11.84         6.51 

$`ITGA7 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        30.90        31.20        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        19.50        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        0.26         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        15.81         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
       29.98        47.05        19.07        12.03         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       26.47         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  ITGA7 MUTATED ITGA7 WILD-TYPE 
           0.26            0.00 
  ITGA7 MUTATED ITGA7 WILD-TYPE 
          32.94          105.07 
  ITGA7 MUTATED ITGA7 WILD-TYPE 
         11.410          12.775 
[1] "0.3 - 32.9 (11.4)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.1"
D592V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ITGA7 MUTATED         0        0        1        1         3         3
  ITGA7 WILD-TYPE       1        9       26       25        28        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ITGA7 MUTATED           0          1          0          2        2
  ITGA7 WILD-TYPE         3         48         36         22       22
D592V3, multiclass
            clus
vv           ITGA7 MUTATED ITGA7 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              3              28
  STAGE IIB              3              41
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             2              22
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITGA7 MUTATED     1   2   4   7
  ITGA7 WILD-TYPE  10  70 118  68
D592V4, multiclass
    clus
vv   ITGA7 MUTATED ITGA7 WILD-TYPE
  T1             1              10
  T2             2              70
  T3             4             118
  T4             7              68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ITGA7 MUTATED    7  3  0  3
  ITGA7 WILD-TYPE 86 78 50 50
D592V5, multiclass
    clus
vv   ITGA7 MUTATED ITGA7 WILD-TYPE
  N0             7              86
  N1             3              78
  N2             0              50
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D592V6, binary
                 cls
clus                0   1
  ITGA7 MUTATED    13   1
  ITGA7 WILD-TYPE 244  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA7 MUTATED     13    1
  ITGA7 WILD-TYPE  244   17
   clus
vv  ITGA7 MUTATED ITGA7 WILD-TYPE
  0            13             244
  1             1              17
[1] 2 2
[1] FALSE
D592V7, binary
                 cls
clus                0   1
  ITGA7 MUTATED     9   5
  ITGA7 WILD-TYPE 101 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA7 MUTATED      9    5
  ITGA7 WILD-TYPE  101  174
        clus
vv       ITGA7 MUTATED ITGA7 WILD-TYPE
  FEMALE             9             101
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ITGA7 MUTATED                                       4
  ITGA7 WILD-TYPE                                    46
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ITGA7 MUTATED                                                        6
  ITGA7 WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ITGA7 MUTATED                                                                   2
  ITGA7 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ITGA7 MUTATED                                                  1
  ITGA7 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ITGA7 MUTATED                                                          1
  ITGA7 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ITGA7 MUTATED                                                           0
  ITGA7 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ITGA7 MUTATED                                          0
  ITGA7 WILD-TYPE                                        3
D592V8, multiclass
                                                                   clus
vv                                                                  ITGA7 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ITGA7 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D592V9, binary
                 cls
clus                0   1
  ITGA7 MUTATED     1  13
  ITGA7 WILD-TYPE   4 271
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA7 MUTATED      1   13
  ITGA7 WILD-TYPE    4  271
     clus
vv    ITGA7 MUTATED ITGA7 WILD-TYPE
  NO              1               4
  YES            13             271
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ITGA7 MUTATED     9   0   1   2
  ITGA7 WILD-TYPE 218  10   9  22
D592V10, multiclass
    clus
vv   ITGA7 MUTATED ITGA7 WILD-TYPE
  R0             9             218
  R1             0              10
  R2             1               9
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D592V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ITGA7 MUTATED       4                         0     7
  ITGA7 WILD-TYPE    72                         4   161
D592V12, multiclass
                           clus
vv                          ITGA7 MUTATED ITGA7 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 7             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(593) Variable = C11ORF63 MUTATION ANALYSIS
D593V1, survival
                    sevent
clus2                  0   1
  C11ORF63 MUTATED    11   2
  C11ORF63 WILD-TYPE 170  78
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
                13                248 
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
                 2                 78 
$`C11ORF63 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-8077 TCGA-BR-8081 TCGA-BR-8372 
       26.70        34.68        19.33         0.69        20.55        19.17 
TCGA-BR-A4QL TCGA-CG-4441 TCGA-D7-6528 TCGA-D7-A4YT TCGA-FP-A4BE TCGA-HU-A4H2 
       11.57        14.01        15.22        14.27        11.08        12.95 
TCGA-HU-A4H4 
       23.84 

$`C11ORF63 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       17.29        13.68        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       12.26         9.60         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 
        7.99         8.05        54.08         4.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H5 
        6.25        10.19         0.26         2.10        19.36        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
              0.69               0.00 
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
             34.68             105.07 
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
             15.22              12.43 
[1] "0.7 - 34.7 (15.2)"  "0.0 - 105.1 (12.4)"
[1] "hr=" "2.6"
D593V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C11ORF63 MUTATED         0        0        1        0         2         4
  C11ORF63 WILD-TYPE       1        9       26       26        29        40
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C11ORF63 MUTATED           0          3          3          1        0
  C11ORF63 WILD-TYPE         3         46         33         23       24
D593V3, multiclass
            clus
vv           C11ORF63 MUTATED C11ORF63 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  1                 26
  STAGE II                  0                 26
  STAGE IIA                 2                 29
  STAGE IIB                 4                 40
  STAGE III                 0                  3
  STAGE IIIA                3                 46
  STAGE IIIB                3                 33
  STAGE IIIC                1                 23
  STAGE IV                  0                 24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C11ORF63 MUTATED     0   4   5   5
  C11ORF63 WILD-TYPE  11  68 117  70
D593V4, multiclass
    clus
vv   C11ORF63 MUTATED C11ORF63 WILD-TYPE
  T1                0                 11
  T2                4                 68
  T3                5                117
  T4                5                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  C11ORF63 MUTATED    6  3  2  4
  C11ORF63 WILD-TYPE 87 78 48 49
D593V5, multiclass
    clus
vv   C11ORF63 MUTATED C11ORF63 WILD-TYPE
  N0                6                 87
  N1                3                 78
  N2                2                 48
  N3                4                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D593V6, binary
                    cls
clus                   0   1
  C11ORF63 MUTATED    15   0
  C11ORF63 WILD-TYPE 242  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF63 MUTATED     15    0
  C11ORF63 WILD-TYPE  242   18
   clus
vv  C11ORF63 MUTATED C11ORF63 WILD-TYPE
  0               15                242
  1                0                 18
[1] 2 2
[1] FALSE
D593V7, binary
                    cls
clus                   0   1
  C11ORF63 MUTATED    10   5
  C11ORF63 WILD-TYPE 100 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF63 MUTATED     10    5
  C11ORF63 WILD-TYPE  100  174
        clus
vv       C11ORF63 MUTATED C11ORF63 WILD-TYPE
  FEMALE               10                100
  MALE                  5                174
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C11ORF63 MUTATED                                       1
  C11ORF63 WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C11ORF63 MUTATED                                                        8
  C11ORF63 WILD-TYPE                                                    127
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C11ORF63 MUTATED                                                                   2
  C11ORF63 WILD-TYPE                                                                38
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C11ORF63 MUTATED                                                  4
  C11ORF63 WILD-TYPE                                               34
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C11ORF63 MUTATED                                                          0
  C11ORF63 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C11ORF63 MUTATED                                                           0
  C11ORF63 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C11ORF63 MUTATED                                          0
  C11ORF63 WILD-TYPE                                        3
D593V8, multiclass
                                                                   clus
vv                                                                  C11ORF63 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  C11ORF63 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D593V9, binary
                    cls
clus                   0   1
  C11ORF63 MUTATED     0  15
  C11ORF63 WILD-TYPE   5 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF63 MUTATED      0   15
  C11ORF63 WILD-TYPE    5  269
     clus
vv    C11ORF63 MUTATED C11ORF63 WILD-TYPE
  NO                 0                  5
  YES               15                269
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C11ORF63 MUTATED    13   0   0   2
  C11ORF63 WILD-TYPE 214  10  10  22
D593V10, multiclass
    clus
vv   C11ORF63 MUTATED C11ORF63 WILD-TYPE
  R0               13                214
  R1                0                 10
  R2                0                 10
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D593V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C11ORF63 MUTATED       2                         1    11
  C11ORF63 WILD-TYPE    74                         3   157
D593V12, multiclass
                           clus
vv                          C11ORF63 MUTATED C11ORF63 WILD-TYPE
  ASIAN                                    2                 74
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                   11                157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(594) Variable = ENOSF1 MUTATION ANALYSIS
D594V1, survival
                  sevent
clus2                0   1
  ENOSF1 MUTATED     4   3
  ENOSF1 WILD-TYPE 177  77
  ENOSF1 MUTATED ENOSF1 WILD-TYPE 
               7              254 
  ENOSF1 MUTATED ENOSF1 WILD-TYPE 
               3               77 
$`ENOSF1 MUTATED`
TCGA-BR-4184 TCGA-BR-7901 TCGA-BR-8360 TCGA-BR-8680 TCGA-CD-A4MJ TCGA-CG-5721 
        6.97         3.45         6.18        15.81        12.62         6.02 
TCGA-D7-A4YV 
        5.92 

$`ENOSF1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73        12.43         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  ENOSF1 MUTATED ENOSF1 WILD-TYPE 
            3.45             0.00 
  ENOSF1 MUTATED ENOSF1 WILD-TYPE 
           15.81           105.07 
  ENOSF1 MUTATED ENOSF1 WILD-TYPE 
           6.180           12.775 
[1] "3.5 - 15.8 (6.2)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "3"  
D594V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ENOSF1 MUTATED         0        0        1        0         1         2
  ENOSF1 WILD-TYPE       1        9       26       26        30        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ENOSF1 MUTATED           0          1          0          0        2
  ENOSF1 WILD-TYPE         3         48         36         24       22
D594V3, multiclass
            clus
vv           ENOSF1 MUTATED ENOSF1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ENOSF1 MUTATED     0   1   4   2
  ENOSF1 WILD-TYPE  11  71 118  73
D594V4, multiclass
    clus
vv   ENOSF1 MUTATED ENOSF1 WILD-TYPE
  T1              0               11
  T2              1               71
  T3              4              118
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ENOSF1 MUTATED    2  4  1  0
  ENOSF1 WILD-TYPE 91 77 49 53
D594V5, multiclass
    clus
vv   ENOSF1 MUTATED ENOSF1 WILD-TYPE
  N0              2               91
  N1              4               77
  N2              1               49
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D594V6, binary
                  cls
clus                 0   1
  ENOSF1 MUTATED     5   1
  ENOSF1 WILD-TYPE 252  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENOSF1 MUTATED      5    1
  ENOSF1 WILD-TYPE  252   17
   clus
vv  ENOSF1 MUTATED ENOSF1 WILD-TYPE
  0              5              252
  1              1               17
[1] 2 2
[1] FALSE
D594V7, binary
                  cls
clus                 0   1
  ENOSF1 MUTATED     1   6
  ENOSF1 WILD-TYPE 109 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENOSF1 MUTATED      1    6
  ENOSF1 WILD-TYPE  109  173
        clus
vv       ENOSF1 MUTATED ENOSF1 WILD-TYPE
  FEMALE              1              109
  MALE                6              173
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ENOSF1 MUTATED                                       0
  ENOSF1 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ENOSF1 MUTATED                                                        3
  ENOSF1 WILD-TYPE                                                    132
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ENOSF1 MUTATED                                                                   2
  ENOSF1 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ENOSF1 MUTATED                                                  2
  ENOSF1 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ENOSF1 MUTATED                                                          0
  ENOSF1 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ENOSF1 MUTATED                                                           0
  ENOSF1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ENOSF1 MUTATED                                          0
  ENOSF1 WILD-TYPE                                        3
D594V8, multiclass
                                                                   clus
vv                                                                  ENOSF1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ENOSF1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D594V9, binary
                  cls
clus                 0   1
  ENOSF1 MUTATED     0   7
  ENOSF1 WILD-TYPE   5 277
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENOSF1 MUTATED      0    7
  ENOSF1 WILD-TYPE    5  277
     clus
vv    ENOSF1 MUTATED ENOSF1 WILD-TYPE
  NO               0                5
  YES              7              277
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ENOSF1 MUTATED     5   0   0   1
  ENOSF1 WILD-TYPE 222  10  10  23
D594V10, multiclass
    clus
vv   ENOSF1 MUTATED ENOSF1 WILD-TYPE
  R0              5              222
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D594V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ENOSF1 MUTATED       2                         0     4
  ENOSF1 WILD-TYPE    74                         4   164
D594V12, multiclass
                           clus
vv                          ENOSF1 MUTATED ENOSF1 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(595) Variable = SLC38A6 MUTATION ANALYSIS
D595V1, survival
                   sevent
clus2                 0   1
  SLC38A6 MUTATED     7   1
  SLC38A6 WILD-TYPE 174  79
  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
                8               253 
  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
                1                79 
$`SLC38A6 MUTATED`
TCGA-BR-8372 TCGA-BR-8487 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4437 TCGA-CG-5721 
       19.17         1.12         0.10         6.58         8.05         6.02 
TCGA-CG-5728 TCGA-FP-7829 
       65.10        19.53 

$`SLC38A6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         7.99        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23        21.27         3.48        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
              0.1               0.0 
  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
            65.10            105.07 
  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
            7.315            12.660 
[1] "0.1 - 65.1 (7.3)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "2.4"
D595V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC38A6 MUTATED         0        0        1        2         2         1
  SLC38A6 WILD-TYPE       1        9       26       24        29        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC38A6 MUTATED           0          0          0          1        1
  SLC38A6 WILD-TYPE         3         49         36         23       23
D595V3, multiclass
            clus
vv           SLC38A6 MUTATED SLC38A6 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 2                24
  STAGE IIA                2                29
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               0                36
  STAGE IIIC               1                23
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC38A6 MUTATED     0   2   4   2
  SLC38A6 WILD-TYPE  11  70 118  73
D595V4, multiclass
    clus
vv   SLC38A6 MUTATED SLC38A6 WILD-TYPE
  T1               0                11
  T2               2                70
  T3               4               118
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  SLC38A6 MUTATED    4  3  0  1
  SLC38A6 WILD-TYPE 89 78 50 52
D595V5, multiclass
    clus
vv   SLC38A6 MUTATED SLC38A6 WILD-TYPE
  N0               4                89
  N1               3                78
  N2               0                50
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D595V6, binary
                   cls
clus                  0   1
  SLC38A6 MUTATED     8   0
  SLC38A6 WILD-TYPE 249  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A6 MUTATED      8    0
  SLC38A6 WILD-TYPE  249   18
   clus
vv  SLC38A6 MUTATED SLC38A6 WILD-TYPE
  0               8               249
  1               0                18
[1] 2 2
[1] FALSE
D595V7, binary
                   cls
clus                  0   1
  SLC38A6 MUTATED     2   6
  SLC38A6 WILD-TYPE 108 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A6 MUTATED      2    6
  SLC38A6 WILD-TYPE  108  173
        clus
vv       SLC38A6 MUTATED SLC38A6 WILD-TYPE
  FEMALE               2               108
  MALE                 6               173
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SLC38A6 MUTATED                                       1
  SLC38A6 WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC38A6 MUTATED                                                        3
  SLC38A6 WILD-TYPE                                                    132
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC38A6 MUTATED                                                                   3
  SLC38A6 WILD-TYPE                                                                37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SLC38A6 MUTATED                                                  0
  SLC38A6 WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SLC38A6 MUTATED                                                          1
  SLC38A6 WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SLC38A6 MUTATED                                                           0
  SLC38A6 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SLC38A6 MUTATED                                          0
  SLC38A6 WILD-TYPE                                        3
D595V8, multiclass
                                                                   clus
vv                                                                  SLC38A6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  SLC38A6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D595V9, binary
                   cls
clus                  0   1
  SLC38A6 MUTATED     0   8
  SLC38A6 WILD-TYPE   5 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A6 MUTATED      0    8
  SLC38A6 WILD-TYPE    5  276
     clus
vv    SLC38A6 MUTATED SLC38A6 WILD-TYPE
  NO                0                 5
  YES               8               276
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC38A6 MUTATED     7   0   0   0
  SLC38A6 WILD-TYPE 220  10  10  24
D595V10, multiclass
    clus
vv   SLC38A6 MUTATED SLC38A6 WILD-TYPE
  R0               7               220
  R1               0                10
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D595V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC38A6 MUTATED       2                         0     3
  SLC38A6 WILD-TYPE    74                         4   165
D595V12, multiclass
                           clus
vv                          SLC38A6 MUTATED SLC38A6 WILD-TYPE
  ASIAN                                   2                74
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   3               165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(596) Variable = KCNC1 MUTATION ANALYSIS
D596V1, survival
                 sevent
clus2               0   1
  KCNC1 MUTATED     7   0
  KCNC1 WILD-TYPE 174  80
  KCNC1 MUTATED KCNC1 WILD-TYPE 
              7             254 
  KCNC1 MUTATED KCNC1 WILD-TYPE 
              0              80 
$`KCNC1 MUTATED`
TCGA-BR-6452 TCGA-BR-8382 TCGA-BR-8487 TCGA-CD-A4MJ TCGA-CG-5728 TCGA-FP-A4BE 
       34.68        15.85         1.12        12.62        65.10        11.08 
TCGA-HU-A4GT 
        6.51 

$`KCNC1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       19.17        14.79         0.26         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        28.96        79.07         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         0.10         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  KCNC1 MUTATED KCNC1 WILD-TYPE 
           1.12            0.00 
  KCNC1 MUTATED KCNC1 WILD-TYPE 
          65.10          105.07 
  KCNC1 MUTATED KCNC1 WILD-TYPE 
         12.620          12.625 
[1] "1.1 - 65.1 (12.6)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "2.6e+07"
D596V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCNC1 MUTATED         0        0        2        0         4         0
  KCNC1 WILD-TYPE       1        9       25       26        27        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCNC1 MUTATED           0          0          0          1        0
  KCNC1 WILD-TYPE         3         49         36         23       24
D596V3, multiclass
            clus
vv           KCNC1 MUTATED KCNC1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              4              27
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCNC1 MUTATED     0   2   4   1
  KCNC1 WILD-TYPE  11  70 118  74
D596V4, multiclass
    clus
vv   KCNC1 MUTATED KCNC1 WILD-TYPE
  T1             0              11
  T2             2              70
  T3             4             118
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  KCNC1 MUTATED    6  0  0  1
  KCNC1 WILD-TYPE 87 81 50 52
D596V5, multiclass
    clus
vv   KCNC1 MUTATED KCNC1 WILD-TYPE
  N0             6              87
  N1             0              81
  N2             0              50
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D596V6, binary
                 cls
clus                0   1
  KCNC1 MUTATED     7   0
  KCNC1 WILD-TYPE 250  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNC1 MUTATED      7    0
  KCNC1 WILD-TYPE  250   18
   clus
vv  KCNC1 MUTATED KCNC1 WILD-TYPE
  0             7             250
  1             0              18
[1] 2 2
[1] FALSE
D596V7, binary
                 cls
clus                0   1
  KCNC1 MUTATED     5   2
  KCNC1 WILD-TYPE 105 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNC1 MUTATED      5    2
  KCNC1 WILD-TYPE  105  177
        clus
vv       KCNC1 MUTATED KCNC1 WILD-TYPE
  FEMALE             5             105
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KCNC1 MUTATED                                       0
  KCNC1 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KCNC1 MUTATED                                                        5
  KCNC1 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KCNC1 MUTATED                                                                   1
  KCNC1 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KCNC1 MUTATED                                                  1
  KCNC1 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KCNC1 MUTATED                                                          0
  KCNC1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KCNC1 MUTATED                                                           0
  KCNC1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KCNC1 MUTATED                                          0
  KCNC1 WILD-TYPE                                        3
D596V8, multiclass
                                                                   clus
vv                                                                  KCNC1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  KCNC1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D596V9, binary
                 cls
clus                0   1
  KCNC1 MUTATED     0   7
  KCNC1 WILD-TYPE   5 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNC1 MUTATED      0    7
  KCNC1 WILD-TYPE    5  277
     clus
vv    KCNC1 MUTATED KCNC1 WILD-TYPE
  NO              0               5
  YES             7             277
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KCNC1 MUTATED     6   0   0   0
  KCNC1 WILD-TYPE 221  10  10  24
D596V10, multiclass
    clus
vv   KCNC1 MUTATED KCNC1 WILD-TYPE
  R0             6             221
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D596V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KCNC1 MUTATED       2                         1     3
  KCNC1 WILD-TYPE    74                         3   165
D596V12, multiclass
                           clus
vv                          KCNC1 MUTATED KCNC1 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(597) Variable = AMPD3 MUTATION ANALYSIS
D597V1, survival
                 sevent
clus2               0   1
  AMPD3 MUTATED    11   7
  AMPD3 WILD-TYPE 170  73
  AMPD3 MUTATED AMPD3 WILD-TYPE 
             18             243 
  AMPD3 MUTATED AMPD3 WILD-TYPE 
              7              73 
$`AMPD3 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6566 TCGA-BR-7703 TCGA-BR-8284 TCGA-BR-8363 
       26.70         6.97        32.78        24.76         8.05         0.26 
TCGA-BR-8370 TCGA-BR-8372 TCGA-CD-8529 TCGA-CD-A4MG TCGA-CG-4436 TCGA-CG-4437 
        3.32        19.17         0.13         6.58         7.99         8.05 
TCGA-CG-4465 TCGA-CG-5726 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
        9.01        28.96        11.84         0.10         6.51         6.25 

$`AMPD3 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 
       31.20        32.94        12.82         9.21        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       12.26         9.60        20.55        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
        2.20        15.58         7.40         6.18        19.50        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 
       17.52         0.95        26.33         4.31        14.04        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.10         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       27.02        15.95         1.02        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
       29.98        47.05        19.07        12.03         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 
        0.99         6.02         0.99       105.07        12.03        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  AMPD3 MUTATED AMPD3 WILD-TYPE 
            0.1             0.0 
  AMPD3 MUTATED AMPD3 WILD-TYPE 
          32.78          105.07 
  AMPD3 MUTATED AMPD3 WILD-TYPE 
           8.02           12.79 
[1] "0.1 - 32.8 (8.0)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.6"
D597V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AMPD3 MUTATED         0        2        2        1         3         3
  AMPD3 WILD-TYPE       1        7       25       25        28        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMPD3 MUTATED           0          1          1          3        2
  AMPD3 WILD-TYPE         3         48         35         21       22
D597V3, multiclass
            clus
vv           AMPD3 MUTATED AMPD3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               2               7
  STAGE IB               2              25
  STAGE II               1              25
  STAGE IIA              3              28
  STAGE IIB              3              41
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             3              21
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AMPD3 MUTATED     3   3   7   6
  AMPD3 WILD-TYPE   8  69 115  69
D597V4, multiclass
    clus
vv   AMPD3 MUTATED AMPD3 WILD-TYPE
  T1             3               8
  T2             3              69
  T3             7             115
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  AMPD3 MUTATED    9  4  1  4
  AMPD3 WILD-TYPE 84 77 49 49
D597V5, multiclass
    clus
vv   AMPD3 MUTATED AMPD3 WILD-TYPE
  N0             9              84
  N1             4              77
  N2             1              49
  N3             4              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D597V6, binary
                 cls
clus                0   1
  AMPD3 MUTATED    16   2
  AMPD3 WILD-TYPE 241  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMPD3 MUTATED     16    2
  AMPD3 WILD-TYPE  241   16
   clus
vv  AMPD3 MUTATED AMPD3 WILD-TYPE
  0            16             241
  1             2              16
[1] 2 2
[1] FALSE
D597V7, binary
                 cls
clus                0   1
  AMPD3 MUTATED     8  11
  AMPD3 WILD-TYPE 102 168
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMPD3 MUTATED      8   11
  AMPD3 WILD-TYPE  102  168
        clus
vv       AMPD3 MUTATED AMPD3 WILD-TYPE
  FEMALE             8             102
  MALE              11             168
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMPD3 MUTATED                                       6
  AMPD3 WILD-TYPE                                    44
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMPD3 MUTATED                                                        5
  AMPD3 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMPD3 MUTATED                                                                   4
  AMPD3 WILD-TYPE                                                                36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMPD3 MUTATED                                                  2
  AMPD3 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMPD3 MUTATED                                                          1
  AMPD3 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMPD3 MUTATED                                                           1
  AMPD3 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMPD3 MUTATED                                          0
  AMPD3 WILD-TYPE                                        3
D597V8, multiclass
                                                                   clus
vv                                                                  AMPD3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  AMPD3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          44
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D597V9, binary
                 cls
clus                0   1
  AMPD3 MUTATED     0  19
  AMPD3 WILD-TYPE   5 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMPD3 MUTATED      0   19
  AMPD3 WILD-TYPE    5  265
     clus
vv    AMPD3 MUTATED AMPD3 WILD-TYPE
  NO              0               5
  YES            19             265
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AMPD3 MUTATED    14   0   1   2
  AMPD3 WILD-TYPE 213  10   9  22
D597V10, multiclass
    clus
vv   AMPD3 MUTATED AMPD3 WILD-TYPE
  R0            14             213
  R1             0              10
  R2             1               9
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D597V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMPD3 MUTATED       6                         0     9
  AMPD3 WILD-TYPE    70                         4   159
D597V12, multiclass
                           clus
vv                          AMPD3 MUTATED AMPD3 WILD-TYPE
  ASIAN                                 6              70
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 9             159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(598) Variable = PPARG MUTATION ANALYSIS
D598V1, survival
                 sevent
clus2               0   1
  PPARG MUTATED     3   0
  PPARG WILD-TYPE 178  80
  PPARG MUTATED PPARG WILD-TYPE 
              3             258 
  PPARG MUTATED PPARG WILD-TYPE 
              0              80 
$`PPARG MUTATED`
TCGA-BR-6852 TCGA-CG-4305 TCGA-HU-A4H8 
       32.94        15.95         8.88 

$`PPARG WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        30.90        31.20        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  PPARG MUTATED PPARG WILD-TYPE 
           8.88            0.00 
  PPARG MUTATED PPARG WILD-TYPE 
          32.94          105.07 
  PPARG MUTATED PPARG WILD-TYPE 
         15.950          12.605 
[1] "8.9 - 32.9 (15.9)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "9200000"
D598V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPARG MUTATED         0        0        1        1         1         0
  PPARG WILD-TYPE       1        9       26       25        30        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPARG MUTATED           0          0          0          0        0
  PPARG WILD-TYPE         3         49         36         24       24
D598V3, multiclass
            clus
vv           PPARG MUTATED PPARG WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PPARG MUTATED     1   1   2   0
  PPARG WILD-TYPE  10  71 120  75
D598V4, multiclass
    clus
vv   PPARG MUTATED PPARG WILD-TYPE
  T1             1              10
  T2             1              71
  T3             2             120
  T4             0              75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PPARG MUTATED    1  2  0  0
  PPARG WILD-TYPE 92 79 50 53
D598V5, multiclass
    clus
vv   PPARG MUTATED PPARG WILD-TYPE
  N0             1              92
  N1             2              79
  N2             0              50
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D598V6, binary
                 cls
clus                0   1
  PPARG MUTATED     3   0
  PPARG WILD-TYPE 254  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPARG MUTATED      3    0
  PPARG WILD-TYPE  254   18
   clus
vv  PPARG MUTATED PPARG WILD-TYPE
  0             3             254
  1             0              18
[1] 2 2
[1] FALSE
D598V7, binary
                 cls
clus                0   1
  PPARG MUTATED     2   2
  PPARG WILD-TYPE 108 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPARG MUTATED      2    2
  PPARG WILD-TYPE  108  177
        clus
vv       PPARG MUTATED PPARG WILD-TYPE
  FEMALE             2             108
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PPARG MUTATED                                       0
  PPARG WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PPARG MUTATED                                                        3
  PPARG WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PPARG MUTATED                                                                   0
  PPARG WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PPARG MUTATED                                                  1
  PPARG WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PPARG MUTATED                                                          0
  PPARG WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PPARG MUTATED                                                           0
  PPARG WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PPARG MUTATED                                          0
  PPARG WILD-TYPE                                        3
D598V8, multiclass
                                                                   clus
vv                                                                  PPARG MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  PPARG WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D598V9, binary
                 cls
clus                0   1
  PPARG MUTATED     0   4
  PPARG WILD-TYPE   5 280
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPARG MUTATED      0    4
  PPARG WILD-TYPE    5  280
     clus
vv    PPARG MUTATED PPARG WILD-TYPE
  NO              0               5
  YES             4             280
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PPARG MUTATED     3   0   0   1
  PPARG WILD-TYPE 224  10  10  23
D598V10, multiclass
    clus
vv   PPARG MUTATED PPARG WILD-TYPE
  R0             3             224
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D598V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPARG MUTATED       1                         0     2
  PPARG WILD-TYPE    75                         4   166
D598V12, multiclass
                           clus
vv                          PPARG MUTATED PPARG WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 2             166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(599) Variable = TRIM27 MUTATION ANALYSIS
D599V1, survival
                  sevent
clus2                0   1
  TRIM27 MUTATED     4   0
  TRIM27 WILD-TYPE 177  80
  TRIM27 MUTATED TRIM27 WILD-TYPE 
               4              257 
  TRIM27 MUTATED TRIM27 WILD-TYPE 
               0               80 
$`TRIM27 MUTATED`
TCGA-B7-5816 TCGA-BR-7707 TCGA-CG-4305 TCGA-F1-6874 
       26.70        23.93        15.95        14.47 

$`TRIM27 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        0.62         7.99        16.24        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  TRIM27 MUTATED TRIM27 WILD-TYPE 
           14.47             0.00 
  TRIM27 MUTATED TRIM27 WILD-TYPE 
           26.70           105.07 
  TRIM27 MUTATED TRIM27 WILD-TYPE 
           19.94            12.56 
[1] "14.5 - 26.7 (19.9)" "0.0 - 105.1 (12.6)"
[1] "hr="     "9300000"
D599V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRIM27 MUTATED         1        0        2        1         0         1
  TRIM27 WILD-TYPE       0        9       25       25        31        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM27 MUTATED           0          0          0          0        0
  TRIM27 WILD-TYPE         3         49         36         24       24
D599V3, multiclass
            clus
vv           TRIM27 MUTATED TRIM27 WILD-TYPE
  STAGE I                 1                0
  STAGE IA                0                9
  STAGE IB                2               25
  STAGE II                1               25
  STAGE IIA               0               31
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM27 MUTATED     1   3   0   1
  TRIM27 WILD-TYPE  10  69 122  74
D599V4, multiclass
    clus
vv   TRIM27 MUTATED TRIM27 WILD-TYPE
  T1              1               10
  T2              3               69
  T3              0              122
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  TRIM27 MUTATED    3  2  0  0
  TRIM27 WILD-TYPE 90 79 50 53
D599V5, multiclass
    clus
vv   TRIM27 MUTATED TRIM27 WILD-TYPE
  N0              3               90
  N1              2               79
  N2              0               50
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D599V6, binary
                  cls
clus                 0   1
  TRIM27 MUTATED     4   0
  TRIM27 WILD-TYPE 253  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM27 MUTATED      4    0
  TRIM27 WILD-TYPE  253   18
   clus
vv  TRIM27 MUTATED TRIM27 WILD-TYPE
  0              4              253
  1              0               18
[1] 2 2
[1] FALSE
D599V7, binary
                  cls
clus                 0   1
  TRIM27 MUTATED     2   3
  TRIM27 WILD-TYPE 108 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM27 MUTATED      2    3
  TRIM27 WILD-TYPE  108  176
        clus
vv       TRIM27 MUTATED TRIM27 WILD-TYPE
  FEMALE              2              108
  MALE                3              176
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TRIM27 MUTATED                                       1
  TRIM27 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TRIM27 MUTATED                                                        3
  TRIM27 WILD-TYPE                                                    132
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TRIM27 MUTATED                                                                   1
  TRIM27 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TRIM27 MUTATED                                                  0
  TRIM27 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TRIM27 MUTATED                                                          0
  TRIM27 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TRIM27 MUTATED                                                           0
  TRIM27 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TRIM27 MUTATED                                          0
  TRIM27 WILD-TYPE                                        3
D599V8, multiclass
                                                                   clus
vv                                                                  TRIM27 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  TRIM27 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D599V9, binary
                  cls
clus                 0   1
  TRIM27 MUTATED     0   5
  TRIM27 WILD-TYPE   5 279
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM27 MUTATED      0    5
  TRIM27 WILD-TYPE    5  279
     clus
vv    TRIM27 MUTATED TRIM27 WILD-TYPE
  NO               0                5
  YES              5              279
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRIM27 MUTATED     5   0   0   0
  TRIM27 WILD-TYPE 222  10  10  24
D599V10, multiclass
    clus
vv   TRIM27 MUTATED TRIM27 WILD-TYPE
  R0              5              222
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D599V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TRIM27 MUTATED       0                         1     3
  TRIM27 WILD-TYPE    76                         3   165
D599V12, multiclass
                           clus
vv                          TRIM27 MUTATED TRIM27 WILD-TYPE
  ASIAN                                  0               76
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  3              165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(600) Variable = MMP3 MUTATION ANALYSIS
D600V1, survival
                sevent
clus2              0   1
  MMP3 MUTATED     7   0
  MMP3 WILD-TYPE 174  80
  MMP3 MUTATED MMP3 WILD-TYPE 
             7            254 
  MMP3 MUTATED MMP3 WILD-TYPE 
             0             80 
$`MMP3 MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8361 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-A4YY 
       34.68        12.26        19.50         6.02       105.07        13.78 
TCGA-HU-8602 
       11.41 

$`MMP3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        5.92        15.16        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  MMP3 MUTATED MMP3 WILD-TYPE 
          6.02           0.00 
  MMP3 MUTATED MMP3 WILD-TYPE 
        105.07          79.07 
  MMP3 MUTATED MMP3 WILD-TYPE 
        13.780         12.605 
[1] "6.0 - 105.1 (13.8)" "0.0 - 79.1 (12.6)" 
[1] "hr="     "2.8e+07"
D600V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MMP3 MUTATED         0        0        0        1         1         2
  MMP3 WILD-TYPE       1        9       27       25        30        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MMP3 MUTATED           0          0          1          1        1
  MMP3 WILD-TYPE         3         49         35         23       23
D600V3, multiclass
            clus
vv           MMP3 MUTATED MMP3 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              1             25
  STAGE IIA             1             30
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            1             35
  STAGE IIIC            1             23
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MMP3 MUTATED     0   1   3   4
  MMP3 WILD-TYPE  11  71 119  71
D600V4, multiclass
    clus
vv   MMP3 MUTATED MMP3 WILD-TYPE
  T1            0             11
  T2            1             71
  T3            3            119
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  MMP3 MUTATED    3  2  1  1
  MMP3 WILD-TYPE 90 79 49 52
D600V5, multiclass
    clus
vv   MMP3 MUTATED MMP3 WILD-TYPE
  N0            3             90
  N1            2             79
  N2            1             49
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D600V6, binary
                cls
clus               0   1
  MMP3 MUTATED     7   0
  MMP3 WILD-TYPE 250  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP3 MUTATED      7    0
  MMP3 WILD-TYPE  250   18
   clus
vv  MMP3 MUTATED MMP3 WILD-TYPE
  0            7            250
  1            0             18
[1] 2 2
[1] FALSE
D600V7, binary
                cls
clus               0   1
  MMP3 MUTATED     5   3
  MMP3 WILD-TYPE 105 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP3 MUTATED      5    3
  MMP3 WILD-TYPE  105  176
        clus
vv       MMP3 MUTATED MMP3 WILD-TYPE
  FEMALE            5            105
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MMP3 MUTATED                                       1
  MMP3 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MMP3 MUTATED                                                        6
  MMP3 WILD-TYPE                                                    129
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MMP3 MUTATED                                                                   1
  MMP3 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MMP3 MUTATED                                                  0
  MMP3 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MMP3 MUTATED                                                          0
  MMP3 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MMP3 MUTATED                                                           0
  MMP3 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MMP3 MUTATED                                          0
  MMP3 WILD-TYPE                                        3
D600V8, multiclass
                                                                   clus
vv                                                                  MMP3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  MMP3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D600V9, binary
                cls
clus               0   1
  MMP3 MUTATED     0   8
  MMP3 WILD-TYPE   5 276
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP3 MUTATED      0    8
  MMP3 WILD-TYPE    5  276
     clus
vv    MMP3 MUTATED MMP3 WILD-TYPE
  NO             0              5
  YES            8            276
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MMP3 MUTATED     7   0   0   1
  MMP3 WILD-TYPE 220  10  10  23
D600V10, multiclass
    clus
vv   MMP3 MUTATED MMP3 WILD-TYPE
  R0            7            220
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D600V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MMP3 MUTATED       1                         0     5
  MMP3 WILD-TYPE    75                         4   163
D600V12, multiclass
                           clus
vv                          MMP3 MUTATED MMP3 WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                5            163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(601) Variable = IDE MUTATION ANALYSIS
D601V1, survival
               sevent
clus2             0   1
  IDE MUTATED     3   5
  IDE WILD-TYPE 178  75
  IDE MUTATED IDE WILD-TYPE 
            8           253 
  IDE MUTATED IDE WILD-TYPE 
            5            75 
$`IDE MUTATED`
TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-4465 TCGA-CG-5726 TCGA-HJ-7597 TCGA-HU-A4GH 
       15.81         6.58         9.01        28.96        26.47        11.77 
TCGA-HU-A4GQ TCGA-HU-A4GT 
        0.10         6.51 

$`IDE WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       19.07        12.03         0.00        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56        11.08         5.52         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       25.81        29.98         8.98         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  IDE MUTATED IDE WILD-TYPE 
          0.1           0.0 
  IDE MUTATED IDE WILD-TYPE 
        28.96        105.07 
  IDE MUTATED IDE WILD-TYPE 
        10.39         12.66 
[1] "0.1 - 29.0 (10.4)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "2.1"
D601V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IDE MUTATED         0        2        1        0         2         0
  IDE WILD-TYPE       1        7       26       26        29        44
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IDE MUTATED           0          1          0          1        2
  IDE WILD-TYPE         3         48         36         23       22
D601V3, multiclass
            clus
vv           IDE MUTATED IDE WILD-TYPE
  STAGE I              0             1
  STAGE IA             2             7
  STAGE IB             1            26
  STAGE II             0            26
  STAGE IIA            2            29
  STAGE IIB            0            44
  STAGE III            0             3
  STAGE IIIA           1            48
  STAGE IIIB           0            36
  STAGE IIIC           1            23
  STAGE IV             2            22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  IDE MUTATED     2   1   2   4
  IDE WILD-TYPE   9  71 120  71
D601V4, multiclass
    clus
vv   IDE MUTATED IDE WILD-TYPE
  T1           2             9
  T2           1            71
  T3           2           120
  T4           4            71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  IDE MUTATED    6  0  2  1
  IDE WILD-TYPE 87 81 48 52
D601V5, multiclass
    clus
vv   IDE MUTATED IDE WILD-TYPE
  N0           6            87
  N1           0            81
  N2           2            48
  N3           1            52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D601V6, binary
               cls
clus              0   1
  IDE MUTATED     6   2
  IDE WILD-TYPE 251  16
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDE MUTATED      6    2
  IDE WILD-TYPE  251   16
   clus
vv  IDE MUTATED IDE WILD-TYPE
  0           6           251
  1           2            16
[1] 2 2
[1] FALSE
D601V7, binary
               cls
clus              0   1
  IDE MUTATED     4   5
  IDE WILD-TYPE 106 174
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDE MUTATED      4    5
  IDE WILD-TYPE  106  174
        clus
vv       IDE MUTATED IDE WILD-TYPE
  FEMALE           4           106
  MALE             5           174
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  IDE MUTATED                                       2
  IDE WILD-TYPE                                    48
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IDE MUTATED                                                        1
  IDE WILD-TYPE                                                    134
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IDE MUTATED                                                                   1
  IDE WILD-TYPE                                                                39
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  IDE MUTATED                                                  4
  IDE WILD-TYPE                                               34
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  IDE MUTATED                                                          0
  IDE WILD-TYPE                                                       16
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  IDE MUTATED                                                           0
  IDE WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  IDE MUTATED                                          1
  IDE WILD-TYPE                                        2
D601V8, multiclass
                                                                   clus
vv                                                                  IDE MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      1
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    1
                                                                   clus
vv                                                                  IDE WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D601V9, binary
               cls
clus              0   1
  IDE MUTATED     0   9
  IDE WILD-TYPE   5 275
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDE MUTATED      0    9
  IDE WILD-TYPE    5  275
     clus
vv    IDE MUTATED IDE WILD-TYPE
  NO            0             5
  YES           9           275
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  IDE MUTATED     6   0   1   1
  IDE WILD-TYPE 221  10   9  23
D601V10, multiclass
    clus
vv   IDE MUTATED IDE WILD-TYPE
  R0           6           221
  R1           0            10
  R2           1             9
  RX           1            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D601V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IDE MUTATED       5                         0     2
  IDE WILD-TYPE    71                         4   166
D601V12, multiclass
                           clus
vv                          IDE MUTATED IDE WILD-TYPE
  ASIAN                               5            71
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                               2           166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(602) Variable = LARP7 MUTATION ANALYSIS
D602V1, survival
                 sevent
clus2               0   1
  LARP7 MUTATED     2   0
  LARP7 WILD-TYPE 179  80
  LARP7 MUTATED LARP7 WILD-TYPE 
              2             259 
  LARP7 MUTATED LARP7 WILD-TYPE 
              0              80 
$`LARP7 MUTATED`
TCGA-BR-6852 TCGA-CD-A486 
       32.94         3.42 

$`LARP7 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        30.90        31.20        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.13         0.10         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  LARP7 MUTATED LARP7 WILD-TYPE 
           3.42            0.00 
  LARP7 MUTATED LARP7 WILD-TYPE 
          32.94          105.07 
  LARP7 MUTATED LARP7 WILD-TYPE 
          18.18           12.62 
[1] "3.4 - 32.9 (18.2)"  "0.0 - 105.1 (12.6)"
[1] "Remove cluster labels:" "LARP7 MUTATED"         
D602V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LARP7 MUTATED         1        0        0        0         2         0
  LARP7 WILD-TYPE       0        9       27       26        29        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LARP7 MUTATED           0          0          0          0        0
  LARP7 WILD-TYPE         3         49         36         24       24
D602V3, multiclass
            clus
vv           LARP7 MUTATED LARP7 WILD-TYPE
  STAGE I                1               0
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LARP7 MUTATED     1   0   2   0
  LARP7 WILD-TYPE  10  72 120  75
D602V4, multiclass
    clus
vv   LARP7 MUTATED LARP7 WILD-TYPE
  T1             1              10
  T2             0              72
  T3             2             120
  T4             0              75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  LARP7 MUTATED    2  1  0  0
  LARP7 WILD-TYPE 91 80 50 53
D602V5, multiclass
    clus
vv   LARP7 MUTATED LARP7 WILD-TYPE
  N0             2              91
  N1             1              80
  N2             0              50
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D602V6, binary
                 cls
clus                0   1
  LARP7 MUTATED     2   0
  LARP7 WILD-TYPE 255  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP7 MUTATED      2    0
  LARP7 WILD-TYPE  255   18
   clus
vv  LARP7 MUTATED LARP7 WILD-TYPE
  0             2             255
  1             0              18
[1] 2 2
[1] FALSE
D602V7, binary
                 cls
clus                0   1
  LARP7 MUTATED     1   2
  LARP7 WILD-TYPE 109 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP7 MUTATED      1    2
  LARP7 WILD-TYPE  109  177
        clus
vv       LARP7 MUTATED LARP7 WILD-TYPE
  FEMALE             1             109
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  LARP7 MUTATED                                       0
  LARP7 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LARP7 MUTATED                                                        3
  LARP7 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LARP7 MUTATED                                                                   0
  LARP7 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  LARP7 MUTATED                                                  0
  LARP7 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  LARP7 MUTATED                                                          0
  LARP7 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  LARP7 MUTATED                                                           0
  LARP7 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  LARP7 MUTATED                                          0
  LARP7 WILD-TYPE                                        3
D602V8, multiclass
                                                                   clus
vv                                                                  LARP7 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  LARP7 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D602V9, binary
                 cls
clus                0   1
  LARP7 MUTATED     0   3
  LARP7 WILD-TYPE   5 281
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP7 MUTATED      0    3
  LARP7 WILD-TYPE    5  281
     clus
vv    LARP7 MUTATED LARP7 WILD-TYPE
  NO              0               5
  YES             3             281
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LARP7 MUTATED     2   0   0   0
  LARP7 WILD-TYPE 225  10  10  24
D602V10, multiclass
[1] "Remove cluster labels:" "LARP7 MUTATED"         
clus
  LARP7 MUTATED LARP7 WILD-TYPE 
              2             269 
     TCGA-B7-5816      TCGA-B7-5818      TCGA-BR-4183      TCGA-BR-4184 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-4187      TCGA-BR-4188      TCGA-BR-4191      TCGA-BR-4201 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256      TCGA-BR-4257 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4292 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-4294      TCGA-BR-4357      TCGA-BR-4361      TCGA-BR-4362 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-4363      TCGA-BR-4366      TCGA-BR-4368      TCGA-BR-4369 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-4370      TCGA-BR-4371      TCGA-BR-6452      TCGA-BR-6453 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703      TCGA-BR-7707 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-7715      TCGA-BR-7716      TCGA-BR-7717      TCGA-BR-7722 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-7723      TCGA-BR-7851      TCGA-BR-7901      TCGA-BR-7957 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-7958      TCGA-BR-7959      TCGA-BR-8058      TCGA-BR-8059 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8077      TCGA-BR-8078      TCGA-BR-8080      TCGA-BR-8081 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8284      TCGA-BR-8286      TCGA-BR-8289      TCGA-BR-8291 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8295      TCGA-BR-8296      TCGA-BR-8297      TCGA-BR-8360 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8361      TCGA-BR-8363      TCGA-BR-8364      TCGA-BR-8365 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8366      TCGA-BR-8367      TCGA-BR-8368      TCGA-BR-8369 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8370      TCGA-BR-8371      TCGA-BR-8372      TCGA-BR-8373 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8380      TCGA-BR-8381      TCGA-BR-8382      TCGA-BR-8384 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8483      TCGA-BR-8484      TCGA-BR-8485      TCGA-BR-8486 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8487      TCGA-BR-8588      TCGA-BR-8589      TCGA-BR-8590 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8591      TCGA-BR-8592      TCGA-BR-8676      TCGA-BR-8677 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8678      TCGA-BR-8679      TCGA-BR-8680      TCGA-BR-8682 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8683      TCGA-BR-8686      TCGA-BR-8687      TCGA-BR-8690 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-A44T      TCGA-BR-A44U      TCGA-BR-A452      TCGA-BR-A453 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-A4CQ      TCGA-BR-A4CR      TCGA-BR-A4CS      TCGA-BR-A4IU 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-A4IV      TCGA-BR-A4IY      TCGA-BR-A4IZ      TCGA-BR-A4J1 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-A4J2      TCGA-BR-A4J4      TCGA-BR-A4J6      TCGA-BR-A4J7 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-A4J8      TCGA-BR-A4PD      TCGA-BR-A4PE      TCGA-BR-A4PF 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-A4QI      TCGA-BR-A4QL      TCGA-BR-A4QM      TCGA-CD-5800 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CD-5801      TCGA-CD-5804      TCGA-CD-8524      TCGA-CD-8525 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CD-8526      TCGA-CD-8527      TCGA-CD-8528      TCGA-CD-8529 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CD-8530      TCGA-CD-8531      TCGA-CD-8532      TCGA-CD-8534 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CD-8535      TCGA-CD-8536      TCGA-CD-A487      TCGA-CG-4300 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CG-4301      TCGA-CG-4304      TCGA-CG-4305      TCGA-CG-4306 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CG-4436      TCGA-CG-4437      TCGA-CG-4438      TCGA-CG-4440 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CG-4441      TCGA-CG-4442      TCGA-CG-4443      TCGA-CG-4444 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CG-4449      TCGA-CG-4455      TCGA-CG-4462      TCGA-CG-4465 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CG-4466      TCGA-CG-4469      TCGA-CG-4474      TCGA-CG-4475 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CG-4476      TCGA-CG-4477      TCGA-CG-5717      TCGA-CG-5718 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CG-5719      TCGA-CG-5720      TCGA-CG-5721      TCGA-CG-5722 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CG-5723      TCGA-CG-5724      TCGA-CG-5726      TCGA-CG-5727 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CG-5728      TCGA-CG-5730      TCGA-CG-5732      TCGA-CG-5733 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CG-5734      TCGA-D7-5577      TCGA-D7-5578      TCGA-D7-5579 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-D7-6518      TCGA-D7-6519      TCGA-D7-6520      TCGA-D7-6521 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-D7-6522      TCGA-D7-6524      TCGA-D7-6525      TCGA-D7-6526 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-D7-6527      TCGA-D7-6528      TCGA-D7-6815      TCGA-D7-6817 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-D7-6818      TCGA-D7-6820      TCGA-D7-6822      TCGA-D7-8570 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-D7-8572      TCGA-D7-8573      TCGA-D7-8574      TCGA-D7-8575 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-D7-8576      TCGA-D7-8578      TCGA-D7-8579      TCGA-D7-A4YT 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-D7-A4YU      TCGA-D7-A4YV      TCGA-D7-A4YX      TCGA-D7-A4YY 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-D7-A4Z0      TCGA-EQ-5647      TCGA-EQ-A4SO      TCGA-F1-6874 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-F1-6875      TCGA-F1-A448      TCGA-FP-7735      TCGA-FP-7829 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-FP-7998      TCGA-FP-8099      TCGA-FP-8209      TCGA-FP-8211 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-FP-8631      TCGA-FP-A4BE      TCGA-FP-A4BF      TCGA-HF-7132 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-HF-7133      TCGA-HF-7136      TCGA-HJ-7597      TCGA-HU-8243 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-HU-8245      TCGA-HU-8249      TCGA-HU-8602      TCGA-HU-8604 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-HU-8608      TCGA-HU-8610      TCGA-HU-A4G2      TCGA-HU-A4G3 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-HU-A4G6      TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-HU-A4GF      TCGA-HU-A4GH      TCGA-HU-A4GN      TCGA-HU-A4GP 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-HU-A4GQ      TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-HU-A4GY      TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-HU-A4H4      TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-HU-A4HD      TCGA-IN-7806      TCGA-IN-8462      TCGA-IN-8663 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-IP-7968 
"LARP7 WILD-TYPE" 
D602V11, continuous
[1] "Remove cluster labels:" "LARP7 MUTATED"         
clus
  LARP7 MUTATED LARP7 WILD-TYPE 
              2             249 
     TCGA-B7-5816      TCGA-BR-4183      TCGA-BR-4184      TCGA-BR-4188 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-4191      TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4361 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-4362      TCGA-BR-4368      TCGA-BR-6452      TCGA-BR-6453 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703      TCGA-BR-7707 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-7715      TCGA-BR-7716      TCGA-BR-7717      TCGA-BR-7722 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-7723      TCGA-BR-7851      TCGA-BR-7901      TCGA-BR-7957 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-7958      TCGA-BR-7959      TCGA-BR-8058      TCGA-BR-8059 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8077      TCGA-BR-8078      TCGA-BR-8080      TCGA-BR-8081 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8284      TCGA-BR-8286      TCGA-BR-8289      TCGA-BR-8291 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8295      TCGA-BR-8296      TCGA-BR-8297      TCGA-BR-8360 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8361      TCGA-BR-8363      TCGA-BR-8364      TCGA-BR-8365 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8366      TCGA-BR-8367      TCGA-BR-8368      TCGA-BR-8369 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8370      TCGA-BR-8371      TCGA-BR-8372      TCGA-BR-8373 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8380      TCGA-BR-8381      TCGA-BR-8382      TCGA-BR-8384 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8483      TCGA-BR-8484      TCGA-BR-8485      TCGA-BR-8486 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8487      TCGA-BR-8588      TCGA-BR-8589      TCGA-BR-8590 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8591      TCGA-BR-8592      TCGA-BR-8676      TCGA-BR-8677 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8678      TCGA-BR-8679      TCGA-BR-8680      TCGA-BR-8682 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-8683      TCGA-BR-8686      TCGA-BR-8687      TCGA-BR-8690 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-A44T      TCGA-BR-A44U      TCGA-BR-A452      TCGA-BR-A453 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-A4CQ      TCGA-BR-A4CR      TCGA-BR-A4CS      TCGA-BR-A4IU 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-A4IV      TCGA-BR-A4IY      TCGA-BR-A4IZ      TCGA-BR-A4J1 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-A4J2      TCGA-BR-A4J4      TCGA-BR-A4J6      TCGA-BR-A4J8 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-A4PD      TCGA-BR-A4PE      TCGA-BR-A4PF      TCGA-BR-A4QI 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-BR-A4QL      TCGA-BR-A4QM      TCGA-CD-5804      TCGA-CD-8525 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CD-8526      TCGA-CD-8531      TCGA-CD-8535      TCGA-CD-A487 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CG-4301      TCGA-CG-4304      TCGA-CG-4305      TCGA-CG-4436 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CG-4437      TCGA-CG-4438      TCGA-CG-4440      TCGA-CG-4441 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CG-4442      TCGA-CG-4443      TCGA-CG-4444      TCGA-CG-4449 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CG-4455      TCGA-CG-4462      TCGA-CG-4465      TCGA-CG-4466 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CG-4469      TCGA-CG-4474      TCGA-CG-4475      TCGA-CG-4476 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CG-4477      TCGA-CG-5717      TCGA-CG-5718      TCGA-CG-5719 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CG-5720      TCGA-CG-5721      TCGA-CG-5722      TCGA-CG-5723 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CG-5724      TCGA-CG-5726      TCGA-CG-5727      TCGA-CG-5728 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-CG-5730      TCGA-CG-5732      TCGA-CG-5733      TCGA-CG-5734 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-D7-5577      TCGA-D7-5578      TCGA-D7-5579      TCGA-D7-6518 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-D7-6519      TCGA-D7-6520      TCGA-D7-6521      TCGA-D7-6522 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-D7-6524      TCGA-D7-6525      TCGA-D7-6526      TCGA-D7-6527 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-D7-6528      TCGA-D7-6815      TCGA-D7-6817      TCGA-D7-6818 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-D7-6820      TCGA-D7-6822      TCGA-D7-8570      TCGA-D7-8572 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-D7-8573      TCGA-D7-8574      TCGA-D7-8575      TCGA-D7-8576 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-D7-8578      TCGA-D7-8579      TCGA-D7-A4YT      TCGA-D7-A4YU 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-D7-A4YV      TCGA-D7-A4YX      TCGA-D7-A4YY      TCGA-D7-A4Z0 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-EQ-5647      TCGA-EQ-8122      TCGA-EQ-A4SO      TCGA-F1-6874 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-F1-6875      TCGA-F1-A448      TCGA-FP-7735      TCGA-FP-7829 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-FP-7916      TCGA-FP-7998      TCGA-FP-8099      TCGA-FP-8209 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-FP-8210      TCGA-FP-8211      TCGA-FP-8631      TCGA-FP-A4BE 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-FP-A4BF      TCGA-HF-7132      TCGA-HF-7133      TCGA-HF-7136 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-HJ-7597      TCGA-HU-8243      TCGA-HU-8245      TCGA-HU-8249 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-HU-8602      TCGA-HU-8604      TCGA-HU-8608      TCGA-HU-8610 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-HU-A4G2      TCGA-HU-A4G3      TCGA-HU-A4G6      TCGA-HU-A4G8 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD      TCGA-HU-A4GF 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-HU-A4GH      TCGA-HU-A4GN      TCGA-HU-A4GP      TCGA-HU-A4GQ 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX      TCGA-HU-A4GY 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3      TCGA-HU-A4H4 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8      TCGA-HU-A4HD 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-IN-7806      TCGA-IN-7808      TCGA-IN-8462      TCGA-IN-8663 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-IP-7968 
"LARP7 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LARP7 MUTATED       1                         1     1
  LARP7 WILD-TYPE    75                         3   167
D602V12, multiclass
                           clus
vv                          LARP7 MUTATED LARP7 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 1             167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(603) Variable = KIF6 MUTATION ANALYSIS
D603V1, survival
                sevent
clus2              0   1
  KIF6 MUTATED     4   1
  KIF6 WILD-TYPE 177  79
  KIF6 MUTATED KIF6 WILD-TYPE 
             5            256 
  KIF6 MUTATED KIF6 WILD-TYPE 
             1             79 
$`KIF6 MUTATED`
TCGA-BR-6452 TCGA-BR-8683 TCGA-BR-8686 TCGA-CD-A4MI TCGA-FP-A4BE 
       34.68         9.86        15.68         0.10        11.08 

$`KIF6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       15.81        16.44         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  KIF6 MUTATED KIF6 WILD-TYPE 
           0.1            0.0 
  KIF6 MUTATED KIF6 WILD-TYPE 
         34.68         105.07 
  KIF6 MUTATED KIF6 WILD-TYPE 
         11.08          12.64 
[1] "0.1 - 34.7 (11.1)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.6"
D603V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIF6 MUTATED         0        0        0        0         2         0
  KIF6 WILD-TYPE       1        9       27       26        29        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIF6 MUTATED           0          1          3          0        0
  KIF6 WILD-TYPE         3         48         33         24       24
D603V3, multiclass
            clus
vv           KIF6 MUTATED KIF6 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              0             26
  STAGE IIA             2             29
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            3             33
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KIF6 MUTATED     0   0   4   2
  KIF6 WILD-TYPE  11  72 118  73
D603V4, multiclass
    clus
vv   KIF6 MUTATED KIF6 WILD-TYPE
  T1            0             11
  T2            0             72
  T3            4            118
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  KIF6 MUTATED    2  4  1  0
  KIF6 WILD-TYPE 91 77 49 53
D603V5, multiclass
    clus
vv   KIF6 MUTATED KIF6 WILD-TYPE
  N0            2             91
  N1            4             77
  N2            1             49
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D603V6, binary
                cls
clus               0   1
  KIF6 MUTATED     7   0
  KIF6 WILD-TYPE 250  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  KIF6 MUTATED      7    0
  KIF6 WILD-TYPE  250   18
   clus
vv  KIF6 MUTATED KIF6 WILD-TYPE
  0            7            250
  1            0             18
[1] 2 2
[1] FALSE
D603V7, binary
                cls
clus               0   1
  KIF6 MUTATED     3   4
  KIF6 WILD-TYPE 107 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  KIF6 MUTATED      3    4
  KIF6 WILD-TYPE  107  175
        clus
vv       KIF6 MUTATED KIF6 WILD-TYPE
  FEMALE            3            107
  MALE              4            175
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KIF6 MUTATED                                       0
  KIF6 WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIF6 MUTATED                                                        5
  KIF6 WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIF6 MUTATED                                                                   0
  KIF6 WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KIF6 MUTATED                                                  2
  KIF6 WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KIF6 MUTATED                                                          0
  KIF6 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KIF6 MUTATED                                                           0
  KIF6 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KIF6 MUTATED                                          0
  KIF6 WILD-TYPE                                        3
D603V8, multiclass
                                                                   clus
vv                                                                  KIF6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  KIF6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D603V9, binary
                cls
clus               0   1
  KIF6 MUTATED     0   7
  KIF6 WILD-TYPE   5 277
[1] "tbl2"
                cls
clus             [,1] [,2]
  KIF6 MUTATED      0    7
  KIF6 WILD-TYPE    5  277
     clus
vv    KIF6 MUTATED KIF6 WILD-TYPE
  NO             0              5
  YES            7            277
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  KIF6 MUTATED     4   0   0   2
  KIF6 WILD-TYPE 223  10  10  22
D603V10, multiclass
    clus
vv   KIF6 MUTATED KIF6 WILD-TYPE
  R0            4            223
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D603V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIF6 MUTATED       3                         1     3
  KIF6 WILD-TYPE    73                         3   165
D603V12, multiclass
                           clus
vv                          KIF6 MUTATED KIF6 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                                3            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(604) Variable = PLEKHH3 MUTATION ANALYSIS
D604V1, survival
                   sevent
clus2                 0   1
  PLEKHH3 MUTATED     7   0
  PLEKHH3 WILD-TYPE 174  80
  PLEKHH3 MUTATED PLEKHH3 WILD-TYPE 
                7               254 
  PLEKHH3 MUTATED PLEKHH3 WILD-TYPE 
                0                80 
$`PLEKHH3 MUTATED`
TCGA-BR-8360 TCGA-BR-8487 TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5727 
        6.18         1.12        15.95         6.02       105.07        79.07 
TCGA-F1-A448 
       21.27 

$`PLEKHH3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        72.23         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  PLEKHH3 MUTATED PLEKHH3 WILD-TYPE 
             1.12              0.00 
  PLEKHH3 MUTATED PLEKHH3 WILD-TYPE 
           105.07             72.23 
  PLEKHH3 MUTATED PLEKHH3 WILD-TYPE 
           15.950            12.605 
[1] "1.1 - 105.1 (15.9)" "0.0 - 72.2 (12.6)" 
[1] "hr="     "4.1e+07"
D604V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLEKHH3 MUTATED         1        0        1        3         2         0
  PLEKHH3 WILD-TYPE       0        9       26       23        29        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHH3 MUTATED           0          0          1          0        1
  PLEKHH3 WILD-TYPE         3         49         35         24       23
D604V3, multiclass
            clus
vv           PLEKHH3 MUTATED PLEKHH3 WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 3                23
  STAGE IIA                2                29
  STAGE IIB                0                44
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               1                35
  STAGE IIIC               0                24
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHH3 MUTATED     1   3   4   1
  PLEKHH3 WILD-TYPE  10  69 118  74
D604V4, multiclass
    clus
vv   PLEKHH3 MUTATED PLEKHH3 WILD-TYPE
  T1               1                10
  T2               3                69
  T3               4               118
  T4               1                74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  PLEKHH3 MUTATED    4  4  0  1
  PLEKHH3 WILD-TYPE 89 77 50 52
D604V5, multiclass
    clus
vv   PLEKHH3 MUTATED PLEKHH3 WILD-TYPE
  N0               4                89
  N1               4                77
  N2               0                50
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D604V6, binary
                   cls
clus                  0   1
  PLEKHH3 MUTATED     8   0
  PLEKHH3 WILD-TYPE 249  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHH3 MUTATED      8    0
  PLEKHH3 WILD-TYPE  249   18
   clus
vv  PLEKHH3 MUTATED PLEKHH3 WILD-TYPE
  0               8               249
  1               0                18
[1] 2 2
[1] FALSE
D604V7, binary
                   cls
clus                  0   1
  PLEKHH3 MUTATED     1   8
  PLEKHH3 WILD-TYPE 109 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHH3 MUTATED      1    8
  PLEKHH3 WILD-TYPE  109  171
        clus
vv       PLEKHH3 MUTATED PLEKHH3 WILD-TYPE
  FEMALE               1               109
  MALE                 8               171
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PLEKHH3 MUTATED                                       0
  PLEKHH3 WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLEKHH3 MUTATED                                                        4
  PLEKHH3 WILD-TYPE                                                    131
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PLEKHH3 MUTATED                                                                   4
  PLEKHH3 WILD-TYPE                                                                36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PLEKHH3 MUTATED                                                  0
  PLEKHH3 WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PLEKHH3 MUTATED                                                          1
  PLEKHH3 WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PLEKHH3 MUTATED                                                           0
  PLEKHH3 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PLEKHH3 MUTATED                                          0
  PLEKHH3 WILD-TYPE                                        3
D604V8, multiclass
                                                                   clus
vv                                                                  PLEKHH3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  PLEKHH3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D604V9, binary
                   cls
clus                  0   1
  PLEKHH3 MUTATED     0   9
  PLEKHH3 WILD-TYPE   5 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHH3 MUTATED      0    9
  PLEKHH3 WILD-TYPE    5  275
     clus
vv    PLEKHH3 MUTATED PLEKHH3 WILD-TYPE
  NO                0                 5
  YES               9               275
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PLEKHH3 MUTATED     9   0   0   0
  PLEKHH3 WILD-TYPE 218  10  10  24
D604V10, multiclass
    clus
vv   PLEKHH3 MUTATED PLEKHH3 WILD-TYPE
  R0               9               218
  R1               0                10
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D604V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLEKHH3 MUTATED       0                         1     3
  PLEKHH3 WILD-TYPE    76                         3   165
D604V12, multiclass
                           clus
vv                          PLEKHH3 MUTATED PLEKHH3 WILD-TYPE
  ASIAN                                   0                76
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   3               165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(605) Variable = WSB2 MUTATION ANALYSIS
D605V1, survival
                sevent
clus2              0   1
  WSB2 MUTATED     7   0
  WSB2 WILD-TYPE 174  80
  WSB2 MUTATED WSB2 WILD-TYPE 
             7            254 
  WSB2 MUTATED WSB2 WILD-TYPE 
             0             80 
$`WSB2 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-8589 TCGA-BR-A4QM TCGA-CG-4437 
       34.68        32.94        24.76        15.81         5.13         8.05 
TCGA-CG-5723 
      105.07 

$`WSB2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 
       21.11        30.90        31.20        12.82         9.21        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        12.79         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         7.99        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         6.02         0.99        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  WSB2 MUTATED WSB2 WILD-TYPE 
          5.13           0.00 
  WSB2 MUTATED WSB2 WILD-TYPE 
        105.07          79.07 
  WSB2 MUTATED WSB2 WILD-TYPE 
        24.760         12.575 
[1] "5.1 - 105.1 (24.8)" "0.0 - 79.1 (12.6)" 
[1] "hr="     "2.9e+07"
D605V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WSB2 MUTATED         1        1        1        2         2         0
  WSB2 WILD-TYPE       0        8       26       24        29        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WSB2 MUTATED           0          1          1          0        0
  WSB2 WILD-TYPE         3         48         35         24       24
D605V3, multiclass
            clus
vv           WSB2 MUTATED WSB2 WILD-TYPE
  STAGE I               1              0
  STAGE IA              1              8
  STAGE IB              1             26
  STAGE II              2             24
  STAGE IIA             2             29
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WSB2 MUTATED     2   3   3   1
  WSB2 WILD-TYPE   9  69 119  74
D605V4, multiclass
    clus
vv   WSB2 MUTATED WSB2 WILD-TYPE
  T1            2              9
  T2            3             69
  T3            3            119
  T4            1             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  WSB2 MUTATED    4  4  1  0
  WSB2 WILD-TYPE 89 77 49 53
D605V5, multiclass
    clus
vv   WSB2 MUTATED WSB2 WILD-TYPE
  N0            4             89
  N1            4             77
  N2            1             49
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D605V6, binary
                cls
clus               0   1
  WSB2 MUTATED     8   0
  WSB2 WILD-TYPE 249  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  WSB2 MUTATED      8    0
  WSB2 WILD-TYPE  249   18
   clus
vv  WSB2 MUTATED WSB2 WILD-TYPE
  0            8            249
  1            0             18
[1] 2 2
[1] FALSE
D605V7, binary
                cls
clus               0   1
  WSB2 MUTATED     2   7
  WSB2 WILD-TYPE 108 172
[1] "tbl2"
                cls
clus             [,1] [,2]
  WSB2 MUTATED      2    7
  WSB2 WILD-TYPE  108  172
        clus
vv       WSB2 MUTATED WSB2 WILD-TYPE
  FEMALE            2            108
  MALE              7            172
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  WSB2 MUTATED                                       0
  WSB2 WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WSB2 MUTATED                                                        6
  WSB2 WILD-TYPE                                                    129
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  WSB2 MUTATED                                                                   2
  WSB2 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  WSB2 MUTATED                                                  0
  WSB2 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  WSB2 MUTATED                                                          0
  WSB2 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  WSB2 MUTATED                                                           1
  WSB2 WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  WSB2 MUTATED                                          0
  WSB2 WILD-TYPE                                        3
D605V8, multiclass
                                                                   clus
vv                                                                  WSB2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  WSB2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D605V9, binary
                cls
clus               0   1
  WSB2 MUTATED     0   9
  WSB2 WILD-TYPE   5 275
[1] "tbl2"
                cls
clus             [,1] [,2]
  WSB2 MUTATED      0    9
  WSB2 WILD-TYPE    5  275
     clus
vv    WSB2 MUTATED WSB2 WILD-TYPE
  NO             0              5
  YES            9            275
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  WSB2 MUTATED     9   0   0   0
  WSB2 WILD-TYPE 218  10  10  24
D605V10, multiclass
    clus
vv   WSB2 MUTATED WSB2 WILD-TYPE
  R0            9            218
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D605V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WSB2 MUTATED       0                         1     5
  WSB2 WILD-TYPE    76                         3   163
D605V12, multiclass
                           clus
vv                          WSB2 MUTATED WSB2 WILD-TYPE
  ASIAN                                0             76
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                                5            163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(606) Variable = KIAA1609 MUTATION ANALYSIS
D606V1, survival
                    sevent
clus2                  0   1
  KIAA1609 MUTATED     5   0
  KIAA1609 WILD-TYPE 176  80
  KIAA1609 MUTATED KIAA1609 WILD-TYPE 
                 5                256 
  KIAA1609 MUTATED KIAA1609 WILD-TYPE 
                 0                 80 
$`KIAA1609 MUTATED`
TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8361 TCGA-CG-5721 TCGA-HU-A4G9 
       12.26         6.18        19.50         6.02        24.20 

$`KIAA1609 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        7.40         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        11.84         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  KIAA1609 MUTATED KIAA1609 WILD-TYPE 
              6.02               0.00 
  KIAA1609 MUTATED KIAA1609 WILD-TYPE 
             24.20             105.07 
  KIAA1609 MUTATED KIAA1609 WILD-TYPE 
             12.26              12.64 
[1] "6.0 - 24.2 (12.3)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "9200000"
D606V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1609 MUTATED         0        1        0        0         1         1
  KIAA1609 WILD-TYPE       1        8       27       26        30        43
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1609 MUTATED           0          0          0          1        1
  KIAA1609 WILD-TYPE         3         49         36         23       23
D606V3, multiclass
            clus
vv           KIAA1609 MUTATED KIAA1609 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  1                  8
  STAGE IB                  0                 27
  STAGE II                  0                 26
  STAGE IIA                 1                 30
  STAGE IIB                 1                 43
  STAGE III                 0                  3
  STAGE IIIA                0                 49
  STAGE IIIB                0                 36
  STAGE IIIC                1                 23
  STAGE IV                  1                 23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1609 MUTATED     1   0   1   3
  KIAA1609 WILD-TYPE  10  72 121  72
D606V4, multiclass
    clus
vv   KIAA1609 MUTATED KIAA1609 WILD-TYPE
  T1                1                 10
  T2                0                 72
  T3                1                121
  T4                3                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  KIAA1609 MUTATED    3  2  1  0
  KIAA1609 WILD-TYPE 90 79 49 53
D606V5, multiclass
    clus
vv   KIAA1609 MUTATED KIAA1609 WILD-TYPE
  N0                3                 90
  N1                2                 79
  N2                1                 49
  N3                0                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D606V6, binary
                    cls
clus                   0   1
  KIAA1609 MUTATED     7   0
  KIAA1609 WILD-TYPE 250  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1609 MUTATED      7    0
  KIAA1609 WILD-TYPE  250   18
   clus
vv  KIAA1609 MUTATED KIAA1609 WILD-TYPE
  0                7                250
  1                0                 18
[1] 2 2
[1] FALSE
D606V7, binary
                    cls
clus                   0   1
  KIAA1609 MUTATED     4   3
  KIAA1609 WILD-TYPE 106 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1609 MUTATED      4    3
  KIAA1609 WILD-TYPE  106  176
        clus
vv       KIAA1609 MUTATED KIAA1609 WILD-TYPE
  FEMALE                4                106
  MALE                  3                176
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KIAA1609 MUTATED                                       0
  KIAA1609 WILD-TYPE                                    50
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA1609 MUTATED                                                        4
  KIAA1609 WILD-TYPE                                                    131
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA1609 MUTATED                                                                   2
  KIAA1609 WILD-TYPE                                                                38
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KIAA1609 MUTATED                                                  1
  KIAA1609 WILD-TYPE                                               37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KIAA1609 MUTATED                                                          0
  KIAA1609 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KIAA1609 MUTATED                                                           0
  KIAA1609 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KIAA1609 MUTATED                                          0
  KIAA1609 WILD-TYPE                                        3
D606V8, multiclass
                                                                   clus
vv                                                                  KIAA1609 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  KIAA1609 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D606V9, binary
                    cls
clus                   0   1
  KIAA1609 MUTATED     0   7
  KIAA1609 WILD-TYPE   5 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1609 MUTATED      0    7
  KIAA1609 WILD-TYPE    5  277
     clus
vv    KIAA1609 MUTATED KIAA1609 WILD-TYPE
  NO                 0                  5
  YES                7                277
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA1609 MUTATED     5   0   0   2
  KIAA1609 WILD-TYPE 222  10  10  22
D606V10, multiclass
    clus
vv   KIAA1609 MUTATED KIAA1609 WILD-TYPE
  R0                5                222
  R1                0                 10
  R2                0                 10
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D606V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA1609 MUTATED       1                         0     5
  KIAA1609 WILD-TYPE    75                         4   163
D606V12, multiclass
                           clus
vv                          KIAA1609 MUTATED KIAA1609 WILD-TYPE
  ASIAN                                    1                 75
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    5                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(607) Variable = AKAP11 MUTATION ANALYSIS
D607V1, survival
                  sevent
clus2                0   1
  AKAP11 MUTATED    11   2
  AKAP11 WILD-TYPE 170  78
  AKAP11 MUTATED AKAP11 WILD-TYPE 
              13              248 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
               2               78 
$`AKAP11 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7851 TCGA-BR-8368 TCGA-BR-8678 TCGA-CG-4465 
        6.97        34.68        12.43         4.31        11.54         9.01 
TCGA-CG-5721 TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
        6.02        25.81        29.98         6.51         6.25        10.19 
TCGA-HU-A4H3 
       19.36 

$`AKAP11 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP 
       11.84        24.20         3.25        22.75        11.77         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.10         0.26         2.10        12.95        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  AKAP11 MUTATED AKAP11 WILD-TYPE 
            4.31             0.00 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
           34.68           105.07 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
          10.190           12.775 
[1] "4.3 - 34.7 (10.2)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "2.1"
D607V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AKAP11 MUTATED         0        0        2        0         4         2
  AKAP11 WILD-TYPE       1        9       25       26        27        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AKAP11 MUTATED           0          2          0          2        2
  AKAP11 WILD-TYPE         3         47         36         22       22
D607V3, multiclass
            clus
vv           AKAP11 MUTATED AKAP11 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                2               25
  STAGE II                0               26
  STAGE IIA               4               27
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              0               36
  STAGE IIIC              2               22
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  AKAP11 MUTATED     0   3   5   6
  AKAP11 WILD-TYPE  11  69 117  69
D607V4, multiclass
    clus
vv   AKAP11 MUTATED AKAP11 WILD-TYPE
  T1              0               11
  T2              3               69
  T3              5              117
  T4              6               69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  AKAP11 MUTATED    7  4  1  2
  AKAP11 WILD-TYPE 86 77 49 51
D607V5, multiclass
    clus
vv   AKAP11 MUTATED AKAP11 WILD-TYPE
  N0              7               86
  N1              4               77
  N2              1               49
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D607V6, binary
                  cls
clus                 0   1
  AKAP11 MUTATED    12   1
  AKAP11 WILD-TYPE 245  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED     12    1
  AKAP11 WILD-TYPE  245   17
   clus
vv  AKAP11 MUTATED AKAP11 WILD-TYPE
  0             12              245
  1              1               17
[1] 2 2
[1] FALSE
D607V7, binary
                  cls
clus                 0   1
  AKAP11 MUTATED     7   7
  AKAP11 WILD-TYPE 103 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED      7    7
  AKAP11 WILD-TYPE  103  172
        clus
vv       AKAP11 MUTATED AKAP11 WILD-TYPE
  FEMALE              7              103
  MALE                7              172
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AKAP11 MUTATED                                       4
  AKAP11 WILD-TYPE                                    46
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AKAP11 MUTATED                                                        5
  AKAP11 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AKAP11 MUTATED                                                                   2
  AKAP11 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AKAP11 MUTATED                                                  3
  AKAP11 WILD-TYPE                                               35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AKAP11 MUTATED                                                          0
  AKAP11 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AKAP11 MUTATED                                                           0
  AKAP11 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AKAP11 MUTATED                                          0
  AKAP11 WILD-TYPE                                        3
D607V8, multiclass
                                                                   clus
vv                                                                  AKAP11 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  AKAP11 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D607V9, binary
                  cls
clus                 0   1
  AKAP11 MUTATED     0  14
  AKAP11 WILD-TYPE   5 270
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED      0   14
  AKAP11 WILD-TYPE    5  270
     clus
vv    AKAP11 MUTATED AKAP11 WILD-TYPE
  NO               0                5
  YES             14              270
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  AKAP11 MUTATED    11   0   1   2
  AKAP11 WILD-TYPE 216  10   9  22
D607V10, multiclass
    clus
vv   AKAP11 MUTATED AKAP11 WILD-TYPE
  R0             11              216
  R1              0               10
  R2              1                9
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D607V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AKAP11 MUTATED       6                         0     6
  AKAP11 WILD-TYPE    70                         4   162
D607V12, multiclass
                           clus
vv                          AKAP11 MUTATED AKAP11 WILD-TYPE
  ASIAN                                  6               70
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(608) Variable = VASH1 MUTATION ANALYSIS
D608V1, survival
                 sevent
clus2               0   1
  VASH1 MUTATED     6   1
  VASH1 WILD-TYPE 175  79
  VASH1 MUTATED VASH1 WILD-TYPE 
              7             254 
  VASH1 MUTATED VASH1 WILD-TYPE 
              1              79 
$`VASH1 MUTATED`
TCGA-BR-6705 TCGA-BR-6852 TCGA-BR-8680 TCGA-CD-A4MJ TCGA-CG-4305 TCGA-HU-A4G9 
       25.61        32.94        15.81        12.62        15.95        24.20 
TCGA-HU-A4GU 
        6.25 

$`VASH1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        32.78        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        11.84         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       11.77        29.98         8.98         0.10         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  VASH1 MUTATED VASH1 WILD-TYPE 
           6.25            0.00 
  VASH1 MUTATED VASH1 WILD-TYPE 
          32.94          105.07 
  VASH1 MUTATED VASH1 WILD-TYPE 
         15.950          12.495 
[1] "6.2 - 32.9 (15.9)"  "0.0 - 105.1 (12.5)"
[1] "hr=" "3"  
D608V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  VASH1 MUTATED         0        1        1        1         1         1
  VASH1 WILD-TYPE       1        8       26       25        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VASH1 MUTATED           0          0          1          0        1
  VASH1 WILD-TYPE         3         49         35         24       23
D608V3, multiclass
            clus
vv           VASH1 MUTATED VASH1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  VASH1 MUTATED     1   2   3   1
  VASH1 WILD-TYPE  10  70 119  74
D608V4, multiclass
    clus
vv   VASH1 MUTATED VASH1 WILD-TYPE
  T1             1              10
  T2             2              70
  T3             3             119
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  VASH1 MUTATED    3  2  1  1
  VASH1 WILD-TYPE 90 79 49 52
D608V5, multiclass
    clus
vv   VASH1 MUTATED VASH1 WILD-TYPE
  N0             3              90
  N1             2              79
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D608V6, binary
                 cls
clus                0   1
  VASH1 MUTATED     6   1
  VASH1 WILD-TYPE 251  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VASH1 MUTATED      6    1
  VASH1 WILD-TYPE  251   17
   clus
vv  VASH1 MUTATED VASH1 WILD-TYPE
  0             6             251
  1             1              17
[1] 2 2
[1] FALSE
D608V7, binary
                 cls
clus                0   1
  VASH1 MUTATED     3   4
  VASH1 WILD-TYPE 107 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VASH1 MUTATED      3    4
  VASH1 WILD-TYPE  107  175
        clus
vv       VASH1 MUTATED VASH1 WILD-TYPE
  FEMALE             3             107
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  VASH1 MUTATED                                       1
  VASH1 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  VASH1 MUTATED                                                        4
  VASH1 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  VASH1 MUTATED                                                                   0
  VASH1 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  VASH1 MUTATED                                                  2
  VASH1 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  VASH1 MUTATED                                                          0
  VASH1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  VASH1 MUTATED                                                           0
  VASH1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  VASH1 MUTATED                                          0
  VASH1 WILD-TYPE                                        3
D608V8, multiclass
                                                                   clus
vv                                                                  VASH1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  VASH1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D608V9, binary
                 cls
clus                0   1
  VASH1 MUTATED     0   7
  VASH1 WILD-TYPE   5 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VASH1 MUTATED      0    7
  VASH1 WILD-TYPE    5  277
     clus
vv    VASH1 MUTATED VASH1 WILD-TYPE
  NO              0               5
  YES             7             277
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  VASH1 MUTATED     6   0   0   0
  VASH1 WILD-TYPE 221  10  10  24
D608V10, multiclass
    clus
vv   VASH1 MUTATED VASH1 WILD-TYPE
  R0             6             221
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D608V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  VASH1 MUTATED       4                         0     2
  VASH1 WILD-TYPE    72                         4   166
D608V12, multiclass
                           clus
vv                          VASH1 MUTATED VASH1 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 2             166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(609) Variable = IFNA17 MUTATION ANALYSIS
D609V1, survival
                  sevent
clus2                0   1
  IFNA17 MUTATED     1   2
  IFNA17 WILD-TYPE 180  78
  IFNA17 MUTATED IFNA17 WILD-TYPE 
               3              258 
  IFNA17 MUTATED IFNA17 WILD-TYPE 
               2               78 
$`IFNA17 MUTATED`
TCGA-BR-8687 TCGA-CG-5721 TCGA-D7-6527 
        8.22         6.02        10.26 

$`IFNA17 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 
       11.54        15.81        16.44         9.86        15.68        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  IFNA17 MUTATED IFNA17 WILD-TYPE 
            6.02             0.00 
  IFNA17 MUTATED IFNA17 WILD-TYPE 
           10.26           105.07 
  IFNA17 MUTATED IFNA17 WILD-TYPE 
            8.22            12.71 
[1] "6.0 - 10.3 (8.2)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "4.3"
D609V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IFNA17 MUTATED         0        0        0        1         0         0
  IFNA17 WILD-TYPE       1        9       27       25        31        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IFNA17 MUTATED           0          0          0          1        1
  IFNA17 WILD-TYPE         3         49         36         23       23
D609V3, multiclass
            clus
vv           IFNA17 MUTATED IFNA17 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                1               25
  STAGE IIA               0               31
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IFNA17 MUTATED     0   1   0   2
  IFNA17 WILD-TYPE  11  71 122  73
D609V4, multiclass
    clus
vv   IFNA17 MUTATED IFNA17 WILD-TYPE
  T1              0               11
  T2              1               71
  T3              0              122
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  IFNA17 MUTATED    0  3  1  0
  IFNA17 WILD-TYPE 93 78 49 53
D609V5, multiclass
    clus
vv   IFNA17 MUTATED IFNA17 WILD-TYPE
  N0              0               93
  N1              3               78
  N2              1               49
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D609V6, binary
                  cls
clus                 0   1
  IFNA17 MUTATED     4   0
  IFNA17 WILD-TYPE 253  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNA17 MUTATED      4    0
  IFNA17 WILD-TYPE  253   18
   clus
vv  IFNA17 MUTATED IFNA17 WILD-TYPE
  0              4              253
  1              0               18
[1] 2 2
[1] FALSE
D609V7, binary
                  cls
clus                 0   1
  IFNA17 MUTATED     2   2
  IFNA17 WILD-TYPE 108 177
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNA17 MUTATED      2    2
  IFNA17 WILD-TYPE  108  177
        clus
vv       IFNA17 MUTATED IFNA17 WILD-TYPE
  FEMALE              2              108
  MALE                2              177
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  IFNA17 MUTATED                                       0
  IFNA17 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IFNA17 MUTATED                                                        2
  IFNA17 WILD-TYPE                                                    133
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IFNA17 MUTATED                                                                   1
  IFNA17 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  IFNA17 MUTATED                                                  0
  IFNA17 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  IFNA17 MUTATED                                                          0
  IFNA17 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  IFNA17 MUTATED                                                           1
  IFNA17 WILD-TYPE                                                         5
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  IFNA17 MUTATED                                          0
  IFNA17 WILD-TYPE                                        3
D609V8, multiclass
                                                                   clus
vv                                                                  IFNA17 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  IFNA17 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D609V9, binary
                  cls
clus                 0   1
  IFNA17 MUTATED     0   4
  IFNA17 WILD-TYPE   5 280
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNA17 MUTATED      0    4
  IFNA17 WILD-TYPE    5  280
     clus
vv    IFNA17 MUTATED IFNA17 WILD-TYPE
  NO               0                5
  YES              4              280
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  IFNA17 MUTATED     2   1   0   1
  IFNA17 WILD-TYPE 225   9  10  23
D609V10, multiclass
    clus
vv   IFNA17 MUTATED IFNA17 WILD-TYPE
  R0              2              225
  R1              1                9
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D609V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IFNA17 MUTATED       0                         0     3
  IFNA17 WILD-TYPE    76                         4   165
D609V12, multiclass
                           clus
vv                          IFNA17 MUTATED IFNA17 WILD-TYPE
  ASIAN                                  0               76
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  3              165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(610) Variable = SBF1 MUTATION ANALYSIS
D610V1, survival
                sevent
clus2              0   1
  SBF1 MUTATED    15   6
  SBF1 WILD-TYPE 166  74
  SBF1 MUTATED SBF1 WILD-TYPE 
            21            240 
  SBF1 MUTATED SBF1 WILD-TYPE 
             6             74 
$`SBF1 MUTATED`
TCGA-BR-7851 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8588 
       12.43        20.55         0.26        15.85         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4CS TCGA-CG-4300 TCGA-CG-4465 
        9.34        13.45        15.81         1.48        20.02         9.01 
TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5728 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4G9 
        6.02        28.96        65.10        11.41        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GN TCGA-HU-A4GT 
        3.25        29.98         6.51 

$`SBF1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       17.49        14.43         0.69        12.26         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        19.50        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        0.26         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8589 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       15.81         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08        22.26        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20         0.10        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 
        1.02         0.99         0.99       105.07        12.03        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.30         5.59        12.30        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  SBF1 MUTATED SBF1 WILD-TYPE 
          0.26           0.00 
  SBF1 MUTATED SBF1 WILD-TYPE 
         65.10         105.07 
  SBF1 MUTATED SBF1 WILD-TYPE 
         12.43          12.64 
[1] "0.3 - 65.1 (12.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D610V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SBF1 MUTATED         0        2        2        0         3         5
  SBF1 WILD-TYPE       1        7       25       26        28        39
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SBF1 MUTATED           0          2          2          4        3
  SBF1 WILD-TYPE         3         47         34         20       21
D610V3, multiclass
            clus
vv           SBF1 MUTATED SBF1 WILD-TYPE
  STAGE I               0              1
  STAGE IA              2              7
  STAGE IB              2             25
  STAGE II              0             26
  STAGE IIA             3             28
  STAGE IIB             5             39
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            2             34
  STAGE IIIC            4             20
  STAGE IV              3             21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SBF1 MUTATED     2   3   6  13
  SBF1 WILD-TYPE   9  69 116  62
D610V4, multiclass
    clus
vv   SBF1 MUTATED SBF1 WILD-TYPE
  T1            2              9
  T2            3             69
  T3            6            116
  T4           13             62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  SBF1 MUTATED   11  5  4  4
  SBF1 WILD-TYPE 82 76 46 49
D610V5, multiclass
    clus
vv   SBF1 MUTATED SBF1 WILD-TYPE
  N0           11             82
  N1            5             76
  N2            4             46
  N3            4             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D610V6, binary
                cls
clus               0   1
  SBF1 MUTATED    24   2
  SBF1 WILD-TYPE 233  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBF1 MUTATED     24    2
  SBF1 WILD-TYPE  233   16
   clus
vv  SBF1 MUTATED SBF1 WILD-TYPE
  0           24            233
  1            2             16
[1] 2 2
[1] FALSE
D610V7, binary
                cls
clus               0   1
  SBF1 MUTATED    16  11
  SBF1 WILD-TYPE  94 168
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBF1 MUTATED     16   11
  SBF1 WILD-TYPE   94  168
        clus
vv       SBF1 MUTATED SBF1 WILD-TYPE
  FEMALE           16             94
  MALE             11            168
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SBF1 MUTATED                                       4
  SBF1 WILD-TYPE                                    46
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SBF1 MUTATED                                                       15
  SBF1 WILD-TYPE                                                    120
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SBF1 MUTATED                                                                   4
  SBF1 WILD-TYPE                                                                36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SBF1 MUTATED                                                  4
  SBF1 WILD-TYPE                                               34
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SBF1 MUTATED                                                          0
  SBF1 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SBF1 MUTATED                                                           0
  SBF1 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SBF1 MUTATED                                          0
  SBF1 WILD-TYPE                                        3
D610V8, multiclass
                                                                   clus
vv                                                                  SBF1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      15
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  SBF1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       120
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D610V9, binary
                cls
clus               0   1
  SBF1 MUTATED     1  26
  SBF1 WILD-TYPE   4 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBF1 MUTATED      1   26
  SBF1 WILD-TYPE    4  258
     clus
vv    SBF1 MUTATED SBF1 WILD-TYPE
  NO             1              4
  YES           26            258
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SBF1 MUTATED    19   1   1   5
  SBF1 WILD-TYPE 208   9   9  19
D610V10, multiclass
    clus
vv   SBF1 MUTATED SBF1 WILD-TYPE
  R0           19            208
  R1            1              9
  R2            1              9
  RX            5             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D610V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SBF1 MUTATED       7                         0    14
  SBF1 WILD-TYPE    69                         4   154
D610V12, multiclass
                           clus
vv                          SBF1 MUTATED SBF1 WILD-TYPE
  ASIAN                                7             69
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               14            154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(611) Variable = SCN9A MUTATION ANALYSIS
D611V1, survival
                 sevent
clus2               0   1
  SCN9A MUTATED    21   5
  SCN9A WILD-TYPE 160  75
  SCN9A MUTATED SCN9A WILD-TYPE 
             26             235 
  SCN9A MUTATED SCN9A WILD-TYPE 
              5              75 
$`SCN9A MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7851 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8368 
        6.97        34.68        12.43         6.18        19.50         4.31 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4J7 
       19.17        14.79         9.21         1.12        15.81        19.36 
TCGA-CD-8527 TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 
        0.07        15.95         6.02        28.96        65.10        69.04 
TCGA-D7-6525 TCGA-D7-6527 TCGA-FP-A4BE TCGA-HU-A4G6 TCGA-HU-A4GH TCGA-HU-A4H3 
       13.35        10.26        11.08        12.30        11.77        19.36 
TCGA-HU-A4H4 TCGA-IP-7968 
       23.84         2.53 

$`SCN9A WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8363 
        2.66        16.31         2.20        15.58         7.40         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       11.80         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.72        14.17         0.53         0.66        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5733 
        0.99       105.07        12.03        79.07         4.01        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6528 
       18.84        18.54        18.61        17.85        17.19        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 
       59.54         5.03        13.58         0.56         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       22.75        25.81        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 
        6.25        10.19         0.26         2.10        12.95        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 
        3.39 

  SCN9A MUTATED SCN9A WILD-TYPE 
           0.07            0.00 
  SCN9A MUTATED SCN9A WILD-TYPE 
          69.04          105.07 
  SCN9A MUTATED SCN9A WILD-TYPE 
          12.89           12.62 
[1] "0.1 - 69.0 (12.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2"  
D611V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SCN9A MUTATED         0        3        2        3         4         3
  SCN9A WILD-TYPE       1        6       25       23        27        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SCN9A MUTATED           0          4          1          5        3
  SCN9A WILD-TYPE         3         45         35         19       21
D611V3, multiclass
            clus
vv           SCN9A MUTATED SCN9A WILD-TYPE
  STAGE I                0               1
  STAGE IA               3               6
  STAGE IB               2              25
  STAGE II               3              23
  STAGE IIA              4              27
  STAGE IIB              3              41
  STAGE III              0               3
  STAGE IIIA             4              45
  STAGE IIIB             1              35
  STAGE IIIC             5              19
  STAGE IV               3              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SCN9A MUTATED     3   8   6  11
  SCN9A WILD-TYPE   8  64 116  64
D611V4, multiclass
    clus
vv   SCN9A MUTATED SCN9A WILD-TYPE
  T1             3               8
  T2             8              64
  T3             6             116
  T4            11              64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  SCN9A MUTATED   11  6  5  5
  SCN9A WILD-TYPE 82 75 45 48
D611V5, multiclass
    clus
vv   SCN9A MUTATED SCN9A WILD-TYPE
  N0            11              82
  N1             6              75
  N2             5              45
  N3             5              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D611V6, binary
                 cls
clus                0   1
  SCN9A MUTATED    25   1
  SCN9A WILD-TYPE 232  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN9A MUTATED     25    1
  SCN9A WILD-TYPE  232   17
   clus
vv  SCN9A MUTATED SCN9A WILD-TYPE
  0            25             232
  1             1              17
[1] 2 2
[1] FALSE
D611V7, binary
                 cls
clus                0   1
  SCN9A MUTATED    11  17
  SCN9A WILD-TYPE  99 162
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN9A MUTATED     11   17
  SCN9A WILD-TYPE   99  162
        clus
vv       SCN9A MUTATED SCN9A WILD-TYPE
  FEMALE            11              99
  MALE              17             162
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SCN9A MUTATED                                       3
  SCN9A WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SCN9A MUTATED                                                       11
  SCN9A WILD-TYPE                                                    124
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SCN9A MUTATED                                                                   8
  SCN9A WILD-TYPE                                                                32
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SCN9A MUTATED                                                  3
  SCN9A WILD-TYPE                                               35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SCN9A MUTATED                                                          1
  SCN9A WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SCN9A MUTATED                                                           2
  SCN9A WILD-TYPE                                                         4
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SCN9A MUTATED                                          0
  SCN9A WILD-TYPE                                        3
D611V8, multiclass
                                                                   clus
vv                                                                  SCN9A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  SCN9A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D611V9, binary
                 cls
clus                0   1
  SCN9A MUTATED     0  28
  SCN9A WILD-TYPE   5 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN9A MUTATED      0   28
  SCN9A WILD-TYPE    5  256
     clus
vv    SCN9A MUTATED SCN9A WILD-TYPE
  NO              0               5
  YES            28             256
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SCN9A MUTATED    26   0   0   2
  SCN9A WILD-TYPE 201  10  10  22
D611V10, multiclass
    clus
vv   SCN9A MUTATED SCN9A WILD-TYPE
  R0            26             201
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D611V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SCN9A MUTATED       7                         1    14
  SCN9A WILD-TYPE    69                         3   154
D611V12, multiclass
                           clus
vv                          SCN9A MUTATED SCN9A WILD-TYPE
  ASIAN                                 7              69
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                14             154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(612) Variable = KIAA0586 MUTATION ANALYSIS
D612V1, survival
                    sevent
clus2                  0   1
  KIAA0586 MUTATED     5   4
  KIAA0586 WILD-TYPE 176  76
  KIAA0586 MUTATED KIAA0586 WILD-TYPE 
                 9                252 
  KIAA0586 MUTATED KIAA0586 WILD-TYPE 
                 4                 76 
$`KIAA0586 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8289 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MG 
        6.97        30.90         2.66        15.81        11.57         6.58 
TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-A4YT 
        6.02       105.07        14.27 

$`KIAA0586 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       12.95        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        13.64         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        1.02         0.99         0.99        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  KIAA0586 MUTATED KIAA0586 WILD-TYPE 
              2.66               0.00 
  KIAA0586 MUTATED KIAA0586 WILD-TYPE 
            105.07              79.07 
  KIAA0586 MUTATED KIAA0586 WILD-TYPE 
             11.57              12.64 
[1] "2.7 - 105.1 (11.6)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.1"
D612V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0586 MUTATED         0        0        0        2         1         0
  KIAA0586 WILD-TYPE       1        9       27       24        30        44
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0586 MUTATED           0          2          1          0        3
  KIAA0586 WILD-TYPE         3         47         35         24       21
D612V3, multiclass
            clus
vv           KIAA0586 MUTATED KIAA0586 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  0                 27
  STAGE II                  2                 24
  STAGE IIA                 1                 30
  STAGE IIB                 0                 44
  STAGE III                 0                  3
  STAGE IIIA                2                 47
  STAGE IIIB                1                 35
  STAGE IIIC                0                 24
  STAGE IV                  3                 21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0586 MUTATED     0   4   3   3
  KIAA0586 WILD-TYPE  11  68 119  72
D612V4, multiclass
    clus
vv   KIAA0586 MUTATED KIAA0586 WILD-TYPE
  T1                0                 11
  T2                4                 68
  T3                3                119
  T4                3                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  KIAA0586 MUTATED    1  4  1  3
  KIAA0586 WILD-TYPE 92 77 49 50
D612V5, multiclass
    clus
vv   KIAA0586 MUTATED KIAA0586 WILD-TYPE
  N0                1                 92
  N1                4                 77
  N2                1                 49
  N3                3                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D612V6, binary
                    cls
clus                   0   1
  KIAA0586 MUTATED     7   2
  KIAA0586 WILD-TYPE 250  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0586 MUTATED      7    2
  KIAA0586 WILD-TYPE  250   16
   clus
vv  KIAA0586 MUTATED KIAA0586 WILD-TYPE
  0                7                250
  1                2                 16
[1] 2 2
[1] FALSE
D612V7, binary
                    cls
clus                   0   1
  KIAA0586 MUTATED     2   8
  KIAA0586 WILD-TYPE 108 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0586 MUTATED      2    8
  KIAA0586 WILD-TYPE  108  171
        clus
vv       KIAA0586 MUTATED KIAA0586 WILD-TYPE
  FEMALE                2                108
  MALE                  8                171
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KIAA0586 MUTATED                                       1
  KIAA0586 WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA0586 MUTATED                                                        4
  KIAA0586 WILD-TYPE                                                    131
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA0586 MUTATED                                                                   2
  KIAA0586 WILD-TYPE                                                                38
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KIAA0586 MUTATED                                                  2
  KIAA0586 WILD-TYPE                                               36
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KIAA0586 MUTATED                                                          1
  KIAA0586 WILD-TYPE                                                       15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KIAA0586 MUTATED                                                           0
  KIAA0586 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KIAA0586 MUTATED                                          0
  KIAA0586 WILD-TYPE                                        3
D612V8, multiclass
                                                                   clus
vv                                                                  KIAA0586 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  KIAA0586 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D612V9, binary
                    cls
clus                   0   1
  KIAA0586 MUTATED     1   9
  KIAA0586 WILD-TYPE   4 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0586 MUTATED      1    9
  KIAA0586 WILD-TYPE    4  275
     clus
vv    KIAA0586 MUTATED KIAA0586 WILD-TYPE
  NO                 1                  4
  YES                9                275
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0586 MUTATED     7   0   0   2
  KIAA0586 WILD-TYPE 220  10  10  22
D612V10, multiclass
    clus
vv   KIAA0586 MUTATED KIAA0586 WILD-TYPE
  R0                7                220
  R1                0                 10
  R2                0                 10
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D612V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA0586 MUTATED       2                         0     5
  KIAA0586 WILD-TYPE    74                         4   163
D612V12, multiclass
                           clus
vv                          KIAA0586 MUTATED KIAA0586 WILD-TYPE
  ASIAN                                    2                 74
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    5                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(613) Variable = MACF1 MUTATION ANALYSIS
D613V1, survival
                 sevent
clus2               0   1
  MACF1 MUTATED    28  12
  MACF1 WILD-TYPE 153  68
  MACF1 MUTATED MACF1 WILD-TYPE 
             40             221 
  MACF1 MUTATED MACF1 WILD-TYPE 
             12              68 
$`MACF1 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7716 
       26.70         6.97        18.35        34.68        32.94        28.01 
TCGA-BR-7851 TCGA-BR-8077 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8361 TCGA-BR-8363 
       12.43         0.69        20.55         8.05        19.50         0.26 
TCGA-BR-8369 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4CS 
       14.04        19.17         1.12        13.45        15.81         1.48 
TCGA-CD-8529 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4466 TCGA-CG-5721 
        0.13         6.58         0.10        12.62        18.97         6.02 
TCGA-CG-5723 TCGA-CG-5726 TCGA-D7-6527 TCGA-D7-A4YT TCGA-F1-A448 TCGA-FP-8631 
      105.07        28.96        10.26        14.27        21.27         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.08         5.52        26.47        29.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-IN-7808 
       10.19        23.84         8.88         3.45 

$`MACF1 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 
       11.70         6.61         4.64         7.43        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
       12.82         9.21        24.76        23.93        15.42        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 
       17.49        14.43        12.26         9.60        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 
       16.31         2.20        15.58         7.40         6.18        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
        9.21        20.22        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
       22.26        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
        0.07         0.07         0.07         0.07         0.10         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 
       11.31        12.43        11.61        12.20        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 
       36.00         1.02         0.99         0.99        12.03        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        7.99        16.24        14.47        72.23         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU 
        3.25        22.75        25.81        11.77         8.98         6.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21        18.81         3.39         2.53 

  MACF1 MUTATED MACF1 WILD-TYPE 
            0.1             0.0 
  MACF1 MUTATED MACF1 WILD-TYPE 
         105.07           79.07 
  MACF1 MUTATED MACF1 WILD-TYPE 
         12.525          12.660 
[1] "0.1 - 105.1 (12.5)" "0.0 - 79.1 (12.7)" 
[1] "hr=" "1.2"
D613V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MACF1 MUTATED         1        1        6        2         7         5
  MACF1 WILD-TYPE       0        8       21       24        24        39
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MACF1 MUTATED           1          5          4          7        3
  MACF1 WILD-TYPE         2         44         32         17       21
D613V3, multiclass
            clus
vv           MACF1 MUTATED MACF1 WILD-TYPE
  STAGE I                1               0
  STAGE IA               1               8
  STAGE IB               6              21
  STAGE II               2              24
  STAGE IIA              7              24
  STAGE IIB              5              39
  STAGE III              1               2
  STAGE IIIA             5              44
  STAGE IIIB             4              32
  STAGE IIIC             7              17
  STAGE IV               3              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MACF1 MUTATED     3  10  14  15
  MACF1 WILD-TYPE   8  62 108  60
D613V4, multiclass
    clus
vv   MACF1 MUTATED MACF1 WILD-TYPE
  T1             3               8
  T2            10              62
  T3            14             108
  T4            15              60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  MACF1 MUTATED   17 12  7  8
  MACF1 WILD-TYPE 76 69 43 45
D613V5, multiclass
    clus
vv   MACF1 MUTATED MACF1 WILD-TYPE
  N0            17              76
  N1            12              69
  N2             7              43
  N3             8              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D613V6, binary
                 cls
clus                0   1
  MACF1 MUTATED    38   3
  MACF1 WILD-TYPE 219  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MACF1 MUTATED     38    3
  MACF1 WILD-TYPE  219   15
   clus
vv  MACF1 MUTATED MACF1 WILD-TYPE
  0            38             219
  1             3              15
[1] 2 2
[1] FALSE
D613V7, binary
                 cls
clus                0   1
  MACF1 MUTATED    18  27
  MACF1 WILD-TYPE  92 152
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MACF1 MUTATED     18   27
  MACF1 WILD-TYPE   92  152
        clus
vv       MACF1 MUTATED MACF1 WILD-TYPE
  FEMALE            18              92
  MALE              27             152
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MACF1 MUTATED                                       4
  MACF1 WILD-TYPE                                    46
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MACF1 MUTATED                                                       21
  MACF1 WILD-TYPE                                                    114
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MACF1 MUTATED                                                                   8
  MACF1 WILD-TYPE                                                                32
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MACF1 MUTATED                                                  7
  MACF1 WILD-TYPE                                               31
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MACF1 MUTATED                                                          2
  MACF1 WILD-TYPE                                                       14
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MACF1 MUTATED                                                           1
  MACF1 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MACF1 MUTATED                                          2
  MACF1 WILD-TYPE                                        1
D613V8, multiclass
                                                                   clus
vv                                                                  MACF1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       21
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      2
                                                                   clus
vv                                                                  MACF1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        114
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               31
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D613V9, binary
                 cls
clus                0   1
  MACF1 MUTATED     0  45
  MACF1 WILD-TYPE   5 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MACF1 MUTATED      0   45
  MACF1 WILD-TYPE    5  239
     clus
vv    MACF1 MUTATED MACF1 WILD-TYPE
  NO              0               5
  YES            45             239
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MACF1 MUTATED    35   1   0   5
  MACF1 WILD-TYPE 192   9  10  19
D613V10, multiclass
    clus
vv   MACF1 MUTATED MACF1 WILD-TYPE
  R0            35             192
  R1             1               9
  R2             0              10
  RX             5              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D613V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MACF1 MUTATED      11                         2    27
  MACF1 WILD-TYPE    65                         2   141
D613V12, multiclass
                           clus
vv                          MACF1 MUTATED MACF1 WILD-TYPE
  ASIAN                                11              65
  BLACK OR AFRICAN AMERICAN             2               2
  WHITE                                27             141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(614) Variable = DYRK1A MUTATION ANALYSIS
D614V1, survival
                  sevent
clus2                0   1
  DYRK1A MUTATED     6   1
  DYRK1A WILD-TYPE 175  79
  DYRK1A MUTATED DYRK1A WILD-TYPE 
               7              254 
  DYRK1A MUTATED DYRK1A WILD-TYPE 
               1               79 
$`DYRK1A MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6802 TCGA-BR-7196 TCGA-BR-8487 TCGA-BR-8680 
       26.70         6.97        30.90        12.82         1.12        15.81 
TCGA-FP-A4BE 
       11.08 

$`DYRK1A WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       31.20        32.94         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  DYRK1A MUTATED DYRK1A WILD-TYPE 
            1.12             0.00 
  DYRK1A MUTATED DYRK1A WILD-TYPE 
           30.90           105.07 
  DYRK1A MUTATED DYRK1A WILD-TYPE 
          12.820           12.605 
[1] "1.1 - 30.9 (12.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.5"
D614V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DYRK1A MUTATED         0        0        0        1         3         1
  DYRK1A WILD-TYPE       1        9       27       25        28        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DYRK1A MUTATED           0          2          0          0        2
  DYRK1A WILD-TYPE         3         47         36         24       22
D614V3, multiclass
            clus
vv           DYRK1A MUTATED DYRK1A WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                1               25
  STAGE IIA               3               28
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DYRK1A MUTATED     0   1   6   2
  DYRK1A WILD-TYPE  11  71 116  73
D614V4, multiclass
    clus
vv   DYRK1A MUTATED DYRK1A WILD-TYPE
  T1              0               11
  T2              1               71
  T3              6              116
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  DYRK1A MUTATED    4  2  2  1
  DYRK1A WILD-TYPE 89 79 48 52
D614V5, multiclass
    clus
vv   DYRK1A MUTATED DYRK1A WILD-TYPE
  N0              4               89
  N1              2               79
  N2              2               48
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D614V6, binary
                  cls
clus                 0   1
  DYRK1A MUTATED     6   2
  DYRK1A WILD-TYPE 251  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DYRK1A MUTATED      6    2
  DYRK1A WILD-TYPE  251   16
   clus
vv  DYRK1A MUTATED DYRK1A WILD-TYPE
  0              6              251
  1              2               16
[1] 2 2
[1] FALSE
D614V7, binary
                  cls
clus                 0   1
  DYRK1A MUTATED     2   7
  DYRK1A WILD-TYPE 108 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DYRK1A MUTATED      2    7
  DYRK1A WILD-TYPE  108  172
        clus
vv       DYRK1A MUTATED DYRK1A WILD-TYPE
  FEMALE              2              108
  MALE                7              172
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DYRK1A MUTATED                                       1
  DYRK1A WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DYRK1A MUTATED                                                        6
  DYRK1A WILD-TYPE                                                    129
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DYRK1A MUTATED                                                                   0
  DYRK1A WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DYRK1A MUTATED                                                  1
  DYRK1A WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DYRK1A MUTATED                                                          1
  DYRK1A WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DYRK1A MUTATED                                                           0
  DYRK1A WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DYRK1A MUTATED                                          0
  DYRK1A WILD-TYPE                                        3
D614V8, multiclass
                                                                   clus
vv                                                                  DYRK1A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  DYRK1A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D614V9, binary
                  cls
clus                 0   1
  DYRK1A MUTATED     1   8
  DYRK1A WILD-TYPE   4 276
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DYRK1A MUTATED      1    8
  DYRK1A WILD-TYPE    4  276
     clus
vv    DYRK1A MUTATED DYRK1A WILD-TYPE
  NO               1                4
  YES              8              276
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DYRK1A MUTATED     8   0   0   1
  DYRK1A WILD-TYPE 219  10  10  23
D614V10, multiclass
    clus
vv   DYRK1A MUTATED DYRK1A WILD-TYPE
  R0              8              219
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D614V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DYRK1A MUTATED       1                         1     6
  DYRK1A WILD-TYPE    75                         3   162
D614V12, multiclass
                           clus
vv                          DYRK1A MUTATED DYRK1A WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(615) Variable = GALK1 MUTATION ANALYSIS
D615V1, survival
                 sevent
clus2               0   1
  GALK1 MUTATED     1   1
  GALK1 WILD-TYPE 180  79
  GALK1 MUTATED GALK1 WILD-TYPE 
              2             259 
  GALK1 MUTATED GALK1 WILD-TYPE 
              1              79 
$`GALK1 MUTATED`
TCGA-CD-A4MG TCGA-FP-A4BE 
        6.58        11.08 

$`GALK1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  GALK1 MUTATED GALK1 WILD-TYPE 
           6.58            0.00 
  GALK1 MUTATED GALK1 WILD-TYPE 
          11.08          105.07 
  GALK1 MUTATED GALK1 WILD-TYPE 
           8.83           12.66 
[1] "6.6 - 11.1 (8.8)"   "0.0 - 105.1 (12.7)"
[1] "Remove cluster labels:" "GALK1 MUTATED"         
D615V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GALK1 MUTATED         0        0        0        0         2         0
  GALK1 WILD-TYPE       1        9       27       26        29        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GALK1 MUTATED           0          1          0          0        0
  GALK1 WILD-TYPE         3         48         36         24       24
D615V3, multiclass
            clus
vv           GALK1 MUTATED GALK1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GALK1 MUTATED     0   0   2   1
  GALK1 WILD-TYPE  11  72 120  74
D615V4, multiclass
    clus
vv   GALK1 MUTATED GALK1 WILD-TYPE
  T1             0              11
  T2             0              72
  T3             2             120
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  GALK1 MUTATED    3  0  0  0
  GALK1 WILD-TYPE 90 81 50 53
D615V5, multiclass
    clus
vv   GALK1 MUTATED GALK1 WILD-TYPE
  N0             3              90
  N1             0              81
  N2             0              50
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D615V6, binary
                 cls
clus                0   1
  GALK1 MUTATED     4   0
  GALK1 WILD-TYPE 253  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GALK1 MUTATED      4    0
  GALK1 WILD-TYPE  253   18
   clus
vv  GALK1 MUTATED GALK1 WILD-TYPE
  0             4             253
  1             0              18
[1] 2 2
[1] FALSE
D615V7, binary
                 cls
clus                0   1
  GALK1 MUTATED     2   2
  GALK1 WILD-TYPE 108 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GALK1 MUTATED      2    2
  GALK1 WILD-TYPE  108  177
        clus
vv       GALK1 MUTATED GALK1 WILD-TYPE
  FEMALE             2             108
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GALK1 MUTATED                                       1
  GALK1 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GALK1 MUTATED                                                        3
  GALK1 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GALK1 MUTATED                                                                   0
  GALK1 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GALK1 MUTATED                                                  0
  GALK1 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GALK1 MUTATED                                                          0
  GALK1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GALK1 MUTATED                                                           0
  GALK1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GALK1 MUTATED                                          0
  GALK1 WILD-TYPE                                        3
D615V8, multiclass
                                                                   clus
vv                                                                  GALK1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  GALK1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D615V9, binary
                 cls
clus                0   1
  GALK1 MUTATED     0   4
  GALK1 WILD-TYPE   5 280
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GALK1 MUTATED      0    4
  GALK1 WILD-TYPE    5  280
     clus
vv    GALK1 MUTATED GALK1 WILD-TYPE
  NO              0               5
  YES             4             280
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GALK1 MUTATED     1   0   0   2
  GALK1 WILD-TYPE 226  10  10  22
D615V10, multiclass
    clus
vv   GALK1 MUTATED GALK1 WILD-TYPE
  R0             1             226
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D615V11, continuous
[1] "Remove cluster labels:" "GALK1 MUTATED"         
clus
  GALK1 MUTATED GALK1 WILD-TYPE 
              2             249 
     TCGA-B7-5816      TCGA-BR-4183      TCGA-BR-4184      TCGA-BR-4188 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-4191      TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4362 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-4368      TCGA-BR-6452      TCGA-BR-6453      TCGA-BR-6454 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457      TCGA-BR-6458 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565      TCGA-BR-6566 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707      TCGA-BR-6710 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803      TCGA-BR-6852 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703      TCGA-BR-7707 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-7715      TCGA-BR-7716      TCGA-BR-7717      TCGA-BR-7722 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-7723      TCGA-BR-7851      TCGA-BR-7901      TCGA-BR-7957 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-7958      TCGA-BR-7959      TCGA-BR-8058      TCGA-BR-8059 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8077      TCGA-BR-8078      TCGA-BR-8080      TCGA-BR-8081 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8284      TCGA-BR-8286      TCGA-BR-8289      TCGA-BR-8291 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8295      TCGA-BR-8296      TCGA-BR-8297      TCGA-BR-8360 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8361      TCGA-BR-8363      TCGA-BR-8364      TCGA-BR-8365 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8366      TCGA-BR-8367      TCGA-BR-8368      TCGA-BR-8369 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8370      TCGA-BR-8371      TCGA-BR-8372      TCGA-BR-8373 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8380      TCGA-BR-8381      TCGA-BR-8382      TCGA-BR-8384 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8483      TCGA-BR-8484      TCGA-BR-8485      TCGA-BR-8486 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8487      TCGA-BR-8588      TCGA-BR-8589      TCGA-BR-8590 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8591      TCGA-BR-8592      TCGA-BR-8676      TCGA-BR-8677 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8678      TCGA-BR-8679      TCGA-BR-8680      TCGA-BR-8682 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8683      TCGA-BR-8686      TCGA-BR-8687      TCGA-BR-8690 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-A44T      TCGA-BR-A44U      TCGA-BR-A452      TCGA-BR-A453 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-A4CQ      TCGA-BR-A4CR      TCGA-BR-A4CS      TCGA-BR-A4IU 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-A4IV      TCGA-BR-A4IY      TCGA-BR-A4IZ      TCGA-BR-A4J1 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-A4J2      TCGA-BR-A4J4      TCGA-BR-A4J6      TCGA-BR-A4J8 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-A4PD      TCGA-BR-A4PE      TCGA-BR-A4PF      TCGA-BR-A4QI 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-A4QL      TCGA-BR-A4QM      TCGA-CD-5804      TCGA-CD-8525 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-CD-8526      TCGA-CD-8531      TCGA-CD-8535      TCGA-CD-A487 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-CG-4301      TCGA-CG-4304      TCGA-CG-4305      TCGA-CG-4436 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-CG-4437      TCGA-CG-4438      TCGA-CG-4440      TCGA-CG-4441 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-CG-4442      TCGA-CG-4443      TCGA-CG-4444      TCGA-CG-4449 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-CG-4455      TCGA-CG-4462      TCGA-CG-4465      TCGA-CG-4466 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-CG-4469      TCGA-CG-4474      TCGA-CG-4475      TCGA-CG-4476 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-CG-4477      TCGA-CG-5717      TCGA-CG-5718      TCGA-CG-5719 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-CG-5720      TCGA-CG-5721      TCGA-CG-5722      TCGA-CG-5723 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-CG-5724      TCGA-CG-5726      TCGA-CG-5727      TCGA-CG-5728 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-CG-5730      TCGA-CG-5732      TCGA-CG-5733      TCGA-CG-5734 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-D7-5577      TCGA-D7-5578      TCGA-D7-5579      TCGA-D7-6518 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-D7-6519      TCGA-D7-6520      TCGA-D7-6521      TCGA-D7-6522 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-D7-6524      TCGA-D7-6525      TCGA-D7-6526      TCGA-D7-6527 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-D7-6528      TCGA-D7-6815      TCGA-D7-6817      TCGA-D7-6818 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-D7-6820      TCGA-D7-6822      TCGA-D7-8570      TCGA-D7-8572 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-D7-8573      TCGA-D7-8574      TCGA-D7-8575      TCGA-D7-8576 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-D7-8578      TCGA-D7-8579      TCGA-D7-A4YT      TCGA-D7-A4YU 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-D7-A4YV      TCGA-D7-A4YX      TCGA-D7-A4YY      TCGA-D7-A4Z0 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-EQ-5647      TCGA-EQ-8122      TCGA-EQ-A4SO      TCGA-F1-6177 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-F1-6874      TCGA-F1-6875      TCGA-F1-A448      TCGA-FP-7735 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-FP-7829      TCGA-FP-7916      TCGA-FP-7998      TCGA-FP-8099 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-FP-8209      TCGA-FP-8210      TCGA-FP-8211      TCGA-FP-8631 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-FP-A4BF      TCGA-HF-7132      TCGA-HF-7133      TCGA-HF-7136 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-HJ-7597      TCGA-HU-8243      TCGA-HU-8245      TCGA-HU-8249 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-HU-8602      TCGA-HU-8604      TCGA-HU-8608      TCGA-HU-8610 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-HU-A4G2      TCGA-HU-A4G3      TCGA-HU-A4G6      TCGA-HU-A4G8 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD      TCGA-HU-A4GF 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-HU-A4GH      TCGA-HU-A4GN      TCGA-HU-A4GP      TCGA-HU-A4GQ 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX      TCGA-HU-A4GY 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3      TCGA-HU-A4H4 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8      TCGA-HU-A4HD 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-IN-7806      TCGA-IN-7808      TCGA-IN-8462      TCGA-IN-8663 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-IP-7968 
"GALK1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GALK1 MUTATED       1                         1     2
  GALK1 WILD-TYPE    75                         3   166
D615V12, multiclass
                           clus
vv                          GALK1 MUTATED GALK1 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 2             166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(616) Variable = DENND1C MUTATION ANALYSIS
D616V1, survival
                   sevent
clus2                 0   1
  DENND1C MUTATED     7   0
  DENND1C WILD-TYPE 174  80
  DENND1C MUTATED DENND1C WILD-TYPE 
                7               254 
  DENND1C MUTATED DENND1C WILD-TYPE 
                0                80 
$`DENND1C MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8360 TCGA-CG-5723 TCGA-FP-A4BE TCGA-HU-8249 
       34.68        12.26         6.18       105.07        11.08        14.17 
TCGA-HU-A4GT 
        6.51 

$`DENND1C WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         0.10         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  DENND1C MUTATED DENND1C WILD-TYPE 
             6.18              0.00 
  DENND1C MUTATED DENND1C WILD-TYPE 
           105.07             79.07 
  DENND1C MUTATED DENND1C WILD-TYPE 
            12.26             12.64 
[1] "6.2 - 105.1 (12.3)" "0.0 - 79.1 (12.6)" 
[1] "hr="     "2.9e+07"
D616V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DENND1C MUTATED         0        0        0        1         4         1
  DENND1C WILD-TYPE       1        9       27       25        27        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DENND1C MUTATED           0          1          0          0        0
  DENND1C WILD-TYPE         3         48         36         24       24
D616V3, multiclass
            clus
vv           DENND1C MUTATED DENND1C WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 0                27
  STAGE II                 1                25
  STAGE IIA                4                27
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               0                36
  STAGE IIIC               0                24
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  DENND1C MUTATED     0   1   5   1
  DENND1C WILD-TYPE  11  71 117  74
D616V4, multiclass
    clus
vv   DENND1C MUTATED DENND1C WILD-TYPE
  T1               0                11
  T2               1                71
  T3               5               117
  T4               1                74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  DENND1C MUTATED    5  1  1  0
  DENND1C WILD-TYPE 88 80 49 53
D616V5, multiclass
    clus
vv   DENND1C MUTATED DENND1C WILD-TYPE
  N0               5                88
  N1               1                80
  N2               1                49
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D616V6, binary
                   cls
clus                  0   1
  DENND1C MUTATED     7   0
  DENND1C WILD-TYPE 250  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND1C MUTATED      7    0
  DENND1C WILD-TYPE  250   18
   clus
vv  DENND1C MUTATED DENND1C WILD-TYPE
  0               7               250
  1               0                18
[1] 2 2
[1] FALSE
D616V7, binary
                   cls
clus                  0   1
  DENND1C MUTATED     3   4
  DENND1C WILD-TYPE 107 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND1C MUTATED      3    4
  DENND1C WILD-TYPE  107  175
        clus
vv       DENND1C MUTATED DENND1C WILD-TYPE
  FEMALE               3               107
  MALE                 4               175
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DENND1C MUTATED                                       0
  DENND1C WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DENND1C MUTATED                                                        4
  DENND1C WILD-TYPE                                                    131
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DENND1C MUTATED                                                                   1
  DENND1C WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DENND1C MUTATED                                                  2
  DENND1C WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DENND1C MUTATED                                                          0
  DENND1C WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DENND1C MUTATED                                                           0
  DENND1C WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DENND1C MUTATED                                          0
  DENND1C WILD-TYPE                                        3
D616V8, multiclass
                                                                   clus
vv                                                                  DENND1C MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  DENND1C WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D616V9, binary
                   cls
clus                  0   1
  DENND1C MUTATED     0   7
  DENND1C WILD-TYPE   5 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND1C MUTATED      0    7
  DENND1C WILD-TYPE    5  277
     clus
vv    DENND1C MUTATED DENND1C WILD-TYPE
  NO                0                 5
  YES               7               277
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  DENND1C MUTATED     7   0   0   0
  DENND1C WILD-TYPE 220  10  10  24
D616V10, multiclass
    clus
vv   DENND1C MUTATED DENND1C WILD-TYPE
  R0               7               220
  R1               0                10
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D616V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DENND1C MUTATED       2                         1     3
  DENND1C WILD-TYPE    74                         3   165
D616V12, multiclass
                           clus
vv                          DENND1C MUTATED DENND1C WILD-TYPE
  ASIAN                                   2                74
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   3               165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(617) Variable = CNKSR1 MUTATION ANALYSIS
D617V1, survival
                  sevent
clus2                0   1
  CNKSR1 MUTATED     4   0
  CNKSR1 WILD-TYPE 177  80
  CNKSR1 MUTATED CNKSR1 WILD-TYPE 
               4              257 
  CNKSR1 MUTATED CNKSR1 WILD-TYPE 
               0               80 
$`CNKSR1 MUTATED`
TCGA-BR-7707 TCGA-BR-8081 TCGA-BR-8372 TCGA-HU-A4GU 
       23.93        20.55        19.17         6.25 

$`CNKSR1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       17.49        14.43         0.69        12.26         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  CNKSR1 MUTATED CNKSR1 WILD-TYPE 
            6.25             0.00 
  CNKSR1 MUTATED CNKSR1 WILD-TYPE 
           23.93           105.07 
  CNKSR1 MUTATED CNKSR1 WILD-TYPE 
           19.86            12.59 
[1] "6.2 - 23.9 (19.9)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "9200000"
D617V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CNKSR1 MUTATED         1        0        1        1         0         2
  CNKSR1 WILD-TYPE       0        9       26       25        31        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNKSR1 MUTATED           0          0          0          1        0
  CNKSR1 WILD-TYPE         3         49         36         23       24
D617V3, multiclass
            clus
vv           CNKSR1 MUTATED CNKSR1 WILD-TYPE
  STAGE I                 1                0
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                1               25
  STAGE IIA               0               31
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CNKSR1 MUTATED     1   2   1   2
  CNKSR1 WILD-TYPE  10  70 121  73
D617V4, multiclass
    clus
vv   CNKSR1 MUTATED CNKSR1 WILD-TYPE
  T1              1               10
  T2              2               70
  T3              1              121
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CNKSR1 MUTATED    2  4  0  1
  CNKSR1 WILD-TYPE 91 77 50 52
D617V5, multiclass
    clus
vv   CNKSR1 MUTATED CNKSR1 WILD-TYPE
  N0              2               91
  N1              4               77
  N2              0               50
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D617V6, binary
                  cls
clus                 0   1
  CNKSR1 MUTATED     6   0
  CNKSR1 WILD-TYPE 251  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNKSR1 MUTATED      6    0
  CNKSR1 WILD-TYPE  251   18
   clus
vv  CNKSR1 MUTATED CNKSR1 WILD-TYPE
  0              6              251
  1              0               18
[1] 2 2
[1] FALSE
D617V7, binary
                  cls
clus                 0   1
  CNKSR1 MUTATED     3   4
  CNKSR1 WILD-TYPE 107 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNKSR1 MUTATED      3    4
  CNKSR1 WILD-TYPE  107  175
        clus
vv       CNKSR1 MUTATED CNKSR1 WILD-TYPE
  FEMALE              3              107
  MALE                4              175
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CNKSR1 MUTATED                                       1
  CNKSR1 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CNKSR1 MUTATED                                                        5
  CNKSR1 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CNKSR1 MUTATED                                                                   0
  CNKSR1 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CNKSR1 MUTATED                                                  0
  CNKSR1 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CNKSR1 MUTATED                                                          1
  CNKSR1 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CNKSR1 MUTATED                                                           0
  CNKSR1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CNKSR1 MUTATED                                          0
  CNKSR1 WILD-TYPE                                        3
D617V8, multiclass
                                                                   clus
vv                                                                  CNKSR1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  CNKSR1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D617V9, binary
                  cls
clus                 0   1
  CNKSR1 MUTATED     1   6
  CNKSR1 WILD-TYPE   4 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNKSR1 MUTATED      1    6
  CNKSR1 WILD-TYPE    4  278
     clus
vv    CNKSR1 MUTATED CNKSR1 WILD-TYPE
  NO               1                4
  YES              6              278
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CNKSR1 MUTATED     6   0   0   1
  CNKSR1 WILD-TYPE 221  10  10  23
D617V10, multiclass
    clus
vv   CNKSR1 MUTATED CNKSR1 WILD-TYPE
  R0              6              221
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D617V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CNKSR1 MUTATED       1                         1     4
  CNKSR1 WILD-TYPE    75                         3   164
D617V12, multiclass
                           clus
vv                          CNKSR1 MUTATED CNKSR1 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(618) Variable = MYCT1 MUTATION ANALYSIS
D618V1, survival
                 sevent
clus2               0   1
  MYCT1 MUTATED     4   1
  MYCT1 WILD-TYPE 177  79
  MYCT1 MUTATED MYCT1 WILD-TYPE 
              5             256 
  MYCT1 MUTATED MYCT1 WILD-TYPE 
              1              79 
$`MYCT1 MUTATED`
TCGA-BR-6452 TCGA-BR-8485 TCGA-CD-8527 TCGA-CG-4469 TCGA-FP-8099 
       34.68         9.21         0.07         7.07        17.06 

$`MYCT1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 
       12.03         0.00         9.01        18.97        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        14.07        22.29        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  MYCT1 MUTATED MYCT1 WILD-TYPE 
           0.07            0.00 
  MYCT1 MUTATED MYCT1 WILD-TYPE 
          34.68          105.07 
  MYCT1 MUTATED MYCT1 WILD-TYPE 
           9.21           12.64 
[1] "0.1 - 34.7 (9.2)"   "0.0 - 105.1 (12.6)"
[1] "hr=" "1.5"
D618V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MYCT1 MUTATED         0        0        0        1         2         0
  MYCT1 WILD-TYPE       1        9       27       25        29        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MYCT1 MUTATED           0          0          0          1        1
  MYCT1 WILD-TYPE         3         49         36         23       23
D618V3, multiclass
            clus
vv           MYCT1 MUTATED MYCT1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              2              29
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYCT1 MUTATED     0   1   3   1
  MYCT1 WILD-TYPE  11  71 119  74
D618V4, multiclass
    clus
vv   MYCT1 MUTATED MYCT1 WILD-TYPE
  T1             0              11
  T2             1              71
  T3             3             119
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  MYCT1 MUTATED    2  2  0  2
  MYCT1 WILD-TYPE 91 79 50 51
D618V5, multiclass
    clus
vv   MYCT1 MUTATED MYCT1 WILD-TYPE
  N0             2              91
  N1             2              79
  N2             0              50
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D618V6, binary
                 cls
clus                0   1
  MYCT1 MUTATED     5   0
  MYCT1 WILD-TYPE 252  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYCT1 MUTATED      5    0
  MYCT1 WILD-TYPE  252   18
   clus
vv  MYCT1 MUTATED MYCT1 WILD-TYPE
  0             5             252
  1             0              18
[1] 2 2
[1] FALSE
D618V7, binary
                 cls
clus                0   1
  MYCT1 MUTATED     4   2
  MYCT1 WILD-TYPE 106 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYCT1 MUTATED      4    2
  MYCT1 WILD-TYPE  106  177
        clus
vv       MYCT1 MUTATED MYCT1 WILD-TYPE
  FEMALE             4             106
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MYCT1 MUTATED                                       0
  MYCT1 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MYCT1 MUTATED                                                        4
  MYCT1 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MYCT1 MUTATED                                                                   2
  MYCT1 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MYCT1 MUTATED                                                  0
  MYCT1 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MYCT1 MUTATED                                                          0
  MYCT1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MYCT1 MUTATED                                                           0
  MYCT1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MYCT1 MUTATED                                          0
  MYCT1 WILD-TYPE                                        3
D618V8, multiclass
                                                                   clus
vv                                                                  MYCT1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  MYCT1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D618V9, binary
                 cls
clus                0   1
  MYCT1 MUTATED     0   6
  MYCT1 WILD-TYPE   5 278
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYCT1 MUTATED      0    6
  MYCT1 WILD-TYPE    5  278
     clus
vv    MYCT1 MUTATED MYCT1 WILD-TYPE
  NO              0               5
  YES             6             278
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MYCT1 MUTATED     4   1   0   1
  MYCT1 WILD-TYPE 223   9  10  23
D618V10, multiclass
    clus
vv   MYCT1 MUTATED MYCT1 WILD-TYPE
  R0             4             223
  R1             1               9
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D618V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MYCT1 MUTATED       1                         0     4
  MYCT1 WILD-TYPE    75                         4   164
D618V12, multiclass
                           clus
vv                          MYCT1 MUTATED MYCT1 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(619) Variable = ATRIP MUTATION ANALYSIS
D619V1, survival
                 sevent
clus2               0   1
  ATRIP MUTATED     4   0
  ATRIP WILD-TYPE 177  80
  ATRIP MUTATED ATRIP WILD-TYPE 
              4             257 
  ATRIP MUTATED ATRIP WILD-TYPE 
              0              80 
$`ATRIP MUTATED`
TCGA-BR-8361 TCGA-BR-8372 TCGA-HU-8602 TCGA-HU-A4GT 
       19.50        19.17        11.41         6.51 

$`ATRIP WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       26.47         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  ATRIP MUTATED ATRIP WILD-TYPE 
           6.51            0.00 
  ATRIP MUTATED ATRIP WILD-TYPE 
          19.50          105.07 
  ATRIP MUTATED ATRIP WILD-TYPE 
          15.29           12.62 
[1] "6.5 - 19.5 (15.3)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "9200000"
D619V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATRIP MUTATED         0        0        0        0         1         1
  ATRIP WILD-TYPE       1        9       27       26        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATRIP MUTATED           0          1          0          2        0
  ATRIP WILD-TYPE         3         48         36         22       24
D619V3, multiclass
            clus
vv           ATRIP MUTATED ATRIP WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             2              22
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ATRIP MUTATED     0   0   1   4
  ATRIP WILD-TYPE  11  72 121  71
D619V4, multiclass
    clus
vv   ATRIP MUTATED ATRIP WILD-TYPE
  T1             0              11
  T2             0              72
  T3             1             121
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ATRIP MUTATED    3  0  1  1
  ATRIP WILD-TYPE 90 81 49 52
D619V5, multiclass
    clus
vv   ATRIP MUTATED ATRIP WILD-TYPE
  N0             3              90
  N1             0              81
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D619V6, binary
                 cls
clus                0   1
  ATRIP MUTATED     5   0
  ATRIP WILD-TYPE 252  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATRIP MUTATED      5    0
  ATRIP WILD-TYPE  252   18
   clus
vv  ATRIP MUTATED ATRIP WILD-TYPE
  0             5             252
  1             0              18
[1] 2 2
[1] FALSE
D619V7, binary
                 cls
clus                0   1
  ATRIP MUTATED     4   1
  ATRIP WILD-TYPE 106 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATRIP MUTATED      4    1
  ATRIP WILD-TYPE  106  178
        clus
vv       ATRIP MUTATED ATRIP WILD-TYPE
  FEMALE             4             106
  MALE               1             178
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ATRIP MUTATED                                       1
  ATRIP WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ATRIP MUTATED                                                        3
  ATRIP WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ATRIP MUTATED                                                                   0
  ATRIP WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ATRIP MUTATED                                                  1
  ATRIP WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ATRIP MUTATED                                                          0
  ATRIP WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ATRIP MUTATED                                                           0
  ATRIP WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ATRIP MUTATED                                          0
  ATRIP WILD-TYPE                                        3
D619V8, multiclass
                                                                   clus
vv                                                                  ATRIP MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ATRIP WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D619V9, binary
                 cls
clus                0   1
  ATRIP MUTATED     0   5
  ATRIP WILD-TYPE   5 279
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATRIP MUTATED      0    5
  ATRIP WILD-TYPE    5  279
     clus
vv    ATRIP MUTATED ATRIP WILD-TYPE
  NO              0               5
  YES             5             279
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ATRIP MUTATED     4   0   0   1
  ATRIP WILD-TYPE 223  10  10  23
D619V10, multiclass
    clus
vv   ATRIP MUTATED ATRIP WILD-TYPE
  R0             4             223
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D619V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATRIP MUTATED       2                         0     3
  ATRIP WILD-TYPE    74                         4   165
D619V12, multiclass
                           clus
vv                          ATRIP MUTATED ATRIP WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(620) Variable = TIMP3 MUTATION ANALYSIS
D620V1, survival
                 sevent
clus2               0   1
  TIMP3 MUTATED     4   0
  TIMP3 WILD-TYPE 177  80
  TIMP3 MUTATED TIMP3 WILD-TYPE 
              4             257 
  TIMP3 MUTATED TIMP3 WILD-TYPE 
              0              80 
$`TIMP3 MUTATED`
TCGA-BR-8487 TCGA-BR-A4J4 TCGA-HU-A4G9 TCGA-HU-A4GT 
        1.12         0.53        24.20         6.51 

$`TIMP3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  TIMP3 MUTATED TIMP3 WILD-TYPE 
           0.53            0.00 
  TIMP3 MUTATED TIMP3 WILD-TYPE 
          24.20          105.07 
  TIMP3 MUTATED TIMP3 WILD-TYPE 
          3.815          12.660 
[1] "0.5 - 24.2 (3.8)"   "0.0 - 105.1 (12.7)"
[1] "hr="     "3300000"
D620V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TIMP3 MUTATED         0        1        0        0         2         0
  TIMP3 WILD-TYPE       1        8       27       26        29        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TIMP3 MUTATED           0          1          1          0        0
  TIMP3 WILD-TYPE         3         48         35         24       24
D620V3, multiclass
            clus
vv           TIMP3 MUTATED TIMP3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TIMP3 MUTATED     1   0   4   1
  TIMP3 WILD-TYPE  10  72 118  74
D620V4, multiclass
    clus
vv   TIMP3 MUTATED TIMP3 WILD-TYPE
  T1             1              10
  T2             0              72
  T3             4             118
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  TIMP3 MUTATED    3  1  1  0
  TIMP3 WILD-TYPE 90 80 49 53
D620V5, multiclass
    clus
vv   TIMP3 MUTATED TIMP3 WILD-TYPE
  N0             3              90
  N1             1              80
  N2             1              49
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D620V6, binary
                 cls
clus                0   1
  TIMP3 MUTATED     5   0
  TIMP3 WILD-TYPE 252  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIMP3 MUTATED      5    0
  TIMP3 WILD-TYPE  252   18
   clus
vv  TIMP3 MUTATED TIMP3 WILD-TYPE
  0             5             252
  1             0              18
[1] 2 2
[1] FALSE
D620V7, binary
                 cls
clus                0   1
  TIMP3 MUTATED     3   3
  TIMP3 WILD-TYPE 107 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIMP3 MUTATED      3    3
  TIMP3 WILD-TYPE  107  176
        clus
vv       TIMP3 MUTATED TIMP3 WILD-TYPE
  FEMALE             3             107
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TIMP3 MUTATED                                       0
  TIMP3 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TIMP3 MUTATED                                                        4
  TIMP3 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TIMP3 MUTATED                                                                   0
  TIMP3 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TIMP3 MUTATED                                                  2
  TIMP3 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TIMP3 MUTATED                                                          0
  TIMP3 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TIMP3 MUTATED                                                           0
  TIMP3 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TIMP3 MUTATED                                          0
  TIMP3 WILD-TYPE                                        3
D620V8, multiclass
                                                                   clus
vv                                                                  TIMP3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  TIMP3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D620V9, binary
                 cls
clus                0   1
  TIMP3 MUTATED     1   5
  TIMP3 WILD-TYPE   4 279
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIMP3 MUTATED      1    5
  TIMP3 WILD-TYPE    4  279
     clus
vv    TIMP3 MUTATED TIMP3 WILD-TYPE
  NO              1               4
  YES             5             279
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TIMP3 MUTATED     4   1   0   1
  TIMP3 WILD-TYPE 223   9  10  23
D620V10, multiclass
    clus
vv   TIMP3 MUTATED TIMP3 WILD-TYPE
  R0             4             223
  R1             1               9
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D620V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TIMP3 MUTATED       3                         0     2
  TIMP3 WILD-TYPE    73                         4   166
D620V12, multiclass
                           clus
vv                          TIMP3 MUTATED TIMP3 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 2             166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(621) Variable = ELK3 MUTATION ANALYSIS
D621V1, survival
                sevent
clus2              0   1
  ELK3 MUTATED     5   1
  ELK3 WILD-TYPE 176  79
  ELK3 MUTATED ELK3 WILD-TYPE 
             6            255 
  ELK3 MUTATED ELK3 WILD-TYPE 
             1             79 
$`ELK3 MUTATED`
TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8361 TCGA-CD-A4MG TCGA-FP-A4BE 
       34.68        30.90        32.94        19.50         6.58        11.08 

$`ELK3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       21.11        31.20        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  ELK3 MUTATED ELK3 WILD-TYPE 
          6.58           0.00 
  ELK3 MUTATED ELK3 WILD-TYPE 
         34.68         105.07 
  ELK3 MUTATED ELK3 WILD-TYPE 
         25.20          12.59 
[1] "6.6 - 34.7 (25.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "3.4"
D621V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ELK3 MUTATED         0        0        0        0         4         0
  ELK3 WILD-TYPE       1        9       27       26        27        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ELK3 MUTATED           0          1          0          1        0
  ELK3 WILD-TYPE         3         48         36         23       24
D621V3, multiclass
            clus
vv           ELK3 MUTATED ELK3 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              0             26
  STAGE IIA             4             27
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            1             23
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ELK3 MUTATED     0   0   5   1
  ELK3 WILD-TYPE  11  72 117  74
D621V4, multiclass
    clus
vv   ELK3 MUTATED ELK3 WILD-TYPE
  T1            0             11
  T2            0             72
  T3            5            117
  T4            1             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  ELK3 MUTATED    4  0  2  0
  ELK3 WILD-TYPE 89 81 48 53
D621V5, multiclass
    clus
vv   ELK3 MUTATED ELK3 WILD-TYPE
  N0            4             89
  N1            0             81
  N2            2             48
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D621V6, binary
                cls
clus               0   1
  ELK3 MUTATED     6   0
  ELK3 WILD-TYPE 251  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELK3 MUTATED      6    0
  ELK3 WILD-TYPE  251   18
   clus
vv  ELK3 MUTATED ELK3 WILD-TYPE
  0            6            251
  1            0             18
[1] 2 2
[1] FALSE
D621V7, binary
                cls
clus               0   1
  ELK3 MUTATED     3   3
  ELK3 WILD-TYPE 107 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELK3 MUTATED      3    3
  ELK3 WILD-TYPE  107  176
        clus
vv       ELK3 MUTATED ELK3 WILD-TYPE
  FEMALE            3            107
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ELK3 MUTATED                                       1
  ELK3 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ELK3 MUTATED                                                        5
  ELK3 WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ELK3 MUTATED                                                                   0
  ELK3 WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ELK3 MUTATED                                                  0
  ELK3 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ELK3 MUTATED                                                          0
  ELK3 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ELK3 MUTATED                                                           0
  ELK3 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ELK3 MUTATED                                          0
  ELK3 WILD-TYPE                                        3
D621V8, multiclass
                                                                   clus
vv                                                                  ELK3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  ELK3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D621V9, binary
                cls
clus               0   1
  ELK3 MUTATED     0   6
  ELK3 WILD-TYPE   5 278
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELK3 MUTATED      0    6
  ELK3 WILD-TYPE    5  278
     clus
vv    ELK3 MUTATED ELK3 WILD-TYPE
  NO             0              5
  YES            6            278
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ELK3 MUTATED     5   0   0   0
  ELK3 WILD-TYPE 222  10  10  24
D621V10, multiclass
    clus
vv   ELK3 MUTATED ELK3 WILD-TYPE
  R0            5            222
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D621V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ELK3 MUTATED       1                         1     4
  ELK3 WILD-TYPE    75                         3   164
D621V12, multiclass
                           clus
vv                          ELK3 MUTATED ELK3 WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                                4            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(622) Variable = CD3EAP MUTATION ANALYSIS
D622V1, survival
                  sevent
clus2                0   1
  CD3EAP MUTATED     4   1
  CD3EAP WILD-TYPE 177  79
  CD3EAP MUTATED CD3EAP WILD-TYPE 
               5              256 
  CD3EAP MUTATED CD3EAP WILD-TYPE 
               1               79 
$`CD3EAP MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-CG-4305 TCGA-CG-5721 TCGA-HU-8602 
        6.97        34.68        15.95         6.02        11.41 

$`CD3EAP WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  CD3EAP MUTATED CD3EAP WILD-TYPE 
            6.02             0.00 
  CD3EAP MUTATED CD3EAP WILD-TYPE 
           34.68           105.07 
  CD3EAP MUTATED CD3EAP WILD-TYPE 
           11.41            12.64 
[1] "6.0 - 34.7 (11.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.6"
D622V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CD3EAP MUTATED         0        0        0        2         1         1
  CD3EAP WILD-TYPE       1        9       27       24        30        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CD3EAP MUTATED           0          1          0          0        1
  CD3EAP WILD-TYPE         3         48         36         24       23
D622V3, multiclass
            clus
vv           CD3EAP MUTATED CD3EAP WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                2               24
  STAGE IIA               1               30
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CD3EAP MUTATED     0   2   2   2
  CD3EAP WILD-TYPE  11  70 120  73
D622V4, multiclass
    clus
vv   CD3EAP MUTATED CD3EAP WILD-TYPE
  T1              0               11
  T2              2               70
  T3              2              120
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CD3EAP MUTATED    2  5  0  0
  CD3EAP WILD-TYPE 91 76 50 53
D622V5, multiclass
    clus
vv   CD3EAP MUTATED CD3EAP WILD-TYPE
  N0              2               91
  N1              5               76
  N2              0               50
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D622V6, binary
                  cls
clus                 0   1
  CD3EAP MUTATED     6   0
  CD3EAP WILD-TYPE 251  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD3EAP MUTATED      6    0
  CD3EAP WILD-TYPE  251   18
   clus
vv  CD3EAP MUTATED CD3EAP WILD-TYPE
  0              6              251
  1              0               18
[1] 2 2
[1] FALSE
D622V7, binary
                  cls
clus                 0   1
  CD3EAP MUTATED     2   5
  CD3EAP WILD-TYPE 108 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD3EAP MUTATED      2    5
  CD3EAP WILD-TYPE  108  174
        clus
vv       CD3EAP MUTATED CD3EAP WILD-TYPE
  FEMALE              2              108
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CD3EAP MUTATED                                       1
  CD3EAP WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CD3EAP MUTATED                                                        4
  CD3EAP WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CD3EAP MUTATED                                                                   1
  CD3EAP WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CD3EAP MUTATED                                                  0
  CD3EAP WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CD3EAP MUTATED                                                          1
  CD3EAP WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CD3EAP MUTATED                                                           0
  CD3EAP WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CD3EAP MUTATED                                          0
  CD3EAP WILD-TYPE                                        3
D622V8, multiclass
                                                                   clus
vv                                                                  CD3EAP MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  CD3EAP WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D622V9, binary
                  cls
clus                 0   1
  CD3EAP MUTATED     1   6
  CD3EAP WILD-TYPE   4 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD3EAP MUTATED      1    6
  CD3EAP WILD-TYPE    4  278
     clus
vv    CD3EAP MUTATED CD3EAP WILD-TYPE
  NO               1                4
  YES              6              278
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CD3EAP MUTATED     5   0   0   2
  CD3EAP WILD-TYPE 222  10  10  22
D622V10, multiclass
    clus
vv   CD3EAP MUTATED CD3EAP WILD-TYPE
  R0              5              222
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D622V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD3EAP MUTATED       1                         0     3
  CD3EAP WILD-TYPE    75                         4   165
D622V12, multiclass
                           clus
vv                          CD3EAP MUTATED CD3EAP WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  3              165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(623) Variable = MAPK15 MUTATION ANALYSIS
D623V1, survival
                  sevent
clus2                0   1
  MAPK15 MUTATED     4   1
  MAPK15 WILD-TYPE 177  79
  MAPK15 MUTATED MAPK15 WILD-TYPE 
               5              256 
  MAPK15 MUTATED MAPK15 WILD-TYPE 
               1               79 
$`MAPK15 MUTATED`
TCGA-BR-7707 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5728 TCGA-HU-8602 
       23.93        15.95         1.02        65.10        11.41 

$`MAPK15 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 
       12.62        20.02         3.02        27.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        0.99       105.07        12.03        28.96        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  MAPK15 MUTATED MAPK15 WILD-TYPE 
            1.02             0.00 
  MAPK15 MUTATED MAPK15 WILD-TYPE 
           65.10           105.07 
  MAPK15 MUTATED MAPK15 WILD-TYPE 
          15.950           12.605 
[1] "1.0 - 65.1 (15.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.3"
D623V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAPK15 MUTATED         0        0        2        1         0         1
  MAPK15 WILD-TYPE       1        9       25       25        31        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAPK15 MUTATED           0          0          0          0        2
  MAPK15 WILD-TYPE         3         49         36         24       22
D623V3, multiclass
            clus
vv           MAPK15 MUTATED MAPK15 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                2               25
  STAGE II                1               25
  STAGE IIA               0               31
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAPK15 MUTATED     0   3   1   2
  MAPK15 WILD-TYPE  11  69 121  73
D623V4, multiclass
    clus
vv   MAPK15 MUTATED MAPK15 WILD-TYPE
  T1              0               11
  T2              3               69
  T3              1              121
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  MAPK15 MUTATED    3  2  2  0
  MAPK15 WILD-TYPE 90 79 48 53
D623V5, multiclass
    clus
vv   MAPK15 MUTATED MAPK15 WILD-TYPE
  N0              3               90
  N1              2               79
  N2              2               48
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D623V6, binary
                  cls
clus                 0   1
  MAPK15 MUTATED     6   1
  MAPK15 WILD-TYPE 251  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAPK15 MUTATED      6    1
  MAPK15 WILD-TYPE  251   17
   clus
vv  MAPK15 MUTATED MAPK15 WILD-TYPE
  0              6              251
  1              1               17
[1] 2 2
[1] FALSE
D623V7, binary
                  cls
clus                 0   1
  MAPK15 MUTATED     5   2
  MAPK15 WILD-TYPE 105 177
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAPK15 MUTATED      5    2
  MAPK15 WILD-TYPE  105  177
        clus
vv       MAPK15 MUTATED MAPK15 WILD-TYPE
  FEMALE              5              105
  MALE                2              177
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MAPK15 MUTATED                                       1
  MAPK15 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MAPK15 MUTATED                                                        5
  MAPK15 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MAPK15 MUTATED                                                                   1
  MAPK15 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MAPK15 MUTATED                                                  0
  MAPK15 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MAPK15 MUTATED                                                          0
  MAPK15 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MAPK15 MUTATED                                                           0
  MAPK15 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MAPK15 MUTATED                                          0
  MAPK15 WILD-TYPE                                        3
D623V8, multiclass
                                                                   clus
vv                                                                  MAPK15 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  MAPK15 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D623V9, binary
                  cls
clus                 0   1
  MAPK15 MUTATED     0   7
  MAPK15 WILD-TYPE   5 277
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAPK15 MUTATED      0    7
  MAPK15 WILD-TYPE    5  277
     clus
vv    MAPK15 MUTATED MAPK15 WILD-TYPE
  NO               0                5
  YES              7              277
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MAPK15 MUTATED     4   0   1   2
  MAPK15 WILD-TYPE 223  10   9  22
D623V10, multiclass
    clus
vv   MAPK15 MUTATED MAPK15 WILD-TYPE
  R0              4              223
  R1              0               10
  R2              1                9
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D623V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAPK15 MUTATED       1                         0     3
  MAPK15 WILD-TYPE    75                         4   165
D623V12, multiclass
                           clus
vv                          MAPK15 MUTATED MAPK15 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  3              165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(624) Variable = PARP15 MUTATION ANALYSIS
D624V1, survival
                  sevent
clus2                0   1
  PARP15 MUTATED     4   0
  PARP15 WILD-TYPE 177  80
  PARP15 MUTATED PARP15 WILD-TYPE 
               4              257 
  PARP15 MUTATED PARP15 WILD-TYPE 
               0               80 
$`PARP15 MUTATED`
TCGA-BR-6852 TCGA-BR-8680 TCGA-CG-5721 TCGA-CG-5728 
       32.94        15.81         6.02        65.10 

$`PARP15 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        30.90        31.20        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        0.99       105.07        12.03        28.96        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  PARP15 MUTATED PARP15 WILD-TYPE 
            6.02             0.00 
  PARP15 MUTATED PARP15 WILD-TYPE 
           65.10           105.07 
  PARP15 MUTATED PARP15 WILD-TYPE 
          24.375           12.590 
[1] "6.0 - 65.1 (24.4)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "2.6e+07"
D624V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PARP15 MUTATED         0        0        1        0         1         0
  PARP15 WILD-TYPE       1        9       26       26        30        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PARP15 MUTATED           0          0          0          0        2
  PARP15 WILD-TYPE         3         49         36         24       22
D624V3, multiclass
            clus
vv           PARP15 MUTATED PARP15 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PARP15 MUTATED     0   1   1   2
  PARP15 WILD-TYPE  11  71 121  73
D624V4, multiclass
    clus
vv   PARP15 MUTATED PARP15 WILD-TYPE
  T1              0               11
  T2              1               71
  T3              1              121
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  PARP15 MUTATED    2  1  1  0
  PARP15 WILD-TYPE 91 80 49 53
D624V5, multiclass
    clus
vv   PARP15 MUTATED PARP15 WILD-TYPE
  N0              2               91
  N1              1               80
  N2              1               49
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D624V6, binary
                  cls
clus                 0   1
  PARP15 MUTATED     3   1
  PARP15 WILD-TYPE 254  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP15 MUTATED      3    1
  PARP15 WILD-TYPE  254   17
   clus
vv  PARP15 MUTATED PARP15 WILD-TYPE
  0              3              254
  1              1               17
[1] 2 2
[1] FALSE
D624V7, binary
                  cls
clus                 0   1
  PARP15 MUTATED     2   2
  PARP15 WILD-TYPE 108 177
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP15 MUTATED      2    2
  PARP15 WILD-TYPE  108  177
        clus
vv       PARP15 MUTATED PARP15 WILD-TYPE
  FEMALE              2              108
  MALE                2              177
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PARP15 MUTATED                                       0
  PARP15 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PARP15 MUTATED                                                        1
  PARP15 WILD-TYPE                                                    134
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PARP15 MUTATED                                                                   2
  PARP15 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PARP15 MUTATED                                                  1
  PARP15 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PARP15 MUTATED                                                          0
  PARP15 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PARP15 MUTATED                                                           0
  PARP15 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PARP15 MUTATED                                          0
  PARP15 WILD-TYPE                                        3
D624V8, multiclass
                                                                   clus
vv                                                                  PARP15 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         1
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  PARP15 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D624V9, binary
                  cls
clus                 0   1
  PARP15 MUTATED     0   4
  PARP15 WILD-TYPE   5 280
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP15 MUTATED      0    4
  PARP15 WILD-TYPE    5  280
     clus
vv    PARP15 MUTATED PARP15 WILD-TYPE
  NO               0                5
  YES              4              280
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PARP15 MUTATED     4   0   0   0
  PARP15 WILD-TYPE 223  10  10  24
D624V10, multiclass
    clus
vv   PARP15 MUTATED PARP15 WILD-TYPE
  R0              4              223
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D624V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PARP15 MUTATED       1                         0     1
  PARP15 WILD-TYPE    75                         4   167
D624V12, multiclass
[1] "Remove cluster labels:" "PARP15 MUTATED"        
clus
  PARP15 MUTATED PARP15 WILD-TYPE 
               2              246 
      TCGA-B7-5816       TCGA-B7-5818       TCGA-BR-4183       TCGA-BR-4184 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-4187       TCGA-BR-4188       TCGA-BR-4191       TCGA-BR-4201 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-4253       TCGA-BR-4255       TCGA-BR-4256       TCGA-BR-4257 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-4267       TCGA-BR-4279       TCGA-BR-4280       TCGA-BR-4292 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-4294       TCGA-BR-4357       TCGA-BR-4361       TCGA-BR-4362 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-4363       TCGA-BR-4366       TCGA-BR-4368       TCGA-BR-4369 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-4370       TCGA-BR-4371       TCGA-BR-6452       TCGA-BR-6453 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-6454       TCGA-BR-6455       TCGA-BR-6456       TCGA-BR-6457 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-6458       TCGA-BR-6563       TCGA-BR-6564       TCGA-BR-6565 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-6566       TCGA-BR-6705       TCGA-BR-6706       TCGA-BR-6707 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-6710       TCGA-BR-6801       TCGA-BR-6802       TCGA-BR-6803 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-7196       TCGA-BR-7197       TCGA-BR-7703       TCGA-BR-7707 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-7715       TCGA-BR-7716       TCGA-BR-7717       TCGA-BR-7722 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-7723       TCGA-BR-7851       TCGA-BR-7901       TCGA-BR-7957 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-7958       TCGA-BR-7959       TCGA-BR-8058       TCGA-BR-8059 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-8077       TCGA-BR-8078       TCGA-BR-8080       TCGA-BR-8081 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-8284       TCGA-BR-8286       TCGA-BR-8289       TCGA-BR-8291 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-8295       TCGA-BR-8296       TCGA-BR-8297       TCGA-BR-8360 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-8361       TCGA-BR-8363       TCGA-BR-8364       TCGA-BR-8365 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-8366       TCGA-BR-8367       TCGA-BR-8368       TCGA-BR-8369 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-8370       TCGA-BR-8371       TCGA-BR-8372       TCGA-BR-8373 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-8380       TCGA-BR-8381       TCGA-BR-8382       TCGA-BR-8384 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-8483       TCGA-BR-8484       TCGA-BR-8485       TCGA-BR-8486 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-8487       TCGA-BR-8588       TCGA-BR-8589       TCGA-BR-8590 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-8591       TCGA-BR-8592       TCGA-BR-8676       TCGA-BR-8677 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-8678       TCGA-BR-8679       TCGA-BR-8682       TCGA-BR-8683 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-8686       TCGA-BR-8687       TCGA-BR-8690       TCGA-BR-A44T 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-A44U       TCGA-BR-A452       TCGA-BR-A453       TCGA-BR-A4CQ 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-A4CR       TCGA-BR-A4CS       TCGA-BR-A4IU       TCGA-BR-A4IV 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-A4IY       TCGA-BR-A4IZ       TCGA-BR-A4J1       TCGA-BR-A4J2 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-A4J4       TCGA-BR-A4J6       TCGA-BR-A4J7       TCGA-BR-A4J8 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-A4PD       TCGA-BR-A4PE       TCGA-BR-A4PF       TCGA-BR-A4QI 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-BR-A4QL       TCGA-BR-A4QM       TCGA-CD-5798       TCGA-CD-5799 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-CD-5800       TCGA-CD-5801       TCGA-CD-5802       TCGA-CD-5803 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-CD-5804       TCGA-CD-5813       TCGA-CD-8524       TCGA-CD-8525 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-CD-8526       TCGA-CD-8527       TCGA-CD-8528       TCGA-CD-8529 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-CD-8530       TCGA-CD-8531       TCGA-CD-8532       TCGA-CD-8534 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-CD-8535       TCGA-CD-8536       TCGA-CD-A486       TCGA-CD-A487 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-CD-A489       TCGA-CD-A48A       TCGA-CD-A48C       TCGA-CD-A4MG 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-CD-A4MH       TCGA-CD-A4MI       TCGA-CD-A4MJ       TCGA-D7-5577 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-D7-5578       TCGA-D7-5579       TCGA-D7-6518       TCGA-D7-6519 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-D7-6520       TCGA-D7-6521       TCGA-D7-6522       TCGA-D7-6524 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-D7-6525       TCGA-D7-6526       TCGA-D7-6527       TCGA-D7-6528 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-D7-6815       TCGA-D7-6817       TCGA-D7-6818       TCGA-D7-6820 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-D7-6822       TCGA-D7-8570       TCGA-D7-8572       TCGA-D7-8573 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-D7-8574       TCGA-D7-8575       TCGA-D7-8576       TCGA-D7-8578 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-D7-8579       TCGA-D7-A4YT       TCGA-D7-A4YU       TCGA-D7-A4YV 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-D7-A4YX       TCGA-D7-A4YY       TCGA-D7-A4Z0       TCGA-EQ-5647 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-EQ-8122       TCGA-EQ-A4SO       TCGA-F1-6177       TCGA-F1-6874 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-F1-6875       TCGA-F1-A448       TCGA-FP-7735       TCGA-FP-7829 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-FP-7916       TCGA-FP-7998       TCGA-FP-8099       TCGA-FP-8209 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-FP-8210       TCGA-FP-8211       TCGA-FP-8631       TCGA-FP-A4BE 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-FP-A4BF       TCGA-HJ-7597       TCGA-HU-8243       TCGA-HU-8245 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-HU-8249       TCGA-HU-8602       TCGA-HU-8604       TCGA-HU-8608 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-HU-8610       TCGA-HU-A4G2       TCGA-HU-A4G3       TCGA-HU-A4G6 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-HU-A4G8       TCGA-HU-A4G9       TCGA-HU-A4GC       TCGA-HU-A4GD 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-HU-A4GF       TCGA-HU-A4GH       TCGA-HU-A4GN       TCGA-HU-A4GP 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-HU-A4GQ       TCGA-HU-A4GT       TCGA-HU-A4GU       TCGA-HU-A4GX 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-HU-A4GY       TCGA-HU-A4H0       TCGA-HU-A4H2       TCGA-HU-A4H3 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-HU-A4H4       TCGA-HU-A4H5       TCGA-HU-A4H6       TCGA-HU-A4H8 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-HU-A4HD       TCGA-IN-7806       TCGA-IN-7808       TCGA-IN-8462 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 
      TCGA-IN-8663       TCGA-IP-7968 
"PARP15 WILD-TYPE" "PARP15 WILD-TYPE" 

Clustering(625) Variable = TM6SF1 MUTATION ANALYSIS
D625V1, survival
                  sevent
clus2                0   1
  TM6SF1 MUTATED     4   1
  TM6SF1 WILD-TYPE 177  79
  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
               5              256 
  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
               1               79 
$`TM6SF1 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8591 TCGA-CD-A4MJ TCGA-CG-4465 
       26.70        34.68        13.45        12.62         9.01 

$`TM6SF1 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
            9.01             0.00 
  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
           34.68           105.07 
  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
          13.450           12.575 
[1] "9.0 - 34.7 (13.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.3"
D625V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TM6SF1 MUTATED         0        0        1        0         1         1
  TM6SF1 WILD-TYPE       1        9       26       26        30        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TM6SF1 MUTATED           0          0          0          1        1
  TM6SF1 WILD-TYPE         3         49         36         23       23
D625V3, multiclass
            clus
vv           TM6SF1 MUTATED TM6SF1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TM6SF1 MUTATED     1   1   1   3
  TM6SF1 WILD-TYPE  10  71 121  72
D625V4, multiclass
    clus
vv   TM6SF1 MUTATED TM6SF1 WILD-TYPE
  T1              1               10
  T2              1               71
  T3              1              121
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  TM6SF1 MUTATED    3  0  0  2
  TM6SF1 WILD-TYPE 90 81 50 51
D625V5, multiclass
    clus
vv   TM6SF1 MUTATED TM6SF1 WILD-TYPE
  N0              3               90
  N1              0               81
  N2              0               50
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D625V6, binary
                  cls
clus                 0   1
  TM6SF1 MUTATED     5   1
  TM6SF1 WILD-TYPE 252  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM6SF1 MUTATED      5    1
  TM6SF1 WILD-TYPE  252   17
   clus
vv  TM6SF1 MUTATED TM6SF1 WILD-TYPE
  0              5              252
  1              1               17
[1] 2 2
[1] FALSE
D625V7, binary
                  cls
clus                 0   1
  TM6SF1 MUTATED     4   2
  TM6SF1 WILD-TYPE 106 177
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM6SF1 MUTATED      4    2
  TM6SF1 WILD-TYPE  106  177
        clus
vv       TM6SF1 MUTATED TM6SF1 WILD-TYPE
  FEMALE              4              106
  MALE                2              177
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TM6SF1 MUTATED                                       2
  TM6SF1 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TM6SF1 MUTATED                                                        4
  TM6SF1 WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TM6SF1 MUTATED                                                                   0
  TM6SF1 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TM6SF1 MUTATED                                                  0
  TM6SF1 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TM6SF1 MUTATED                                                          0
  TM6SF1 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TM6SF1 MUTATED                                                           0
  TM6SF1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TM6SF1 MUTATED                                          0
  TM6SF1 WILD-TYPE                                        3
D625V8, multiclass
                                                                   clus
vv                                                                  TM6SF1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  TM6SF1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D625V9, binary
                  cls
clus                 0   1
  TM6SF1 MUTATED     0   6
  TM6SF1 WILD-TYPE   5 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM6SF1 MUTATED      0    6
  TM6SF1 WILD-TYPE    5  278
     clus
vv    TM6SF1 MUTATED TM6SF1 WILD-TYPE
  NO               0                5
  YES              6              278
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TM6SF1 MUTATED     3   0   1   1
  TM6SF1 WILD-TYPE 224  10   9  23
D625V10, multiclass
    clus
vv   TM6SF1 MUTATED TM6SF1 WILD-TYPE
  R0              3              224
  R1              0               10
  R2              1                9
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D625V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TM6SF1 MUTATED       1                         0     4
  TM6SF1 WILD-TYPE    75                         4   164
D625V12, multiclass
                           clus
vv                          TM6SF1 MUTATED TM6SF1 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(626) Variable = DDX50 MUTATION ANALYSIS
D626V1, survival
                 sevent
clus2               0   1
  DDX50 MUTATED     6   3
  DDX50 WILD-TYPE 175  77
  DDX50 MUTATED DDX50 WILD-TYPE 
              9             252 
  DDX50 MUTATED DDX50 WILD-TYPE 
              3              77 
$`DDX50 MUTATED`
TCGA-BR-4201 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CG-5721 
       30.90        24.76        23.93         1.12         6.58         6.02 
TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GQ 
       11.41        11.84         0.10 

$`DDX50 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  DDX50 MUTATED DDX50 WILD-TYPE 
            0.1             0.0 
  DDX50 MUTATED DDX50 WILD-TYPE 
          30.90          105.07 
  DDX50 MUTATED DDX50 WILD-TYPE 
          11.41           12.71 
[1] "0.1 - 30.9 (11.4)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.2"
D626V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDX50 MUTATED         1        1        1        0         2         2
  DDX50 WILD-TYPE       0        8       26       26        29        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DDX50 MUTATED           0          0          0          1        2
  DDX50 WILD-TYPE         3         49         36         23       22
D626V3, multiclass
            clus
vv           DDX50 MUTATED DDX50 WILD-TYPE
  STAGE I                1               0
  STAGE IA               1               8
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDX50 MUTATED     2   2   3   4
  DDX50 WILD-TYPE   9  70 119  71
D626V4, multiclass
    clus
vv   DDX50 MUTATED DDX50 WILD-TYPE
  T1             2               9
  T2             2              70
  T3             3             119
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  DDX50 MUTATED    5  3  2  0
  DDX50 WILD-TYPE 88 78 48 53
D626V5, multiclass
    clus
vv   DDX50 MUTATED DDX50 WILD-TYPE
  N0             5              88
  N1             3              78
  N2             2              48
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D626V6, binary
                 cls
clus                0   1
  DDX50 MUTATED    10   0
  DDX50 WILD-TYPE 247  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX50 MUTATED     10    0
  DDX50 WILD-TYPE  247   18
   clus
vv  DDX50 MUTATED DDX50 WILD-TYPE
  0            10             247
  1             0              18
[1] 2 2
[1] FALSE
D626V7, binary
                 cls
clus                0   1
  DDX50 MUTATED     6   5
  DDX50 WILD-TYPE 104 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX50 MUTATED      6    5
  DDX50 WILD-TYPE  104  174
        clus
vv       DDX50 MUTATED DDX50 WILD-TYPE
  FEMALE             6             104
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DDX50 MUTATED                                       3
  DDX50 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DDX50 MUTATED                                                        5
  DDX50 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DDX50 MUTATED                                                                   1
  DDX50 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DDX50 MUTATED                                                  1
  DDX50 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DDX50 MUTATED                                                          0
  DDX50 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DDX50 MUTATED                                                           1
  DDX50 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DDX50 MUTATED                                          0
  DDX50 WILD-TYPE                                        3
D626V8, multiclass
                                                                   clus
vv                                                                  DDX50 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  DDX50 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D626V9, binary
                 cls
clus                0   1
  DDX50 MUTATED     0  11
  DDX50 WILD-TYPE   5 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX50 MUTATED      0   11
  DDX50 WILD-TYPE    5  273
     clus
vv    DDX50 MUTATED DDX50 WILD-TYPE
  NO              0               5
  YES            11             273
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DDX50 MUTATED     7   0   0   2
  DDX50 WILD-TYPE 220  10  10  22
D626V10, multiclass
    clus
vv   DDX50 MUTATED DDX50 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D626V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDX50 MUTATED       4                         1     5
  DDX50 WILD-TYPE    72                         3   163
D626V12, multiclass
                           clus
vv                          DDX50 MUTATED DDX50 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(627) Variable = CCDC27 MUTATION ANALYSIS
D627V1, survival
                  sevent
clus2                0   1
  CCDC27 MUTATED     2   3
  CCDC27 WILD-TYPE 179  77
  CCDC27 MUTATED CCDC27 WILD-TYPE 
               5              256 
  CCDC27 MUTATED CCDC27 WILD-TYPE 
               3               77 
$`CCDC27 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7717 TCGA-BR-8590 TCGA-CG-5721 
       30.90        34.68        18.15         9.34         6.02 

$`CCDC27 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       18.35         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       23.93        15.42        28.01        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        12.79        15.81        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  CCDC27 MUTATED CCDC27 WILD-TYPE 
            6.02             0.00 
  CCDC27 MUTATED CCDC27 WILD-TYPE 
           34.68           105.07 
  CCDC27 MUTATED CCDC27 WILD-TYPE 
          18.150           12.605 
[1] "6.0 - 34.7 (18.1)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D627V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC27 MUTATED         1        0        0        0         1         0
  CCDC27 WILD-TYPE       0        9       27       26        30        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC27 MUTATED           0          0          0          1        2
  CCDC27 WILD-TYPE         3         49         36         23       22
D627V3, multiclass
            clus
vv           CCDC27 MUTATED CCDC27 WILD-TYPE
  STAGE I                 1                0
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CCDC27 MUTATED     1   1   1   3
  CCDC27 WILD-TYPE  10  71 121  72
D627V4, multiclass
    clus
vv   CCDC27 MUTATED CCDC27 WILD-TYPE
  T1              1               10
  T2              1               71
  T3              1              121
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CCDC27 MUTATED    1  3  1  0
  CCDC27 WILD-TYPE 92 78 49 53
D627V5, multiclass
    clus
vv   CCDC27 MUTATED CCDC27 WILD-TYPE
  N0              1               92
  N1              3               78
  N2              1               49
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D627V6, binary
                  cls
clus                 0   1
  CCDC27 MUTATED     5   0
  CCDC27 WILD-TYPE 252  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC27 MUTATED      5    0
  CCDC27 WILD-TYPE  252   18
   clus
vv  CCDC27 MUTATED CCDC27 WILD-TYPE
  0              5              252
  1              0               18
[1] 2 2
[1] FALSE
D627V7, binary
                  cls
clus                 0   1
  CCDC27 MUTATED     2   4
  CCDC27 WILD-TYPE 108 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC27 MUTATED      2    4
  CCDC27 WILD-TYPE  108  175
        clus
vv       CCDC27 MUTATED CCDC27 WILD-TYPE
  FEMALE              2              108
  MALE                4              175
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CCDC27 MUTATED                                       0
  CCDC27 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CCDC27 MUTATED                                                        5
  CCDC27 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CCDC27 MUTATED                                                                   1
  CCDC27 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CCDC27 MUTATED                                                  0
  CCDC27 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CCDC27 MUTATED                                                          0
  CCDC27 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CCDC27 MUTATED                                                           0
  CCDC27 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CCDC27 MUTATED                                          0
  CCDC27 WILD-TYPE                                        3
D627V8, multiclass
                                                                   clus
vv                                                                  CCDC27 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  CCDC27 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D627V9, binary
                  cls
clus                 0   1
  CCDC27 MUTATED     0   6
  CCDC27 WILD-TYPE   5 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC27 MUTATED      0    6
  CCDC27 WILD-TYPE    5  278
     clus
vv    CCDC27 MUTATED CCDC27 WILD-TYPE
  NO               0                5
  YES              6              278
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CCDC27 MUTATED     5   0   0   1
  CCDC27 WILD-TYPE 222  10  10  23
D627V10, multiclass
    clus
vv   CCDC27 MUTATED CCDC27 WILD-TYPE
  R0              5              222
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D627V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC27 MUTATED       0                         1     4
  CCDC27 WILD-TYPE    76                         3   164
D627V12, multiclass
                           clus
vv                          CCDC27 MUTATED CCDC27 WILD-TYPE
  ASIAN                                  0               76
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(628) Variable = EPHB6 MUTATION ANALYSIS
D628V1, survival
                 sevent
clus2               0   1
  EPHB6 MUTATED    10   1
  EPHB6 WILD-TYPE 171  79
  EPHB6 MUTATED EPHB6 WILD-TYPE 
             11             250 
  EPHB6 MUTATED EPHB6 WILD-TYPE 
              1              79 
$`EPHB6 MUTATED`
TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8591 TCGA-BR-8680 
       34.68        30.90        12.26        19.50        13.45        15.81 
TCGA-CD-A4MG TCGA-CG-5728 TCGA-F1-6874 TCGA-HU-A4H3 TCGA-HU-A4H5 
        6.58        65.10        14.47        19.36        12.30 

$`EPHB6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        15.81         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 
       14.76         0.62         7.99        16.24        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       12.95        23.84         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  EPHB6 MUTATED EPHB6 WILD-TYPE 
           6.58            0.00 
  EPHB6 MUTATED EPHB6 WILD-TYPE 
          65.10          105.07 
  EPHB6 MUTATED EPHB6 WILD-TYPE 
         15.810          12.495 
[1] "6.6 - 65.1 (15.8)"  "0.0 - 105.1 (12.5)"
[1] "hr=" "5.5"
D628V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPHB6 MUTATED         0        0        3        0         2         1
  EPHB6 WILD-TYPE       1        9       24       26        29        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EPHB6 MUTATED           0          1          0          3        1
  EPHB6 WILD-TYPE         3         48         36         21       23
D628V3, multiclass
            clus
vv           EPHB6 MUTATED EPHB6 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               3              24
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             3              21
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EPHB6 MUTATED     0   3   3   5
  EPHB6 WILD-TYPE  11  69 119  70
D628V4, multiclass
    clus
vv   EPHB6 MUTATED EPHB6 WILD-TYPE
  T1             0              11
  T2             3              69
  T3             3             119
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  EPHB6 MUTATED    6  0  3  2
  EPHB6 WILD-TYPE 87 81 47 51
D628V5, multiclass
    clus
vv   EPHB6 MUTATED EPHB6 WILD-TYPE
  N0             6              87
  N1             0              81
  N2             3              47
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D628V6, binary
                 cls
clus                0   1
  EPHB6 MUTATED    10   1
  EPHB6 WILD-TYPE 247  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB6 MUTATED     10    1
  EPHB6 WILD-TYPE  247   17
   clus
vv  EPHB6 MUTATED EPHB6 WILD-TYPE
  0            10             247
  1             1              17
[1] 2 2
[1] FALSE
D628V7, binary
                 cls
clus                0   1
  EPHB6 MUTATED     5   6
  EPHB6 WILD-TYPE 105 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB6 MUTATED      5    6
  EPHB6 WILD-TYPE  105  173
        clus
vv       EPHB6 MUTATED EPHB6 WILD-TYPE
  FEMALE             5             105
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  EPHB6 MUTATED                                       2
  EPHB6 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EPHB6 MUTATED                                                        5
  EPHB6 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EPHB6 MUTATED                                                                   2
  EPHB6 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  EPHB6 MUTATED                                                  1
  EPHB6 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  EPHB6 MUTATED                                                          0
  EPHB6 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  EPHB6 MUTATED                                                           1
  EPHB6 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  EPHB6 MUTATED                                          0
  EPHB6 WILD-TYPE                                        3
D628V8, multiclass
                                                                   clus
vv                                                                  EPHB6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  EPHB6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D628V9, binary
                 cls
clus                0   1
  EPHB6 MUTATED     0  11
  EPHB6 WILD-TYPE   5 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB6 MUTATED      0   11
  EPHB6 WILD-TYPE    5  273
     clus
vv    EPHB6 MUTATED EPHB6 WILD-TYPE
  NO              0               5
  YES            11             273
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EPHB6 MUTATED    10   0   0   0
  EPHB6 WILD-TYPE 217  10  10  24
D628V10, multiclass
    clus
vv   EPHB6 MUTATED EPHB6 WILD-TYPE
  R0            10             217
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D628V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EPHB6 MUTATED       4                         0     6
  EPHB6 WILD-TYPE    72                         4   162
D628V12, multiclass
                           clus
vv                          EPHB6 MUTATED EPHB6 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(629) Variable = TRIP11 MUTATION ANALYSIS
D629V1, survival
                  sevent
clus2                0   1
  TRIP11 MUTATED     8   5
  TRIP11 WILD-TYPE 173  75
  TRIP11 MUTATED TRIP11 WILD-TYPE 
              13              248 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
               5               75 
$`TRIP11 MUTATED`
TCGA-BR-7703 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8680 TCGA-CD-5800 
       24.76        14.43        12.26         4.31        15.81        13.15 
TCGA-CD-5801 TCGA-CG-4466 TCGA-CG-5721 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 
       13.18        18.97         6.02        65.10        69.04        21.07 
TCGA-HU-A4GQ 
        0.10 

$`TRIP11 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       17.49         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
        2.83         3.25         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       47.05        19.07        12.03         0.00         9.01         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        0.99       105.07        12.03        28.96        79.07         4.01 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  TRIP11 MUTATED TRIP11 WILD-TYPE 
             0.1              0.0 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
           69.04           105.07 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
          14.430           12.495 
[1] "0.1 - 69.0 (14.4)"  "0.0 - 105.1 (12.5)"
[1] "hr=" "1.1"
D629V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRIP11 MUTATED         0        1        3        1         0         1
  TRIP11 WILD-TYPE       1        8       24       25        31        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIP11 MUTATED           1          2          0          1        3
  TRIP11 WILD-TYPE         2         47         36         23       21
D629V3, multiclass
            clus
vv           TRIP11 MUTATED TRIP11 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                3               24
  STAGE II                1               25
  STAGE IIA               0               31
  STAGE IIB               1               43
  STAGE III               1                2
  STAGE IIIA              2               47
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                3               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIP11 MUTATED     1   5   2   5
  TRIP11 WILD-TYPE  10  67 120  70
D629V4, multiclass
    clus
vv   TRIP11 MUTATED TRIP11 WILD-TYPE
  T1              1               10
  T2              5               67
  T3              2              120
  T4              5               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  TRIP11 MUTATED    6  3  3  1
  TRIP11 WILD-TYPE 87 78 47 52
D629V5, multiclass
    clus
vv   TRIP11 MUTATED TRIP11 WILD-TYPE
  N0              6               87
  N1              3               78
  N2              3               47
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D629V6, binary
                  cls
clus                 0   1
  TRIP11 MUTATED    12   1
  TRIP11 WILD-TYPE 245  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED     12    1
  TRIP11 WILD-TYPE  245   17
   clus
vv  TRIP11 MUTATED TRIP11 WILD-TYPE
  0             12              245
  1              1               17
[1] 2 2
[1] FALSE
D629V7, binary
                  cls
clus                 0   1
  TRIP11 MUTATED     6   7
  TRIP11 WILD-TYPE 104 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED      6    7
  TRIP11 WILD-TYPE  104  172
        clus
vv       TRIP11 MUTATED TRIP11 WILD-TYPE
  FEMALE              6              104
  MALE                7              172
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TRIP11 MUTATED                                       0
  TRIP11 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TRIP11 MUTATED                                                        3
  TRIP11 WILD-TYPE                                                    132
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TRIP11 MUTATED                                                                   6
  TRIP11 WILD-TYPE                                                                34
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TRIP11 MUTATED                                                  2
  TRIP11 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TRIP11 MUTATED                                                          0
  TRIP11 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TRIP11 MUTATED                                                           2
  TRIP11 WILD-TYPE                                                         4
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TRIP11 MUTATED                                          0
  TRIP11 WILD-TYPE                                        3
D629V8, multiclass
                                                                   clus
vv                                                                  TRIP11 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  TRIP11 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D629V9, binary
                  cls
clus                 0   1
  TRIP11 MUTATED     0  13
  TRIP11 WILD-TYPE   5 271
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED      0   13
  TRIP11 WILD-TYPE    5  271
     clus
vv    TRIP11 MUTATED TRIP11 WILD-TYPE
  NO               0                5
  YES             13              271
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRIP11 MUTATED    13   0   0   0
  TRIP11 WILD-TYPE 214  10  10  24
D629V10, multiclass
    clus
vv   TRIP11 MUTATED TRIP11 WILD-TYPE
  R0             13              214
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D629V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TRIP11 MUTATED       4                         0     4
  TRIP11 WILD-TYPE    72                         4   164
D629V12, multiclass
                           clus
vv                          TRIP11 MUTATED TRIP11 WILD-TYPE
  ASIAN                                  4               72
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(630) Variable = ITGAV MUTATION ANALYSIS
D630V1, survival
                 sevent
clus2               0   1
  ITGAV MUTATED    10   2
  ITGAV WILD-TYPE 171  78
  ITGAV MUTATED ITGAV WILD-TYPE 
             12             249 
  ITGAV MUTATED ITGAV WILD-TYPE 
              2              78 
$`ITGAV MUTATED`
TCGA-BR-6458 TCGA-BR-7197 TCGA-BR-7722 TCGA-BR-8078 TCGA-BR-8487 TCGA-CG-4305 
       19.33         9.21        15.32        12.26         1.12        15.95 
TCGA-CG-5730 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4H8 
        4.01        12.59        11.41        25.81         6.51         8.88 

$`ITGAV WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       21.11        30.90        31.20        32.94        12.82        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 
       23.93        15.42        28.01        18.15        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        65.10        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        5.52        26.47         5.92        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        11.77        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  ITGAV MUTATED ITGAV WILD-TYPE 
           1.12            0.00 
  ITGAV MUTATED ITGAV WILD-TYPE 
          25.81          105.07 
  ITGAV MUTATED ITGAV WILD-TYPE 
         11.835          12.760 
[1] "1.1 - 25.8 (11.8)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.5"
D630V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ITGAV MUTATED         0        0        1        2         4         4
  ITGAV WILD-TYPE       1        9       26       24        27        40
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ITGAV MUTATED           0          0          0          0        2
  ITGAV WILD-TYPE         3         49         36         24       22
D630V3, multiclass
            clus
vv           ITGAV MUTATED ITGAV WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               2              24
  STAGE IIA              4              27
  STAGE IIB              4              40
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITGAV MUTATED     1   2   7   3
  ITGAV WILD-TYPE  10  70 115  72
D630V4, multiclass
    clus
vv   ITGAV MUTATED ITGAV WILD-TYPE
  T1             1              10
  T2             2              70
  T3             7             115
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ITGAV MUTATED    7  5  1  0
  ITGAV WILD-TYPE 86 76 49 53
D630V5, multiclass
    clus
vv   ITGAV MUTATED ITGAV WILD-TYPE
  N0             7              86
  N1             5              76
  N2             1              49
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D630V6, binary
                 cls
clus                0   1
  ITGAV MUTATED    12   1
  ITGAV WILD-TYPE 245  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAV MUTATED     12    1
  ITGAV WILD-TYPE  245   17
   clus
vv  ITGAV MUTATED ITGAV WILD-TYPE
  0            12             245
  1             1              17
[1] 2 2
[1] FALSE
D630V7, binary
                 cls
clus                0   1
  ITGAV MUTATED     7   6
  ITGAV WILD-TYPE 103 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAV MUTATED      7    6
  ITGAV WILD-TYPE  103  173
        clus
vv       ITGAV MUTATED ITGAV WILD-TYPE
  FEMALE             7             103
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ITGAV MUTATED                                       1
  ITGAV WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ITGAV MUTATED                                                        7
  ITGAV WILD-TYPE                                                    128
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ITGAV MUTATED                                                                   1
  ITGAV WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ITGAV MUTATED                                                  3
  ITGAV WILD-TYPE                                               35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ITGAV MUTATED                                                          0
  ITGAV WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ITGAV MUTATED                                                           1
  ITGAV WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ITGAV MUTATED                                          0
  ITGAV WILD-TYPE                                        3
D630V8, multiclass
                                                                   clus
vv                                                                  ITGAV MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ITGAV WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D630V9, binary
                 cls
clus                0   1
  ITGAV MUTATED     0  13
  ITGAV WILD-TYPE   5 271
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAV MUTATED      0   13
  ITGAV WILD-TYPE    5  271
     clus
vv    ITGAV MUTATED ITGAV WILD-TYPE
  NO              0               5
  YES            13             271
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ITGAV MUTATED    11   0   1   1
  ITGAV WILD-TYPE 216  10   9  23
D630V10, multiclass
    clus
vv   ITGAV MUTATED ITGAV WILD-TYPE
  R0            11             216
  R1             0              10
  R2             1               9
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D630V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ITGAV MUTATED       5                         0     6
  ITGAV WILD-TYPE    71                         4   162
D630V12, multiclass
                           clus
vv                          ITGAV MUTATED ITGAV WILD-TYPE
  ASIAN                                 5              71
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(631) Variable = BCL2L14 MUTATION ANALYSIS
D631V1, survival
                   sevent
clus2                 0   1
  BCL2L14 MUTATED     2   0
  BCL2L14 WILD-TYPE 179  80
  BCL2L14 MUTATED BCL2L14 WILD-TYPE 
                2               259 
  BCL2L14 MUTATED BCL2L14 WILD-TYPE 
                0                80 
$`BCL2L14 MUTATED`
TCGA-BR-A4QI TCGA-F1-6874 
       13.64        14.47 

$`BCL2L14 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
       13.78        14.76         0.62         7.99        16.24        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  BCL2L14 MUTATED BCL2L14 WILD-TYPE 
            13.64              0.00 
  BCL2L14 MUTATED BCL2L14 WILD-TYPE 
            14.47            105.07 
  BCL2L14 MUTATED BCL2L14 WILD-TYPE 
           14.055            12.590 
[1] "13.6 - 14.5 (14.1)" "0.0 - 105.1 (12.6)"
[1] "Remove cluster labels:" "BCL2L14 MUTATED"       
D631V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BCL2L14 MUTATED         0        0        2        0         1         0
  BCL2L14 WILD-TYPE       1        9       25       26        30        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BCL2L14 MUTATED           0          0          0          0        0
  BCL2L14 WILD-TYPE         3         49         36         24       24
D631V3, multiclass
            clus
vv           BCL2L14 MUTATED BCL2L14 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 2                25
  STAGE II                 0                26
  STAGE IIA                1                30
  STAGE IIB                0                44
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               0                36
  STAGE IIIC               0                24
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  BCL2L14 MUTATED     0   2   1   0
  BCL2L14 WILD-TYPE  11  70 121  75
D631V4, multiclass
    clus
vv   BCL2L14 MUTATED BCL2L14 WILD-TYPE
  T1               0                11
  T2               2                70
  T3               1               121
  T4               0                75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  BCL2L14 MUTATED    3  0  0  0
  BCL2L14 WILD-TYPE 90 81 50 53
D631V5, multiclass
    clus
vv   BCL2L14 MUTATED BCL2L14 WILD-TYPE
  N0               3                90
  N1               0                81
  N2               0                50
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D631V6, binary
                   cls
clus                  0   1
  BCL2L14 MUTATED     3   0
  BCL2L14 WILD-TYPE 254  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  BCL2L14 MUTATED      3    0
  BCL2L14 WILD-TYPE  254   18
   clus
vv  BCL2L14 MUTATED BCL2L14 WILD-TYPE
  0               3               254
  1               0                18
[1] 2 2
[1] FALSE
D631V7, binary
                   cls
clus                  0   1
  BCL2L14 MUTATED     1   2
  BCL2L14 WILD-TYPE 109 177
[1] "tbl2"
                   cls
clus                [,1] [,2]
  BCL2L14 MUTATED      1    2
  BCL2L14 WILD-TYPE  109  177
        clus
vv       BCL2L14 MUTATED BCL2L14 WILD-TYPE
  FEMALE               1               109
  MALE                 2               177
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  BCL2L14 MUTATED                                       0
  BCL2L14 WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BCL2L14 MUTATED                                                        1
  BCL2L14 WILD-TYPE                                                    134
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BCL2L14 MUTATED                                                                   2
  BCL2L14 WILD-TYPE                                                                38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  BCL2L14 MUTATED                                                  0
  BCL2L14 WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  BCL2L14 MUTATED                                                          0
  BCL2L14 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  BCL2L14 MUTATED                                                           0
  BCL2L14 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  BCL2L14 MUTATED                                          0
  BCL2L14 WILD-TYPE                                        3
D631V8, multiclass
                                                                   clus
vv                                                                  BCL2L14 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          1
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  BCL2L14 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D631V9, binary
                   cls
clus                  0   1
  BCL2L14 MUTATED     0   3
  BCL2L14 WILD-TYPE   5 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  BCL2L14 MUTATED      0    3
  BCL2L14 WILD-TYPE    5  281
     clus
vv    BCL2L14 MUTATED BCL2L14 WILD-TYPE
  NO                0                 5
  YES               3               281
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  BCL2L14 MUTATED     3   0   0   0
  BCL2L14 WILD-TYPE 224  10  10  24
D631V10, multiclass
    clus
vv   BCL2L14 MUTATED BCL2L14 WILD-TYPE
  R0               3               224
  R1               0                10
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D631V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCL2L14 MUTATED       0                         0     2
  BCL2L14 WILD-TYPE    76                         4   166
D631V12, multiclass
[1] "Remove cluster labels:" "BCL2L14 MUTATED"       
clus
  BCL2L14 MUTATED BCL2L14 WILD-TYPE 
                2               246 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-4187        TCGA-BR-4188        TCGA-BR-4191        TCGA-BR-4201 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-4294        TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-4363        TCGA-BR-4366        TCGA-BR-4368        TCGA-BR-4369 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-4370        TCGA-BR-4371        TCGA-BR-6452        TCGA-BR-6453 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-6710        TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-6852        TCGA-BR-7196        TCGA-BR-7197        TCGA-BR-7703 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-7707        TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-7722        TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-7957        TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8058 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-8059        TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-8081        TCGA-BR-8284        TCGA-BR-8286        TCGA-BR-8289 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-8360        TCGA-BR-8361        TCGA-BR-8363        TCGA-BR-8364 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-8365        TCGA-BR-8366        TCGA-BR-8367        TCGA-BR-8368 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-8369        TCGA-BR-8370        TCGA-BR-8371        TCGA-BR-8372 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-8373        TCGA-BR-8380        TCGA-BR-8381        TCGA-BR-8382 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-8384        TCGA-BR-8483        TCGA-BR-8484        TCGA-BR-8485 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-8486        TCGA-BR-8487        TCGA-BR-8588        TCGA-BR-8589 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-8590        TCGA-BR-8591        TCGA-BR-8592        TCGA-BR-8676 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-8677        TCGA-BR-8678        TCGA-BR-8679        TCGA-BR-8680 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-8682        TCGA-BR-8683        TCGA-BR-8686        TCGA-BR-8687 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-8690        TCGA-BR-A44T        TCGA-BR-A44U        TCGA-BR-A452 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-A453        TCGA-BR-A4CQ        TCGA-BR-A4CR        TCGA-BR-A4CS 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY        TCGA-BR-A4IZ 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4        TCGA-BR-A4J6 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-A4J7        TCGA-BR-A4J8        TCGA-BR-A4PD        TCGA-BR-A4PE 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QL        TCGA-BR-A4QM        TCGA-CD-5798 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-CD-5803        TCGA-CD-5804        TCGA-CD-5813        TCGA-CD-8524 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-CD-8525        TCGA-CD-8526        TCGA-CD-8527        TCGA-CD-8528 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-CD-8529        TCGA-CD-8530        TCGA-CD-8531        TCGA-CD-8532 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-CD-8534        TCGA-CD-8535        TCGA-CD-8536        TCGA-CD-A486 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-CD-A487        TCGA-CD-A489        TCGA-CD-A48A        TCGA-CD-A48C 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-CD-A4MG        TCGA-CD-A4MH        TCGA-CD-A4MI        TCGA-CD-A4MJ 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-D7-8570        TCGA-D7-8572 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-D7-8573        TCGA-D7-8574        TCGA-D7-8575        TCGA-D7-8576 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-D7-8578        TCGA-D7-8579        TCGA-D7-A4YT        TCGA-D7-A4YU 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-D7-A4YV        TCGA-D7-A4YX        TCGA-D7-A4YY        TCGA-D7-A4Z0 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-EQ-A4SO        TCGA-F1-6177 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-F1-6875        TCGA-F1-A448        TCGA-FP-7735        TCGA-FP-7829 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-FP-8210        TCGA-FP-8211        TCGA-FP-8631        TCGA-FP-A4BE 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-FP-A4BF        TCGA-HJ-7597        TCGA-HU-8243        TCGA-HU-8245 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-HU-8249        TCGA-HU-8602        TCGA-HU-8604        TCGA-HU-8608 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-HU-8610        TCGA-HU-A4G2        TCGA-HU-A4G3        TCGA-HU-A4G6 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-HU-A4G8        TCGA-HU-A4G9        TCGA-HU-A4GC        TCGA-HU-A4GD 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-HU-A4GF        TCGA-HU-A4GH        TCGA-HU-A4GN        TCGA-HU-A4GP 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-HU-A4GQ        TCGA-HU-A4GT        TCGA-HU-A4GU        TCGA-HU-A4GX 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-HU-A4GY        TCGA-HU-A4H0        TCGA-HU-A4H2        TCGA-HU-A4H3 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-HU-A4H4        TCGA-HU-A4H5        TCGA-HU-A4H6        TCGA-HU-A4H8 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-HU-A4HD        TCGA-IN-7806        TCGA-IN-7808        TCGA-IN-8462 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 
       TCGA-IN-8663        TCGA-IP-7968 
"BCL2L14 WILD-TYPE" "BCL2L14 WILD-TYPE" 

Clustering(632) Variable = CDX2 MUTATION ANALYSIS
D632V1, survival
                sevent
clus2              0   1
  CDX2 MUTATED     2   0
  CDX2 WILD-TYPE 179  80
  CDX2 MUTATED CDX2 WILD-TYPE 
             2            259 
  CDX2 MUTATED CDX2 WILD-TYPE 
             0             80 
$`CDX2 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 
       26.70        34.68 

$`CDX2 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  CDX2 MUTATED CDX2 WILD-TYPE 
          26.7            0.0 
  CDX2 MUTATED CDX2 WILD-TYPE 
         34.68         105.07 
  CDX2 MUTATED CDX2 WILD-TYPE 
         30.69          12.59 
[1] "26.7 - 34.7 (30.7)" "0.0 - 105.1 (12.6)"
[1] "Remove cluster labels:" "CDX2 MUTATED"          
D632V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDX2 MUTATED         0        0        0        0         1         1
  CDX2 WILD-TYPE       1        9       27       26        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDX2 MUTATED           0          0          0          0        1
  CDX2 WILD-TYPE         3         49         36         24       23
D632V3, multiclass
            clus
vv           CDX2 MUTATED CDX2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              0             26
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CDX2 MUTATED     0   0   1   2
  CDX2 WILD-TYPE  11  72 121  73
D632V4, multiclass
    clus
vv   CDX2 MUTATED CDX2 WILD-TYPE
  T1            0             11
  T2            0             72
  T3            1            121
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  CDX2 MUTATED    2  0  1  0
  CDX2 WILD-TYPE 91 81 49 53
D632V5, multiclass
    clus
vv   CDX2 MUTATED CDX2 WILD-TYPE
  N0            2             91
  N1            0             81
  N2            1             49
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D632V6, binary
                cls
clus               0   1
  CDX2 MUTATED     3   0
  CDX2 WILD-TYPE 254  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDX2 MUTATED      3    0
  CDX2 WILD-TYPE  254   18
   clus
vv  CDX2 MUTATED CDX2 WILD-TYPE
  0            3            254
  1            0             18
[1] 2 2
[1] FALSE
D632V7, binary
                cls
clus               0   1
  CDX2 MUTATED     3   0
  CDX2 WILD-TYPE 107 179
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDX2 MUTATED      3    0
  CDX2 WILD-TYPE  107  179
        clus
vv       CDX2 MUTATED CDX2 WILD-TYPE
  FEMALE            3            107
  MALE              0            179
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CDX2 MUTATED                                       1
  CDX2 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CDX2 MUTATED                                                        2
  CDX2 WILD-TYPE                                                    133
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CDX2 MUTATED                                                                   0
  CDX2 WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CDX2 MUTATED                                                  0
  CDX2 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CDX2 MUTATED                                                          0
  CDX2 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CDX2 MUTATED                                                           0
  CDX2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CDX2 MUTATED                                          0
  CDX2 WILD-TYPE                                        3
D632V8, multiclass
                                                                   clus
vv                                                                  CDX2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  CDX2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D632V9, binary
                cls
clus               0   1
  CDX2 MUTATED     0   3
  CDX2 WILD-TYPE   5 281
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDX2 MUTATED      0    3
  CDX2 WILD-TYPE    5  281
     clus
vv    CDX2 MUTATED CDX2 WILD-TYPE
  NO             0              5
  YES            3            281
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CDX2 MUTATED     2   0   0   1
  CDX2 WILD-TYPE 225  10  10  23
D632V10, multiclass
    clus
vv   CDX2 MUTATED CDX2 WILD-TYPE
  R0            2            225
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D632V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDX2 MUTATED       0                         0     3
  CDX2 WILD-TYPE    76                         4   165
D632V12, multiclass
                           clus
vv                          CDX2 MUTATED CDX2 WILD-TYPE
  ASIAN                                0             76
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                3            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(633) Variable = SLC7A10 MUTATION ANALYSIS
D633V1, survival
                   sevent
clus2                 0   1
  SLC7A10 MUTATED     4   0
  SLC7A10 WILD-TYPE 177  80
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                4               257 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                0                80 
$`SLC7A10 MUTATED`
TCGA-BR-7851 TCGA-CD-8536 TCGA-CG-5721 TCGA-FP-A4BE 
       12.43         0.10         6.02        11.08 

$`SLC7A10 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.13         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
        5.03        13.58         0.56         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
              0.1               0.0 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
            12.43            105.07 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
             8.55             12.76 
[1] "0.1 - 12.4 (8.6)"   "0.0 - 105.1 (12.8)"
[1] "hr="     "3300000"
D633V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC7A10 MUTATED         0        0        0        2         1         1
  SLC7A10 WILD-TYPE       1        9       27       24        30        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC7A10 MUTATED           0          0          0          0        1
  SLC7A10 WILD-TYPE         3         49         36         24       23
D633V3, multiclass
            clus
vv           SLC7A10 MUTATED SLC7A10 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 0                27
  STAGE II                 2                24
  STAGE IIA                1                30
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               0                36
  STAGE IIIC               0                24
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC7A10 MUTATED     0   1   2   2
  SLC7A10 WILD-TYPE  11  71 120  73
D633V4, multiclass
    clus
vv   SLC7A10 MUTATED SLC7A10 WILD-TYPE
  T1               0                11
  T2               1                71
  T3               2               120
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  SLC7A10 MUTATED    3  2  0  0
  SLC7A10 WILD-TYPE 90 79 50 53
D633V5, multiclass
    clus
vv   SLC7A10 MUTATED SLC7A10 WILD-TYPE
  N0               3                90
  N1               2                79
  N2               0                50
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D633V6, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     5   0
  SLC7A10 WILD-TYPE 252  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      5    0
  SLC7A10 WILD-TYPE  252   18
   clus
vv  SLC7A10 MUTATED SLC7A10 WILD-TYPE
  0               5               252
  1               0                18
[1] 2 2
[1] FALSE
D633V7, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     0   5
  SLC7A10 WILD-TYPE 110 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      0    5
  SLC7A10 WILD-TYPE  110  174
        clus
vv       SLC7A10 MUTATED SLC7A10 WILD-TYPE
  FEMALE               0               110
  MALE                 5               174
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SLC7A10 MUTATED                                       0
  SLC7A10 WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC7A10 MUTATED                                                        2
  SLC7A10 WILD-TYPE                                                    133
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC7A10 MUTATED                                                                   2
  SLC7A10 WILD-TYPE                                                                38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SLC7A10 MUTATED                                                  0
  SLC7A10 WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SLC7A10 MUTATED                                                          1
  SLC7A10 WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SLC7A10 MUTATED                                                           0
  SLC7A10 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SLC7A10 MUTATED                                          0
  SLC7A10 WILD-TYPE                                        3
D633V8, multiclass
                                                                   clus
vv                                                                  SLC7A10 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  SLC7A10 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D633V9, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     1   4
  SLC7A10 WILD-TYPE   4 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      1    4
  SLC7A10 WILD-TYPE    4  280
     clus
vv    SLC7A10 MUTATED SLC7A10 WILD-TYPE
  NO                1                 4
  YES               4               280
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC7A10 MUTATED     5   0   0   0
  SLC7A10 WILD-TYPE 222  10  10  24
D633V10, multiclass
    clus
vv   SLC7A10 MUTATED SLC7A10 WILD-TYPE
  R0               5               222
  R1               0                10
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D633V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC7A10 MUTATED       1                         1     1
  SLC7A10 WILD-TYPE    75                         3   167
D633V12, multiclass
                           clus
vv                          SLC7A10 MUTATED SLC7A10 WILD-TYPE
  ASIAN                                   1                75
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   1               167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(634) Variable = RGS2 MUTATION ANALYSIS
D634V1, survival
                sevent
clus2              0   1
  RGS2 MUTATED     1   0
  RGS2 WILD-TYPE 180  80
  RGS2 MUTATED RGS2 WILD-TYPE 
             1            260 
  RGS2 MUTATED RGS2 WILD-TYPE 
             0             80 
$`RGS2 MUTATED`
TCGA-D7-6520 
       18.84 

$`RGS2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  RGS2 MUTATED RGS2 WILD-TYPE 
         18.84           0.00 
  RGS2 MUTATED RGS2 WILD-TYPE 
         18.84         105.07 
  RGS2 MUTATED RGS2 WILD-TYPE 
        18.840         12.605 
[1] "18.8 - 18.8 (18.8)" "0.0 - 105.1 (12.6)"
[1] "Remove cluster labels:" "RGS2 MUTATED"          
D634V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RGS2 MUTATED         0        0        0        0         0         0
  RGS2 WILD-TYPE       1        9       27       26        31        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RGS2 MUTATED           0          1          0          0        0
  RGS2 WILD-TYPE         3         48         36         24       24
D634V3, multiclass
[1] "Remove cluster labels:" "RGS2 MUTATED"          
clus
  RGS2 MUTATED RGS2 WILD-TYPE 
             1            273 
    TCGA-B7-5816     TCGA-B7-5818     TCGA-BR-4183     TCGA-BR-4184 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-4253     TCGA-BR-4255     TCGA-BR-4267     TCGA-BR-4279 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-4280     TCGA-BR-4361     TCGA-BR-4368     TCGA-BR-6452 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-6453     TCGA-BR-6454     TCGA-BR-6455     TCGA-BR-6456 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-6457     TCGA-BR-6458     TCGA-BR-6563     TCGA-BR-6564 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-6565     TCGA-BR-6566     TCGA-BR-6705     TCGA-BR-6706 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-6707     TCGA-BR-6710     TCGA-BR-6801     TCGA-BR-6802 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-6803     TCGA-BR-6852     TCGA-BR-7196     TCGA-BR-7197 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-7703     TCGA-BR-7707     TCGA-BR-7715     TCGA-BR-7716 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-7717     TCGA-BR-7722     TCGA-BR-7723     TCGA-BR-7851 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-7901     TCGA-BR-7957     TCGA-BR-7958     TCGA-BR-7959 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8058     TCGA-BR-8059     TCGA-BR-8077     TCGA-BR-8078 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8080     TCGA-BR-8081     TCGA-BR-8284     TCGA-BR-8286 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8289     TCGA-BR-8291     TCGA-BR-8295     TCGA-BR-8296 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8297     TCGA-BR-8360     TCGA-BR-8361     TCGA-BR-8363 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8364     TCGA-BR-8365     TCGA-BR-8366     TCGA-BR-8367 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8368     TCGA-BR-8369     TCGA-BR-8370     TCGA-BR-8371 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8372     TCGA-BR-8373     TCGA-BR-8380     TCGA-BR-8381 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8382     TCGA-BR-8384     TCGA-BR-8483     TCGA-BR-8484 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8485     TCGA-BR-8486     TCGA-BR-8487     TCGA-BR-8588 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8589     TCGA-BR-8590     TCGA-BR-8591     TCGA-BR-8592 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8676     TCGA-BR-8677     TCGA-BR-8678     TCGA-BR-8679 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8680     TCGA-BR-8682     TCGA-BR-8683     TCGA-BR-8686 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8687     TCGA-BR-8690     TCGA-BR-A44T     TCGA-BR-A44U 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A452     TCGA-BR-A453     TCGA-BR-A4CQ     TCGA-BR-A4CR 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A4CS     TCGA-BR-A4IU     TCGA-BR-A4IV     TCGA-BR-A4IY 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A4IZ     TCGA-BR-A4J1     TCGA-BR-A4J2     TCGA-BR-A4J4 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A4J6     TCGA-BR-A4J7     TCGA-BR-A4J8     TCGA-BR-A4PD 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A4PE     TCGA-BR-A4PF     TCGA-BR-A4QI     TCGA-BR-A4QL 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A4QM     TCGA-CD-5798     TCGA-CD-5799     TCGA-CD-5800 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-5801     TCGA-CD-5802     TCGA-CD-5803     TCGA-CD-5804 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-5813     TCGA-CD-8524     TCGA-CD-8525     TCGA-CD-8526 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-8527     TCGA-CD-8528     TCGA-CD-8529     TCGA-CD-8530 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-8531     TCGA-CD-8532     TCGA-CD-8534     TCGA-CD-8535 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-8536     TCGA-CD-A486     TCGA-CD-A487     TCGA-CD-A489 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-A48A     TCGA-CD-A48C     TCGA-CD-A4MG     TCGA-CD-A4MH 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-A4MI     TCGA-CD-A4MJ     TCGA-CG-4300     TCGA-CG-4301 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4304     TCGA-CG-4305     TCGA-CG-4306     TCGA-CG-4436 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4437     TCGA-CG-4438     TCGA-CG-4440     TCGA-CG-4441 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4442     TCGA-CG-4443     TCGA-CG-4444     TCGA-CG-4449 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4455     TCGA-CG-4462     TCGA-CG-4465     TCGA-CG-4466 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4469     TCGA-CG-4474     TCGA-CG-4475     TCGA-CG-4476 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4477     TCGA-CG-5717     TCGA-CG-5718     TCGA-CG-5719 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-5720     TCGA-CG-5721     TCGA-CG-5722     TCGA-CG-5723 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-5724     TCGA-CG-5726     TCGA-CG-5727     TCGA-CG-5728 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-5730     TCGA-CG-5732     TCGA-CG-5733     TCGA-CG-5734 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-5577     TCGA-D7-5578     TCGA-D7-5579     TCGA-D7-6518 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-6519     TCGA-D7-6521     TCGA-D7-6522     TCGA-D7-6524 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-6525     TCGA-D7-6526     TCGA-D7-6527     TCGA-D7-6528 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-6815     TCGA-D7-6817     TCGA-D7-6818     TCGA-D7-6820 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-6822     TCGA-D7-8570     TCGA-D7-8572     TCGA-D7-8573 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-8574     TCGA-D7-8575     TCGA-D7-8576     TCGA-D7-8578 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-8579     TCGA-D7-A4YT     TCGA-D7-A4YU     TCGA-D7-A4YV 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-A4YX     TCGA-D7-A4YY     TCGA-D7-A4Z0     TCGA-EQ-5647 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-EQ-8122     TCGA-EQ-A4SO     TCGA-F1-6177     TCGA-F1-6874 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-F1-6875     TCGA-F1-A448     TCGA-FP-7735     TCGA-FP-7829 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-FP-7916     TCGA-FP-7998     TCGA-FP-8099     TCGA-FP-8209 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-FP-8210     TCGA-FP-8211     TCGA-FP-8631     TCGA-FP-A4BE 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-FP-A4BF     TCGA-HF-7132     TCGA-HF-7133     TCGA-HF-7136 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HJ-7597     TCGA-HU-8243     TCGA-HU-8245     TCGA-HU-8249 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-8602     TCGA-HU-8604     TCGA-HU-8608     TCGA-HU-8610 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4G2     TCGA-HU-A4G3     TCGA-HU-A4G6     TCGA-HU-A4G8 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4G9     TCGA-HU-A4GC     TCGA-HU-A4GD     TCGA-HU-A4GF 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4GH     TCGA-HU-A4GN     TCGA-HU-A4GP     TCGA-HU-A4GQ 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4GT     TCGA-HU-A4GU     TCGA-HU-A4GX     TCGA-HU-A4GY 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4H0     TCGA-HU-A4H2     TCGA-HU-A4H3     TCGA-HU-A4H4 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4H5     TCGA-HU-A4H6     TCGA-HU-A4H8     TCGA-HU-A4HD 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-IN-7806     TCGA-IN-7808     TCGA-IN-8462     TCGA-IN-8663 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-IP-7968 
"RGS2 WILD-TYPE" 
                vv
clus              T1  T2  T3  T4
  RGS2 MUTATED     1   1   0   0
  RGS2 WILD-TYPE  10  71 122  75
D634V4, multiclass
[1] "Remove cluster labels:" "RGS2 MUTATED"          
clus
  RGS2 MUTATED RGS2 WILD-TYPE 
             2            278 
    TCGA-B7-5816     TCGA-B7-5818     TCGA-BR-4183     TCGA-BR-4184 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-4201     TCGA-BR-4253     TCGA-BR-4255     TCGA-BR-4267 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-4279     TCGA-BR-4280     TCGA-BR-4294     TCGA-BR-4357 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-4361     TCGA-BR-4363     TCGA-BR-4368     TCGA-BR-4371 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-6452     TCGA-BR-6453     TCGA-BR-6454     TCGA-BR-6455 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-6456     TCGA-BR-6457     TCGA-BR-6458     TCGA-BR-6563 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-6564     TCGA-BR-6565     TCGA-BR-6566     TCGA-BR-6705 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-6706     TCGA-BR-6707     TCGA-BR-6710     TCGA-BR-6801 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-6802     TCGA-BR-6803     TCGA-BR-6852     TCGA-BR-7196 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-7197     TCGA-BR-7703     TCGA-BR-7707     TCGA-BR-7715 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-7716     TCGA-BR-7717     TCGA-BR-7722     TCGA-BR-7723 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-7851     TCGA-BR-7901     TCGA-BR-7957     TCGA-BR-7958 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-7959     TCGA-BR-8058     TCGA-BR-8059     TCGA-BR-8077 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8078     TCGA-BR-8080     TCGA-BR-8081     TCGA-BR-8284 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8286     TCGA-BR-8289     TCGA-BR-8291     TCGA-BR-8295 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8296     TCGA-BR-8297     TCGA-BR-8360     TCGA-BR-8361 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8363     TCGA-BR-8364     TCGA-BR-8365     TCGA-BR-8366 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8367     TCGA-BR-8368     TCGA-BR-8369     TCGA-BR-8370 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8371     TCGA-BR-8372     TCGA-BR-8373     TCGA-BR-8380 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8381     TCGA-BR-8382     TCGA-BR-8384     TCGA-BR-8483 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8484     TCGA-BR-8485     TCGA-BR-8486     TCGA-BR-8487 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8588     TCGA-BR-8589     TCGA-BR-8590     TCGA-BR-8591 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8592     TCGA-BR-8676     TCGA-BR-8677     TCGA-BR-8678 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8679     TCGA-BR-8680     TCGA-BR-8682     TCGA-BR-8683 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8686     TCGA-BR-8687     TCGA-BR-8690     TCGA-BR-A44T 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A44U     TCGA-BR-A452     TCGA-BR-A453     TCGA-BR-A4CQ 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A4CR     TCGA-BR-A4CS     TCGA-BR-A4IU     TCGA-BR-A4IV 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A4IY     TCGA-BR-A4IZ     TCGA-BR-A4J1     TCGA-BR-A4J2 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A4J4     TCGA-BR-A4J6     TCGA-BR-A4J7     TCGA-BR-A4J8 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A4PD     TCGA-BR-A4PE     TCGA-BR-A4PF     TCGA-BR-A4QI 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A4QL     TCGA-BR-A4QM     TCGA-CD-5798     TCGA-CD-5799 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-5800     TCGA-CD-5801     TCGA-CD-5802     TCGA-CD-5803 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-5804     TCGA-CD-5813     TCGA-CD-8524     TCGA-CD-8525 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-8526     TCGA-CD-8527     TCGA-CD-8528     TCGA-CD-8529 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-8530     TCGA-CD-8531     TCGA-CD-8532     TCGA-CD-8534 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-8535     TCGA-CD-8536     TCGA-CD-A486     TCGA-CD-A487 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-A489     TCGA-CD-A48A     TCGA-CD-A48C     TCGA-CD-A4MG 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-A4MH     TCGA-CD-A4MI     TCGA-CD-A4MJ     TCGA-CG-4300 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4301     TCGA-CG-4304     TCGA-CG-4305     TCGA-CG-4306 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4436     TCGA-CG-4437     TCGA-CG-4438     TCGA-CG-4440 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4441     TCGA-CG-4442     TCGA-CG-4443     TCGA-CG-4444 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4449     TCGA-CG-4455     TCGA-CG-4462     TCGA-CG-4465 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4466     TCGA-CG-4469     TCGA-CG-4474     TCGA-CG-4475 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4476     TCGA-CG-4477     TCGA-CG-5717     TCGA-CG-5718 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-5719     TCGA-CG-5720     TCGA-CG-5721     TCGA-CG-5722 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-5723     TCGA-CG-5724     TCGA-CG-5726     TCGA-CG-5727 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-5728     TCGA-CG-5730     TCGA-CG-5732     TCGA-CG-5733 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-5734     TCGA-D7-5577     TCGA-D7-5578     TCGA-D7-5579 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-6518     TCGA-D7-6519     TCGA-D7-6521     TCGA-D7-6522 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-6524     TCGA-D7-6525     TCGA-D7-6526     TCGA-D7-6527 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-6528     TCGA-D7-6815     TCGA-D7-6817     TCGA-D7-6818 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-6820     TCGA-D7-6822     TCGA-D7-8570     TCGA-D7-8572 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-8573     TCGA-D7-8574     TCGA-D7-8575     TCGA-D7-8576 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-8578     TCGA-D7-8579     TCGA-D7-A4YT     TCGA-D7-A4YU 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-A4YV     TCGA-D7-A4YX     TCGA-D7-A4YY     TCGA-D7-A4Z0 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-EQ-5647     TCGA-EQ-8122     TCGA-EQ-A4SO     TCGA-F1-6177 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-F1-6874     TCGA-F1-6875     TCGA-F1-A448     TCGA-FP-7735 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-FP-7829     TCGA-FP-7916     TCGA-FP-7998     TCGA-FP-8099 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-FP-8209     TCGA-FP-8210     TCGA-FP-8211     TCGA-FP-8631 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-FP-A4BE     TCGA-FP-A4BF     TCGA-HF-7132     TCGA-HF-7133 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HF-7136     TCGA-HJ-7597     TCGA-HU-8243     TCGA-HU-8245 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-8249     TCGA-HU-8602     TCGA-HU-8604     TCGA-HU-8608 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-8610     TCGA-HU-A4G2     TCGA-HU-A4G3     TCGA-HU-A4G6 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4G8     TCGA-HU-A4G9     TCGA-HU-A4GC     TCGA-HU-A4GD 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4GF     TCGA-HU-A4GH     TCGA-HU-A4GN     TCGA-HU-A4GP 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4GQ     TCGA-HU-A4GT     TCGA-HU-A4GU     TCGA-HU-A4GX 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4GY     TCGA-HU-A4H0     TCGA-HU-A4H2     TCGA-HU-A4H3 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4H4     TCGA-HU-A4H5     TCGA-HU-A4H6     TCGA-HU-A4H8 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4HD     TCGA-IN-7806     TCGA-IN-7808     TCGA-IN-8462 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-IN-8663     TCGA-IP-7968 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
                vv
clus             N0 N1 N2 N3
  RGS2 MUTATED    0  1  1  0
  RGS2 WILD-TYPE 93 80 49 53
D634V5, multiclass
[1] "Remove cluster labels:" "RGS2 MUTATED"          
clus
  RGS2 MUTATED RGS2 WILD-TYPE 
             2            275 
    TCGA-B7-5816     TCGA-B7-5818     TCGA-BR-4183     TCGA-BR-4184 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-4188     TCGA-BR-4191     TCGA-BR-4253     TCGA-BR-4255 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-4256     TCGA-BR-4267     TCGA-BR-4279     TCGA-BR-4280 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-4361     TCGA-BR-4368     TCGA-BR-6452     TCGA-BR-6453 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-6454     TCGA-BR-6455     TCGA-BR-6456     TCGA-BR-6457 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-6458     TCGA-BR-6563     TCGA-BR-6564     TCGA-BR-6565 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-6566     TCGA-BR-6705     TCGA-BR-6706     TCGA-BR-6707 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-6710     TCGA-BR-6801     TCGA-BR-6802     TCGA-BR-6803 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-6852     TCGA-BR-7196     TCGA-BR-7197     TCGA-BR-7703 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-7707     TCGA-BR-7715     TCGA-BR-7716     TCGA-BR-7717 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-7722     TCGA-BR-7723     TCGA-BR-7851     TCGA-BR-7901 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-7957     TCGA-BR-7958     TCGA-BR-7959     TCGA-BR-8058 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8059     TCGA-BR-8077     TCGA-BR-8078     TCGA-BR-8080 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8081     TCGA-BR-8284     TCGA-BR-8286     TCGA-BR-8289 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8291     TCGA-BR-8295     TCGA-BR-8296     TCGA-BR-8297 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8360     TCGA-BR-8361     TCGA-BR-8363     TCGA-BR-8364 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8365     TCGA-BR-8366     TCGA-BR-8367     TCGA-BR-8368 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8369     TCGA-BR-8370     TCGA-BR-8371     TCGA-BR-8372 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8373     TCGA-BR-8380     TCGA-BR-8381     TCGA-BR-8382 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8384     TCGA-BR-8483     TCGA-BR-8484     TCGA-BR-8485 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8486     TCGA-BR-8487     TCGA-BR-8588     TCGA-BR-8589 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8590     TCGA-BR-8591     TCGA-BR-8592     TCGA-BR-8676 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8677     TCGA-BR-8678     TCGA-BR-8679     TCGA-BR-8680 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8682     TCGA-BR-8683     TCGA-BR-8686     TCGA-BR-8687 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8690     TCGA-BR-A44T     TCGA-BR-A44U     TCGA-BR-A452 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A453     TCGA-BR-A4CQ     TCGA-BR-A4CR     TCGA-BR-A4CS 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A4IU     TCGA-BR-A4IV     TCGA-BR-A4IY     TCGA-BR-A4IZ 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A4J1     TCGA-BR-A4J2     TCGA-BR-A4J4     TCGA-BR-A4J6 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A4J8     TCGA-BR-A4PD     TCGA-BR-A4PE     TCGA-BR-A4PF 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A4QI     TCGA-BR-A4QL     TCGA-BR-A4QM     TCGA-CD-5798 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-5799     TCGA-CD-5800     TCGA-CD-5801     TCGA-CD-5802 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-5803     TCGA-CD-5804     TCGA-CD-5813     TCGA-CD-8524 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-8525     TCGA-CD-8526     TCGA-CD-8527     TCGA-CD-8528 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-8529     TCGA-CD-8530     TCGA-CD-8531     TCGA-CD-8532 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-8534     TCGA-CD-8535     TCGA-CD-8536     TCGA-CD-A486 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-A487     TCGA-CD-A489     TCGA-CD-A48A     TCGA-CD-A48C 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-A4MG     TCGA-CD-A4MH     TCGA-CD-A4MI     TCGA-CD-A4MJ 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4300     TCGA-CG-4301     TCGA-CG-4304     TCGA-CG-4305 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4306     TCGA-CG-4436     TCGA-CG-4437     TCGA-CG-4438 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4440     TCGA-CG-4441     TCGA-CG-4442     TCGA-CG-4443 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4444     TCGA-CG-4449     TCGA-CG-4455     TCGA-CG-4462 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4465     TCGA-CG-4466     TCGA-CG-4469     TCGA-CG-4474 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4475     TCGA-CG-4476     TCGA-CG-4477     TCGA-CG-5717 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-5718     TCGA-CG-5719     TCGA-CG-5720     TCGA-CG-5721 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-5722     TCGA-CG-5723     TCGA-CG-5724     TCGA-CG-5726 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-5727     TCGA-CG-5728     TCGA-CG-5730     TCGA-CG-5732 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-5733     TCGA-CG-5734     TCGA-D7-5577     TCGA-D7-5578 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-5579     TCGA-D7-6518     TCGA-D7-6519     TCGA-D7-6521 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-6522     TCGA-D7-6524     TCGA-D7-6525     TCGA-D7-6526 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-6527     TCGA-D7-6528     TCGA-D7-6815     TCGA-D7-6817 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-6818     TCGA-D7-6820     TCGA-D7-6822     TCGA-D7-8570 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-8572     TCGA-D7-8573     TCGA-D7-8574     TCGA-D7-8575 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-8576     TCGA-D7-8578     TCGA-D7-8579     TCGA-D7-A4YT 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-A4YU     TCGA-D7-A4YV     TCGA-D7-A4YX     TCGA-D7-A4YY 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-A4Z0     TCGA-EQ-5647     TCGA-EQ-8122     TCGA-EQ-A4SO 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-F1-6177     TCGA-F1-6874     TCGA-F1-6875     TCGA-F1-A448 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-FP-7735     TCGA-FP-7829     TCGA-FP-7916     TCGA-FP-7998 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-FP-8099     TCGA-FP-8209     TCGA-FP-8210     TCGA-FP-8211 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-FP-8631     TCGA-FP-A4BE     TCGA-FP-A4BF     TCGA-HF-7132 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HF-7133     TCGA-HF-7136     TCGA-HJ-7597     TCGA-HU-8243 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-8245     TCGA-HU-8249     TCGA-HU-8602     TCGA-HU-8604 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-8608     TCGA-HU-8610     TCGA-HU-A4G2     TCGA-HU-A4G3 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4G6     TCGA-HU-A4G8     TCGA-HU-A4G9     TCGA-HU-A4GC 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4GD     TCGA-HU-A4GF     TCGA-HU-A4GH     TCGA-HU-A4GN 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4GP     TCGA-HU-A4GQ     TCGA-HU-A4GT     TCGA-HU-A4GU 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4GX     TCGA-HU-A4GY     TCGA-HU-A4H0     TCGA-HU-A4H2 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4H3     TCGA-HU-A4H4     TCGA-HU-A4H5     TCGA-HU-A4H6 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4H8     TCGA-HU-A4HD     TCGA-IN-7806     TCGA-IN-7808 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-IN-8462     TCGA-IN-8663     TCGA-IP-7968 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
D634V6, binary
                cls
clus               0   1
  RGS2 MUTATED     3   0
  RGS2 WILD-TYPE 254  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGS2 MUTATED      3    0
  RGS2 WILD-TYPE  254   18
   clus
vv  RGS2 MUTATED RGS2 WILD-TYPE
  0            3            254
  1            0             18
[1] 2 2
[1] FALSE
D634V7, binary
                cls
clus               0   1
  RGS2 MUTATED     2   1
  RGS2 WILD-TYPE 108 178
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGS2 MUTATED      2    1
  RGS2 WILD-TYPE  108  178
        clus
vv       RGS2 MUTATED RGS2 WILD-TYPE
  FEMALE            2            108
  MALE              1            178
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RGS2 MUTATED                                       0
  RGS2 WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RGS2 MUTATED                                                        2
  RGS2 WILD-TYPE                                                    133
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RGS2 MUTATED                                                                   0
  RGS2 WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RGS2 MUTATED                                                  1
  RGS2 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RGS2 MUTATED                                                          0
  RGS2 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RGS2 MUTATED                                                           0
  RGS2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RGS2 MUTATED                                          0
  RGS2 WILD-TYPE                                        3
D634V8, multiclass
                                                                   clus
vv                                                                  RGS2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  RGS2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D634V9, binary
                cls
clus               0   1
  RGS2 MUTATED     0   3
  RGS2 WILD-TYPE   5 281
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGS2 MUTATED      0    3
  RGS2 WILD-TYPE    5  281
     clus
vv    RGS2 MUTATED RGS2 WILD-TYPE
  NO             0              5
  YES            3            281
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RGS2 MUTATED     1   0   0   2
  RGS2 WILD-TYPE 226  10  10  22
D634V10, multiclass
    clus
vv   RGS2 MUTATED RGS2 WILD-TYPE
  R0            1            226
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D634V11, continuous
[1] "Remove cluster labels:" "RGS2 MUTATED"          
clus
  RGS2 MUTATED RGS2 WILD-TYPE 
             2            249 
    TCGA-B7-5816     TCGA-BR-4183     TCGA-BR-4184     TCGA-BR-4188 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-4191     TCGA-BR-4253     TCGA-BR-4255     TCGA-BR-4256 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-4267     TCGA-BR-4279     TCGA-BR-4280     TCGA-BR-4361 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-4368     TCGA-BR-6452     TCGA-BR-6453     TCGA-BR-6454 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-6455     TCGA-BR-6456     TCGA-BR-6457     TCGA-BR-6458 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-6563     TCGA-BR-6564     TCGA-BR-6565     TCGA-BR-6566 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-6705     TCGA-BR-6706     TCGA-BR-6707     TCGA-BR-6710 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-6801     TCGA-BR-6802     TCGA-BR-6803     TCGA-BR-6852 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-7196     TCGA-BR-7197     TCGA-BR-7703     TCGA-BR-7707 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-7715     TCGA-BR-7716     TCGA-BR-7717     TCGA-BR-7722 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-7723     TCGA-BR-7851     TCGA-BR-7901     TCGA-BR-7957 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-7958     TCGA-BR-7959     TCGA-BR-8058     TCGA-BR-8059 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8077     TCGA-BR-8078     TCGA-BR-8080     TCGA-BR-8081 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8284     TCGA-BR-8286     TCGA-BR-8289     TCGA-BR-8291 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8295     TCGA-BR-8296     TCGA-BR-8297     TCGA-BR-8360 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8361     TCGA-BR-8363     TCGA-BR-8364     TCGA-BR-8365 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8366     TCGA-BR-8367     TCGA-BR-8368     TCGA-BR-8369 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8370     TCGA-BR-8371     TCGA-BR-8372     TCGA-BR-8373 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8380     TCGA-BR-8381     TCGA-BR-8382     TCGA-BR-8384 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8483     TCGA-BR-8484     TCGA-BR-8485     TCGA-BR-8486 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8487     TCGA-BR-8588     TCGA-BR-8589     TCGA-BR-8590 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8591     TCGA-BR-8592     TCGA-BR-8676     TCGA-BR-8677 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8678     TCGA-BR-8679     TCGA-BR-8680     TCGA-BR-8682 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-8683     TCGA-BR-8686     TCGA-BR-8687     TCGA-BR-8690 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A44T     TCGA-BR-A44U     TCGA-BR-A452     TCGA-BR-A453 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A4CQ     TCGA-BR-A4CR     TCGA-BR-A4CS     TCGA-BR-A4IU 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A4IV     TCGA-BR-A4IY     TCGA-BR-A4IZ     TCGA-BR-A4J1 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A4J2     TCGA-BR-A4J4     TCGA-BR-A4J6     TCGA-BR-A4J8 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A4PD     TCGA-BR-A4PE     TCGA-BR-A4PF     TCGA-BR-A4QI 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-BR-A4QL     TCGA-BR-A4QM     TCGA-CD-5804     TCGA-CD-8525 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CD-8526     TCGA-CD-8531     TCGA-CD-8535     TCGA-CD-A487 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4301     TCGA-CG-4304     TCGA-CG-4305     TCGA-CG-4436 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4437     TCGA-CG-4438     TCGA-CG-4440     TCGA-CG-4441 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4442     TCGA-CG-4443     TCGA-CG-4444     TCGA-CG-4449 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4455     TCGA-CG-4462     TCGA-CG-4465     TCGA-CG-4466 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4469     TCGA-CG-4474     TCGA-CG-4475     TCGA-CG-4476 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-4477     TCGA-CG-5717     TCGA-CG-5718     TCGA-CG-5719 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-5720     TCGA-CG-5721     TCGA-CG-5722     TCGA-CG-5723 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-5724     TCGA-CG-5726     TCGA-CG-5727     TCGA-CG-5728 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-CG-5730     TCGA-CG-5732     TCGA-CG-5733     TCGA-CG-5734 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-5577     TCGA-D7-5578     TCGA-D7-5579     TCGA-D7-6518 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-6519     TCGA-D7-6521     TCGA-D7-6522     TCGA-D7-6524 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-6525     TCGA-D7-6526     TCGA-D7-6527     TCGA-D7-6528 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-6815     TCGA-D7-6817     TCGA-D7-6818     TCGA-D7-6820 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-6822     TCGA-D7-8570     TCGA-D7-8572     TCGA-D7-8573 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-8574     TCGA-D7-8575     TCGA-D7-8576     TCGA-D7-8578 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-8579     TCGA-D7-A4YT     TCGA-D7-A4YU     TCGA-D7-A4YV 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-D7-A4YX     TCGA-D7-A4YY     TCGA-D7-A4Z0     TCGA-EQ-5647 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-EQ-8122     TCGA-EQ-A4SO     TCGA-F1-6177     TCGA-F1-6874 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-F1-6875     TCGA-F1-A448     TCGA-FP-7735     TCGA-FP-7829 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-FP-7916     TCGA-FP-7998     TCGA-FP-8099     TCGA-FP-8209 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-FP-8210     TCGA-FP-8211     TCGA-FP-8631     TCGA-FP-A4BE 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-FP-A4BF     TCGA-HF-7132     TCGA-HF-7133     TCGA-HF-7136 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HJ-7597     TCGA-HU-8243     TCGA-HU-8245     TCGA-HU-8249 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-8602     TCGA-HU-8604     TCGA-HU-8608     TCGA-HU-8610 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4G2     TCGA-HU-A4G3     TCGA-HU-A4G6     TCGA-HU-A4G8 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4G9     TCGA-HU-A4GC     TCGA-HU-A4GD     TCGA-HU-A4GF 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4GH     TCGA-HU-A4GN     TCGA-HU-A4GP     TCGA-HU-A4GQ 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4GT     TCGA-HU-A4GU     TCGA-HU-A4GX     TCGA-HU-A4GY 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4H0     TCGA-HU-A4H2     TCGA-HU-A4H3     TCGA-HU-A4H4 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-HU-A4H5     TCGA-HU-A4H6     TCGA-HU-A4H8     TCGA-HU-A4HD 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-IN-7806     TCGA-IN-7808     TCGA-IN-8462     TCGA-IN-8663 
"RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" "RGS2 WILD-TYPE" 
    TCGA-IP-7968 
"RGS2 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RGS2 MUTATED       0                         0     3
  RGS2 WILD-TYPE    76                         4   165
D634V12, multiclass
                           clus
vv                          RGS2 MUTATED RGS2 WILD-TYPE
  ASIAN                                0             76
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                3            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(635) Variable = SAMD9L MUTATION ANALYSIS
D635V1, survival
                  sevent
clus2                0   1
  SAMD9L MUTATED    12   3
  SAMD9L WILD-TYPE 169  77
  SAMD9L MUTATED SAMD9L WILD-TYPE 
              15              246 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
               3               77 
$`SAMD9L MUTATED`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8370 TCGA-BR-8484 
       26.70        11.70        34.68         0.26         3.32        25.18 
TCGA-BR-8680 TCGA-CD-A4MJ TCGA-CG-5721 TCGA-CG-5728 TCGA-HU-8602 TCGA-HU-8604 
       15.81        12.62         6.02        65.10        11.41        12.10 
TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-IN-8663 
        6.25        12.30         3.39 

$`SAMD9L WILD-TYPE`
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       19.50        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        0.99       105.07        12.03        28.96        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       12.59        14.17        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       11.77        29.98         8.98         0.10         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        23.84         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IP-7968 
        8.88        27.42        21.21         3.45        18.81         2.53 

  SAMD9L MUTATED SAMD9L WILD-TYPE 
            0.26             0.00 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
           65.10           105.07 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
          12.100           12.775 
[1] "0.3 - 65.1 (12.1)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.7"
D635V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SAMD9L MUTATED         0        0        5        0         2         4
  SAMD9L WILD-TYPE       1        9       22       26        29        40
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SAMD9L MUTATED           0          2          1          0        3
  SAMD9L WILD-TYPE         3         47         35         24       21
D635V3, multiclass
            clus
vv           SAMD9L MUTATED SAMD9L WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                5               22
  STAGE II                0               26
  STAGE IIA               2               29
  STAGE IIB               4               40
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              1               35
  STAGE IIIC              0               24
  STAGE IV                3               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SAMD9L MUTATED     0   6   4   7
  SAMD9L WILD-TYPE  11  66 118  68
D635V4, multiclass
    clus
vv   SAMD9L MUTATED SAMD9L WILD-TYPE
  T1              0               11
  T2              6               66
  T3              4              118
  T4              7               68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  SAMD9L MUTATED   10  4  3  1
  SAMD9L WILD-TYPE 83 77 47 52
D635V5, multiclass
    clus
vv   SAMD9L MUTATED SAMD9L WILD-TYPE
  N0             10               83
  N1              4               77
  N2              3               47
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D635V6, binary
                  cls
clus                 0   1
  SAMD9L MUTATED    17   1
  SAMD9L WILD-TYPE 240  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED     17    1
  SAMD9L WILD-TYPE  240   17
   clus
vv  SAMD9L MUTATED SAMD9L WILD-TYPE
  0             17              240
  1              1               17
[1] 2 2
[1] FALSE
D635V7, binary
                  cls
clus                 0   1
  SAMD9L MUTATED     9   9
  SAMD9L WILD-TYPE 101 170
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED      9    9
  SAMD9L WILD-TYPE  101  170
        clus
vv       SAMD9L MUTATED SAMD9L WILD-TYPE
  FEMALE              9              101
  MALE                9              170
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SAMD9L MUTATED                                       5
  SAMD9L WILD-TYPE                                    45
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SAMD9L MUTATED                                                        8
  SAMD9L WILD-TYPE                                                    127
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SAMD9L MUTATED                                                                   2
  SAMD9L WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SAMD9L MUTATED                                                  2
  SAMD9L WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SAMD9L MUTATED                                                          0
  SAMD9L WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SAMD9L MUTATED                                                           1
  SAMD9L WILD-TYPE                                                         5
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SAMD9L MUTATED                                          0
  SAMD9L WILD-TYPE                                        3
D635V8, multiclass
                                                                   clus
vv                                                                  SAMD9L MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  SAMD9L WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D635V9, binary
                  cls
clus                 0   1
  SAMD9L MUTATED     0  18
  SAMD9L WILD-TYPE   5 266
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED      0   18
  SAMD9L WILD-TYPE    5  266
     clus
vv    SAMD9L MUTATED SAMD9L WILD-TYPE
  NO               0                5
  YES             18              266
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SAMD9L MUTATED    14   0   0   3
  SAMD9L WILD-TYPE 213  10  10  21
D635V10, multiclass
    clus
vv   SAMD9L MUTATED SAMD9L WILD-TYPE
  R0             14              213
  R1              0               10
  R2              0               10
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D635V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SAMD9L MUTATED       6                         0    10
  SAMD9L WILD-TYPE    70                         4   158
D635V12, multiclass
                           clus
vv                          SAMD9L MUTATED SAMD9L WILD-TYPE
  ASIAN                                  6               70
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                 10              158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(636) Variable = DUSP11 MUTATION ANALYSIS
D636V1, survival
                  sevent
clus2                0   1
  DUSP11 MUTATED     3   1
  DUSP11 WILD-TYPE 178  79
  DUSP11 MUTATED DUSP11 WILD-TYPE 
               4              257 
  DUSP11 MUTATED DUSP11 WILD-TYPE 
               1               79 
$`DUSP11 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-F1-6874 TCGA-HU-A4G8 
        6.97        34.68        14.47        11.84 

$`DUSP11 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 
       14.76         0.62         7.99        16.24        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  DUSP11 MUTATED DUSP11 WILD-TYPE 
            6.97             0.00 
  DUSP11 MUTATED DUSP11 WILD-TYPE 
           34.68           105.07 
  DUSP11 MUTATED DUSP11 WILD-TYPE 
          13.155           12.620 
[1] "7.0 - 34.7 (13.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.5"
D636V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DUSP11 MUTATED         0        0        1        0         1         1
  DUSP11 WILD-TYPE       1        9       26       26        30        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DUSP11 MUTATED           0          1          0          0        0
  DUSP11 WILD-TYPE         3         48         36         24       24
D636V3, multiclass
            clus
vv           DUSP11 MUTATED DUSP11 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DUSP11 MUTATED     0   1   3   0
  DUSP11 WILD-TYPE  11  71 119  75
D636V4, multiclass
    clus
vv   DUSP11 MUTATED DUSP11 WILD-TYPE
  T1              0               11
  T2              1               71
  T3              3              119
  T4              0               75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  DUSP11 MUTATED    2  2  0  0
  DUSP11 WILD-TYPE 91 79 50 53
D636V5, multiclass
    clus
vv   DUSP11 MUTATED DUSP11 WILD-TYPE
  N0              2               91
  N1              2               79
  N2              0               50
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D636V6, binary
                  cls
clus                 0   1
  DUSP11 MUTATED     3   0
  DUSP11 WILD-TYPE 254  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP11 MUTATED      3    0
  DUSP11 WILD-TYPE  254   18
   clus
vv  DUSP11 MUTATED DUSP11 WILD-TYPE
  0              3              254
  1              0               18
[1] 2 2
[1] FALSE
D636V7, binary
                  cls
clus                 0   1
  DUSP11 MUTATED     2   2
  DUSP11 WILD-TYPE 108 177
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP11 MUTATED      2    2
  DUSP11 WILD-TYPE  108  177
        clus
vv       DUSP11 MUTATED DUSP11 WILD-TYPE
  FEMALE              2              108
  MALE                2              177
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DUSP11 MUTATED                                       1
  DUSP11 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DUSP11 MUTATED                                                        2
  DUSP11 WILD-TYPE                                                    133
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DUSP11 MUTATED                                                                   1
  DUSP11 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DUSP11 MUTATED                                                  0
  DUSP11 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DUSP11 MUTATED                                                          0
  DUSP11 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DUSP11 MUTATED                                                           0
  DUSP11 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DUSP11 MUTATED                                          0
  DUSP11 WILD-TYPE                                        3
D636V8, multiclass
                                                                   clus
vv                                                                  DUSP11 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  DUSP11 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D636V9, binary
                  cls
clus                 0   1
  DUSP11 MUTATED     0   4
  DUSP11 WILD-TYPE   5 280
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP11 MUTATED      0    4
  DUSP11 WILD-TYPE    5  280
     clus
vv    DUSP11 MUTATED DUSP11 WILD-TYPE
  NO               0                5
  YES              4              280
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DUSP11 MUTATED     2   0   0   1
  DUSP11 WILD-TYPE 225  10  10  23
D636V10, multiclass
    clus
vv   DUSP11 MUTATED DUSP11 WILD-TYPE
  R0              2              225
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D636V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DUSP11 MUTATED       1                         0     3
  DUSP11 WILD-TYPE    75                         4   165
D636V12, multiclass
                           clus
vv                          DUSP11 MUTATED DUSP11 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  3              165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(637) Variable = MRPL2 MUTATION ANALYSIS
D637V1, survival
                 sevent
clus2               0   1
  MRPL2 MUTATED     4   1
  MRPL2 WILD-TYPE 177  79
  MRPL2 MUTATED MRPL2 WILD-TYPE 
              5             256 
  MRPL2 MUTATED MRPL2 WILD-TYPE 
              1              79 
$`MRPL2 MUTATED`
TCGA-BR-4280 TCGA-BR-8372 TCGA-CD-8536 TCGA-CG-5721 TCGA-FP-A4BE 
        6.61        19.17         0.10         6.02        11.08 

$`MRPL2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  MRPL2 MUTATED MRPL2 WILD-TYPE 
            0.1             0.0 
  MRPL2 MUTATED MRPL2 WILD-TYPE 
          19.17          105.07 
  MRPL2 MUTATED MRPL2 WILD-TYPE 
           6.61           12.71 
[1] "0.1 - 19.2 (6.6)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.2"
D637V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MRPL2 MUTATED         0        0        0        1         1         0
  MRPL2 WILD-TYPE       1        9       27       25        30        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRPL2 MUTATED           1          0          0          1        1
  MRPL2 WILD-TYPE         2         49         36         23       23
D637V3, multiclass
            clus
vv           MRPL2 MUTATED MRPL2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              0              44
  STAGE III              1               2
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MRPL2 MUTATED     0   1   2   2
  MRPL2 WILD-TYPE  11  71 120  73
D637V4, multiclass
    clus
vv   MRPL2 MUTATED MRPL2 WILD-TYPE
  T1             0              11
  T2             1              71
  T3             2             120
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  MRPL2 MUTATED    2  2  0  1
  MRPL2 WILD-TYPE 91 79 50 52
D637V5, multiclass
    clus
vv   MRPL2 MUTATED MRPL2 WILD-TYPE
  N0             2              91
  N1             2              79
  N2             0              50
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D637V6, binary
                 cls
clus                0   1
  MRPL2 MUTATED     6   0
  MRPL2 WILD-TYPE 251  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPL2 MUTATED      6    0
  MRPL2 WILD-TYPE  251   18
   clus
vv  MRPL2 MUTATED MRPL2 WILD-TYPE
  0             6             251
  1             0              18
[1] 2 2
[1] FALSE
D637V7, binary
                 cls
clus                0   1
  MRPL2 MUTATED     2   4
  MRPL2 WILD-TYPE 108 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPL2 MUTATED      2    4
  MRPL2 WILD-TYPE  108  175
        clus
vv       MRPL2 MUTATED MRPL2 WILD-TYPE
  FEMALE             2             108
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MRPL2 MUTATED                                       0
  MRPL2 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MRPL2 MUTATED                                                        5
  MRPL2 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MRPL2 MUTATED                                                                   1
  MRPL2 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MRPL2 MUTATED                                                  0
  MRPL2 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MRPL2 MUTATED                                                          0
  MRPL2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MRPL2 MUTATED                                                           0
  MRPL2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MRPL2 MUTATED                                          0
  MRPL2 WILD-TYPE                                        3
D637V8, multiclass
                                                                   clus
vv                                                                  MRPL2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  MRPL2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D637V9, binary
                 cls
clus                0   1
  MRPL2 MUTATED     0   6
  MRPL2 WILD-TYPE   5 278
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPL2 MUTATED      0    6
  MRPL2 WILD-TYPE    5  278
     clus
vv    MRPL2 MUTATED MRPL2 WILD-TYPE
  NO              0               5
  YES             6             278
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MRPL2 MUTATED     4   0   0   2
  MRPL2 WILD-TYPE 223  10  10  22
D637V10, multiclass
    clus
vv   MRPL2 MUTATED MRPL2 WILD-TYPE
  R0             4             223
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D637V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MRPL2 MUTATED       1                         1     3
  MRPL2 WILD-TYPE    75                         3   165
D637V12, multiclass
                           clus
vv                          MRPL2 MUTATED MRPL2 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(638) Variable = SLC4A3 MUTATION ANALYSIS
D638V1, survival
                  sevent
clus2                0   1
  SLC4A3 MUTATED     9   3
  SLC4A3 WILD-TYPE 172  77
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
              12              249 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
               3               77 
$`SLC4A3 MUTATED`
TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8382 
       32.94        23.93        12.43        12.26        19.50        15.85 
TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5733 TCGA-D7-A4YV TCGA-HU-A4GH TCGA-HU-A4H3 
        1.02         6.02        21.07         5.92        11.77        19.36 

$`SLC4A3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        30.90        31.20        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
       16.31         2.20        15.58         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
        3.32        11.80        19.17        14.79         0.26         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       14.27        16.44        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       22.75        25.81        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.25        10.19         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
            1.02             0.00 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
           32.94           105.07 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
           14.14            12.62 
[1] "1.0 - 32.9 (14.1)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D638V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC4A3 MUTATED         1        1        1        0         1         3
  SLC4A3 WILD-TYPE       0        8       26       26        30        41
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC4A3 MUTATED           0          1          0          3        3
  SLC4A3 WILD-TYPE         3         48         36         21       21
D638V3, multiclass
            clus
vv           SLC4A3 MUTATED SLC4A3 WILD-TYPE
  STAGE I                 1                0
  STAGE IA                1                8
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               3               41
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              3               21
  STAGE IV                3               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SLC4A3 MUTATED     2   2   3   7
  SLC4A3 WILD-TYPE   9  70 119  68
D638V4, multiclass
    clus
vv   SLC4A3 MUTATED SLC4A3 WILD-TYPE
  T1              2                9
  T2              2               70
  T3              3              119
  T4              7               68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  SLC4A3 MUTATED    5  3  4  2
  SLC4A3 WILD-TYPE 88 78 46 51
D638V5, multiclass
    clus
vv   SLC4A3 MUTATED SLC4A3 WILD-TYPE
  N0              5               88
  N1              3               78
  N2              4               46
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D638V6, binary
                  cls
clus                 0   1
  SLC4A3 MUTATED    13   1
  SLC4A3 WILD-TYPE 244  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED     13    1
  SLC4A3 WILD-TYPE  244   17
   clus
vv  SLC4A3 MUTATED SLC4A3 WILD-TYPE
  0             13              244
  1              1               17
[1] 2 2
[1] FALSE
D638V7, binary
                  cls
clus                 0   1
  SLC4A3 MUTATED    10   5
  SLC4A3 WILD-TYPE 100 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED     10    5
  SLC4A3 WILD-TYPE  100  174
        clus
vv       SLC4A3 MUTATED SLC4A3 WILD-TYPE
  FEMALE             10              100
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SLC4A3 MUTATED                                       1
  SLC4A3 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC4A3 MUTATED                                                        9
  SLC4A3 WILD-TYPE                                                    126
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC4A3 MUTATED                                                                   3
  SLC4A3 WILD-TYPE                                                                37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SLC4A3 MUTATED                                                  2
  SLC4A3 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SLC4A3 MUTATED                                                          0
  SLC4A3 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SLC4A3 MUTATED                                                           0
  SLC4A3 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SLC4A3 MUTATED                                          0
  SLC4A3 WILD-TYPE                                        3
D638V8, multiclass
                                                                   clus
vv                                                                  SLC4A3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  SLC4A3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D638V9, binary
                  cls
clus                 0   1
  SLC4A3 MUTATED     0  15
  SLC4A3 WILD-TYPE   5 269
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED      0   15
  SLC4A3 WILD-TYPE    5  269
     clus
vv    SLC4A3 MUTATED SLC4A3 WILD-TYPE
  NO               0                5
  YES             15              269
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SLC4A3 MUTATED    12   0   1   2
  SLC4A3 WILD-TYPE 215  10   9  22
D638V10, multiclass
    clus
vv   SLC4A3 MUTATED SLC4A3 WILD-TYPE
  R0             12              215
  R1              0               10
  R2              1                9
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D638V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC4A3 MUTATED       2                         1     9
  SLC4A3 WILD-TYPE    74                         3   159
D638V12, multiclass
                           clus
vv                          SLC4A3 MUTATED SLC4A3 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  9              159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(639) Variable = ZDHHC5 MUTATION ANALYSIS
D639V1, survival
                  sevent
clus2                0   1
  ZDHHC5 MUTATED     6   3
  ZDHHC5 WILD-TYPE 175  77
  ZDHHC5 MUTATED ZDHHC5 WILD-TYPE 
               9              252 
  ZDHHC5 MUTATED ZDHHC5 WILD-TYPE 
               3               77 
$`ZDHHC5 MUTATED`
TCGA-BR-6452 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5723 
       34.68        15.81         6.58         1.02         6.02       105.07 
TCGA-HU-A4GH TCGA-HU-A4GQ TCGA-HU-A4H5 
       11.77         0.10        12.30 

$`ZDHHC5 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
        6.97        36.00         1.02         0.99         0.99        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        19.36        23.84         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  ZDHHC5 MUTATED ZDHHC5 WILD-TYPE 
             0.1              0.0 
  ZDHHC5 MUTATED ZDHHC5 WILD-TYPE 
          105.07            79.07 
  ZDHHC5 MUTATED ZDHHC5 WILD-TYPE 
           11.77            12.71 
[1] "0.1 - 105.1 (11.8)" "0.0 - 79.1 (12.7)" 
[1] "hr=" "1.2"
D639V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZDHHC5 MUTATED         0        1        1        2         2         0
  ZDHHC5 WILD-TYPE       1        8       26       24        29        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZDHHC5 MUTATED           0          0          0          1        3
  ZDHHC5 WILD-TYPE         3         49         36         23       21
D639V3, multiclass
            clus
vv           ZDHHC5 MUTATED ZDHHC5 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                1               26
  STAGE II                2               24
  STAGE IIA               2               29
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                3               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZDHHC5 MUTATED     1   3   3   3
  ZDHHC5 WILD-TYPE  10  69 119  72
D639V4, multiclass
    clus
vv   ZDHHC5 MUTATED ZDHHC5 WILD-TYPE
  T1              1               10
  T2              3               69
  T3              3              119
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZDHHC5 MUTATED    4  3  3  0
  ZDHHC5 WILD-TYPE 89 78 47 53
D639V5, multiclass
    clus
vv   ZDHHC5 MUTATED ZDHHC5 WILD-TYPE
  N0              4               89
  N1              3               78
  N2              3               47
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D639V6, binary
                  cls
clus                 0   1
  ZDHHC5 MUTATED     8   2
  ZDHHC5 WILD-TYPE 249  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC5 MUTATED      8    2
  ZDHHC5 WILD-TYPE  249   16
   clus
vv  ZDHHC5 MUTATED ZDHHC5 WILD-TYPE
  0              8              249
  1              2               16
[1] 2 2
[1] FALSE
D639V7, binary
                  cls
clus                 0   1
  ZDHHC5 MUTATED     1   9
  ZDHHC5 WILD-TYPE 109 170
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC5 MUTATED      1    9
  ZDHHC5 WILD-TYPE  109  170
        clus
vv       ZDHHC5 MUTATED ZDHHC5 WILD-TYPE
  FEMALE              1              109
  MALE                9              170
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZDHHC5 MUTATED                                       1
  ZDHHC5 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZDHHC5 MUTATED                                                        3
  ZDHHC5 WILD-TYPE                                                    132
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZDHHC5 MUTATED                                                                   1
  ZDHHC5 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZDHHC5 MUTATED                                                  3
  ZDHHC5 WILD-TYPE                                               35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZDHHC5 MUTATED                                                          1
  ZDHHC5 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZDHHC5 MUTATED                                                           1
  ZDHHC5 WILD-TYPE                                                         5
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZDHHC5 MUTATED                                          0
  ZDHHC5 WILD-TYPE                                        3
D639V8, multiclass
                                                                   clus
vv                                                                  ZDHHC5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ZDHHC5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D639V9, binary
                  cls
clus                 0   1
  ZDHHC5 MUTATED     1   9
  ZDHHC5 WILD-TYPE   4 275
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC5 MUTATED      1    9
  ZDHHC5 WILD-TYPE    4  275
     clus
vv    ZDHHC5 MUTATED ZDHHC5 WILD-TYPE
  NO               1                4
  YES              9              275
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZDHHC5 MUTATED     8   0   1   0
  ZDHHC5 WILD-TYPE 219  10   9  24
D639V10, multiclass
    clus
vv   ZDHHC5 MUTATED ZDHHC5 WILD-TYPE
  R0              8              219
  R1              0               10
  R2              1                9
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D639V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZDHHC5 MUTATED       5                         0     1
  ZDHHC5 WILD-TYPE    71                         4   167
D639V12, multiclass
                           clus
vv                          ZDHHC5 MUTATED ZDHHC5 WILD-TYPE
  ASIAN                                  5               71
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  1              167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(640) Variable = GCDH MUTATION ANALYSIS
D640V1, survival
                sevent
clus2              0   1
  GCDH MUTATED     4   2
  GCDH WILD-TYPE 177  78
  GCDH MUTATED GCDH WILD-TYPE 
             6            255 
  GCDH MUTATED GCDH WILD-TYPE 
             2             78 
$`GCDH MUTATED`
TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-A4QL TCGA-CG-4306 TCGA-CG-5723 TCGA-HJ-7597 
       34.68        19.50        11.57         1.02       105.07        26.47 

$`GCDH WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56        11.08         5.52         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  GCDH MUTATED GCDH WILD-TYPE 
          1.02           0.00 
  GCDH MUTATED GCDH WILD-TYPE 
        105.07          79.07 
  GCDH MUTATED GCDH WILD-TYPE 
        22.985         12.590 
[1] "1.0 - 105.1 (23.0)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "2.1"
D640V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GCDH MUTATED         0        0        2        1         1         0
  GCDH WILD-TYPE       1        9       25       25        30        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GCDH MUTATED           0          0          1          1        1
  GCDH WILD-TYPE         3         49         35         23       23
D640V3, multiclass
            clus
vv           GCDH MUTATED GCDH WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              1             25
  STAGE IIA             1             30
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            1             35
  STAGE IIIC            1             23
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GCDH MUTATED     0   3   3   1
  GCDH WILD-TYPE  11  69 119  74
D640V4, multiclass
    clus
vv   GCDH MUTATED GCDH WILD-TYPE
  T1            0             11
  T2            3             69
  T3            3            119
  T4            1             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  GCDH MUTATED    3  2  2  1
  GCDH WILD-TYPE 90 79 48 52
D640V5, multiclass
    clus
vv   GCDH MUTATED GCDH WILD-TYPE
  N0            3             90
  N1            2             79
  N2            2             48
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D640V6, binary
                cls
clus               0   1
  GCDH MUTATED     6   1
  GCDH WILD-TYPE 251  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCDH MUTATED      6    1
  GCDH WILD-TYPE  251   17
   clus
vv  GCDH MUTATED GCDH WILD-TYPE
  0            6            251
  1            1             17
[1] 2 2
[1] FALSE
D640V7, binary
                cls
clus               0   1
  GCDH MUTATED     5   3
  GCDH WILD-TYPE 105 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCDH MUTATED      5    3
  GCDH WILD-TYPE  105  176
        clus
vv       GCDH MUTATED GCDH WILD-TYPE
  FEMALE            5            105
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GCDH MUTATED                                       0
  GCDH WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GCDH MUTATED                                                        6
  GCDH WILD-TYPE                                                    129
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GCDH MUTATED                                                                   1
  GCDH WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GCDH MUTATED                                                  0
  GCDH WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GCDH MUTATED                                                          0
  GCDH WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GCDH MUTATED                                                           0
  GCDH WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GCDH MUTATED                                          1
  GCDH WILD-TYPE                                        2
D640V8, multiclass
                                                                   clus
vv                                                                  GCDH MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  GCDH WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D640V9, binary
                cls
clus               0   1
  GCDH MUTATED     0   8
  GCDH WILD-TYPE   5 276
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCDH MUTATED      0    8
  GCDH WILD-TYPE    5  276
     clus
vv    GCDH MUTATED GCDH WILD-TYPE
  NO             0              5
  YES            8            276
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GCDH MUTATED     6   0   1   1
  GCDH WILD-TYPE 221  10   9  23
D640V10, multiclass
    clus
vv   GCDH MUTATED GCDH WILD-TYPE
  R0            6            221
  R1            0             10
  R2            1              9
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D640V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GCDH MUTATED       0                         0     5
  GCDH WILD-TYPE    76                         4   163
D640V12, multiclass
                           clus
vv                          GCDH MUTATED GCDH WILD-TYPE
  ASIAN                                0             76
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                5            163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(641) Variable = BTNL8 MUTATION ANALYSIS
D641V1, survival
                 sevent
clus2               0   1
  BTNL8 MUTATED     4   1
  BTNL8 WILD-TYPE 177  79
  BTNL8 MUTATED BTNL8 WILD-TYPE 
              5             256 
  BTNL8 MUTATED BTNL8 WILD-TYPE 
              1              79 
$`BTNL8 MUTATED`
TCGA-BR-7716 TCGA-BR-8487 TCGA-BR-8687 TCGA-CG-5721 TCGA-CG-5723 
       28.01         1.12         8.22         6.02       105.07 

$`BTNL8 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        23.93        15.42        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         9.86        15.68        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  BTNL8 MUTATED BTNL8 WILD-TYPE 
           1.12            0.00 
  BTNL8 MUTATED BTNL8 WILD-TYPE 
         105.07           79.07 
  BTNL8 MUTATED BTNL8 WILD-TYPE 
           8.22           12.64 
[1] "1.1 - 105.1 (8.2)" "0.0 - 79.1 (12.6)"
[1] "hr=" "2.9"
D641V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BTNL8 MUTATED         0        0        1        1         1         1
  BTNL8 WILD-TYPE       1        9       26       25        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BTNL8 MUTATED           0          0          0          1        1
  BTNL8 WILD-TYPE         3         49         36         23       23
D641V3, multiclass
            clus
vv           BTNL8 MUTATED BTNL8 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BTNL8 MUTATED     0   2   2   2
  BTNL8 WILD-TYPE  11  70 120  73
D641V4, multiclass
    clus
vv   BTNL8 MUTATED BTNL8 WILD-TYPE
  T1             0              11
  T2             2              70
  T3             2             120
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  BTNL8 MUTATED    2  3  1  0
  BTNL8 WILD-TYPE 91 78 49 53
D641V5, multiclass
    clus
vv   BTNL8 MUTATED BTNL8 WILD-TYPE
  N0             2              91
  N1             3              78
  N2             1              49
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D641V6, binary
                 cls
clus                0   1
  BTNL8 MUTATED     6   0
  BTNL8 WILD-TYPE 251  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL8 MUTATED      6    0
  BTNL8 WILD-TYPE  251   18
   clus
vv  BTNL8 MUTATED BTNL8 WILD-TYPE
  0             6             251
  1             0              18
[1] 2 2
[1] FALSE
D641V7, binary
                 cls
clus                0   1
  BTNL8 MUTATED     3   3
  BTNL8 WILD-TYPE 107 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL8 MUTATED      3    3
  BTNL8 WILD-TYPE  107  176
        clus
vv       BTNL8 MUTATED BTNL8 WILD-TYPE
  FEMALE             3             107
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  BTNL8 MUTATED                                       0
  BTNL8 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BTNL8 MUTATED                                                        4
  BTNL8 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BTNL8 MUTATED                                                                   2
  BTNL8 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  BTNL8 MUTATED                                                  0
  BTNL8 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  BTNL8 MUTATED                                                          0
  BTNL8 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  BTNL8 MUTATED                                                           0
  BTNL8 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  BTNL8 MUTATED                                          0
  BTNL8 WILD-TYPE                                        3
D641V8, multiclass
                                                                   clus
vv                                                                  BTNL8 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  BTNL8 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D641V9, binary
                 cls
clus                0   1
  BTNL8 MUTATED     0   6
  BTNL8 WILD-TYPE   5 278
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL8 MUTATED      0    6
  BTNL8 WILD-TYPE    5  278
     clus
vv    BTNL8 MUTATED BTNL8 WILD-TYPE
  NO              0               5
  YES             6             278
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BTNL8 MUTATED     5   1   0   0
  BTNL8 WILD-TYPE 222   9  10  24
D641V10, multiclass
    clus
vv   BTNL8 MUTATED BTNL8 WILD-TYPE
  R0             5             222
  R1             1               9
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D641V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BTNL8 MUTATED       0                         0     3
  BTNL8 WILD-TYPE    76                         4   165
D641V12, multiclass
                           clus
vv                          BTNL8 MUTATED BTNL8 WILD-TYPE
  ASIAN                                 0              76
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(642) Variable = RASA2 MUTATION ANALYSIS
D642V1, survival
                 sevent
clus2               0   1
  RASA2 MUTATED     6   1
  RASA2 WILD-TYPE 175  79
  RASA2 MUTATED RASA2 WILD-TYPE 
              7             254 
  RASA2 MUTATED RASA2 WILD-TYPE 
              1              79 
$`RASA2 MUTATED`
TCGA-BR-4184 TCGA-CD-5803 TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-5721 TCGA-HU-A4GT 
        6.97         0.07        12.62        15.95         6.02         6.51 
TCGA-HU-A4GU 
        6.25 

$`RASA2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.15        13.18         0.30         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 
       12.43        11.61         6.58        12.20         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX 
       25.81        11.77        29.98         8.98         0.10        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  RASA2 MUTATED RASA2 WILD-TYPE 
           0.07            0.00 
  RASA2 MUTATED RASA2 WILD-TYPE 
          15.95          105.07 
  RASA2 MUTATED RASA2 WILD-TYPE 
          6.510          12.775 
[1] "0.1 - 15.9 (6.5)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1"  
D642V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RASA2 MUTATED         0        0        1        2         1         1
  RASA2 WILD-TYPE       1        9       26       24        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RASA2 MUTATED           0          1          0          0        1
  RASA2 WILD-TYPE         3         48         36         24       23
D642V3, multiclass
            clus
vv           RASA2 MUTATED RASA2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               2              24
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RASA2 MUTATED     0   2   4   1
  RASA2 WILD-TYPE  11  70 118  74
D642V4, multiclass
    clus
vv   RASA2 MUTATED RASA2 WILD-TYPE
  T1             0              11
  T2             2              70
  T3             4             118
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  RASA2 MUTATED    3  4  0  0
  RASA2 WILD-TYPE 90 77 50 53
D642V5, multiclass
    clus
vv   RASA2 MUTATED RASA2 WILD-TYPE
  N0             3              90
  N1             4              77
  N2             0              50
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D642V6, binary
                 cls
clus                0   1
  RASA2 MUTATED     7   0
  RASA2 WILD-TYPE 250  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA2 MUTATED      7    0
  RASA2 WILD-TYPE  250   18
   clus
vv  RASA2 MUTATED RASA2 WILD-TYPE
  0             7             250
  1             0              18
[1] 2 2
[1] FALSE
D642V7, binary
                 cls
clus                0   1
  RASA2 MUTATED     3   5
  RASA2 WILD-TYPE 107 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA2 MUTATED      3    5
  RASA2 WILD-TYPE  107  174
        clus
vv       RASA2 MUTATED RASA2 WILD-TYPE
  FEMALE             3             107
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RASA2 MUTATED                                       1
  RASA2 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RASA2 MUTATED                                                        5
  RASA2 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RASA2 MUTATED                                                                   1
  RASA2 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RASA2 MUTATED                                                  1
  RASA2 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RASA2 MUTATED                                                          0
  RASA2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RASA2 MUTATED                                                           0
  RASA2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RASA2 MUTATED                                          0
  RASA2 WILD-TYPE                                        3
D642V8, multiclass
                                                                   clus
vv                                                                  RASA2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  RASA2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D642V9, binary
                 cls
clus                0   1
  RASA2 MUTATED     0   8
  RASA2 WILD-TYPE   5 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA2 MUTATED      0    8
  RASA2 WILD-TYPE    5  276
     clus
vv    RASA2 MUTATED RASA2 WILD-TYPE
  NO              0               5
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RASA2 MUTATED     4   0   0   2
  RASA2 WILD-TYPE 223  10  10  22
D642V10, multiclass
    clus
vv   RASA2 MUTATED RASA2 WILD-TYPE
  R0             4             223
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D642V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RASA2 MUTATED       4                         0     2
  RASA2 WILD-TYPE    72                         4   166
D642V12, multiclass
                           clus
vv                          RASA2 MUTATED RASA2 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 2             166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(643) Variable = PIK3R1 MUTATION ANALYSIS
D643V1, survival
                  sevent
clus2                0   1
  PIK3R1 MUTATED     6   1
  PIK3R1 WILD-TYPE 175  79
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               7              254 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               1               79 
$`PIK3R1 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-CG-5721 TCGA-D7-6528 TCGA-D7-8572 TCGA-HU-A4GN 
        6.97        34.68         6.02        15.22        16.80        29.98 
TCGA-HU-A4GU 
        6.25 

$`PIK3R1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        10.26        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 
       10.55        11.31        12.33        24.72        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       25.81        11.77         8.98         0.10         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
            6.02             0.00 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
           34.68           105.07 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
          15.220           12.605 
[1] "6.0 - 34.7 (15.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.7"
D643V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIK3R1 MUTATED         1        0        1        0         2         2
  PIK3R1 WILD-TYPE       0        9       26       26        29        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3R1 MUTATED           0          2          0          0        1
  PIK3R1 WILD-TYPE         3         47         36         24       23
D643V3, multiclass
            clus
vv           PIK3R1 MUTATED PIK3R1 WILD-TYPE
  STAGE I                 1                0
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               2               29
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PIK3R1 MUTATED     1   3   3   2
  PIK3R1 WILD-TYPE  10  69 119  73
D643V4, multiclass
    clus
vv   PIK3R1 MUTATED PIK3R1 WILD-TYPE
  T1              1               10
  T2              3               69
  T3              3              119
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  PIK3R1 MUTATED    3  5  1  0
  PIK3R1 WILD-TYPE 90 76 49 53
D643V5, multiclass
    clus
vv   PIK3R1 MUTATED PIK3R1 WILD-TYPE
  N0              3               90
  N1              5               76
  N2              1               49
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D643V6, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED     8   0
  PIK3R1 WILD-TYPE 249  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      8    0
  PIK3R1 WILD-TYPE  249   18
   clus
vv  PIK3R1 MUTATED PIK3R1 WILD-TYPE
  0              8              249
  1              0               18
[1] 2 2
[1] FALSE
D643V7, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED     3   7
  PIK3R1 WILD-TYPE 107 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      3    7
  PIK3R1 WILD-TYPE  107  172
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  FEMALE              3              107
  MALE                7              172
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PIK3R1 MUTATED                                       1
  PIK3R1 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIK3R1 MUTATED                                                        6
  PIK3R1 WILD-TYPE                                                    129
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIK3R1 MUTATED                                                                   1
  PIK3R1 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PIK3R1 MUTATED                                                  2
  PIK3R1 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PIK3R1 MUTATED                                                          0
  PIK3R1 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PIK3R1 MUTATED                                                           0
  PIK3R1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PIK3R1 MUTATED                                          0
  PIK3R1 WILD-TYPE                                        3
D643V8, multiclass
                                                                   clus
vv                                                                  PIK3R1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  PIK3R1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D643V9, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED     0  10
  PIK3R1 WILD-TYPE   5 274
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      0   10
  PIK3R1 WILD-TYPE    5  274
     clus
vv    PIK3R1 MUTATED PIK3R1 WILD-TYPE
  NO               0                5
  YES             10              274
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PIK3R1 MUTATED     7   0   0   3
  PIK3R1 WILD-TYPE 220  10  10  21
D643V10, multiclass
    clus
vv   PIK3R1 MUTATED PIK3R1 WILD-TYPE
  R0              7              220
  R1              0               10
  R2              0               10
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D643V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3R1 MUTATED       2                         1     6
  PIK3R1 WILD-TYPE    74                         3   162
D643V12, multiclass
                           clus
vv                          PIK3R1 MUTATED PIK3R1 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(644) Variable = CDC5L MUTATION ANALYSIS
D644V1, survival
                 sevent
clus2               0   1
  CDC5L MUTATED     9   3
  CDC5L WILD-TYPE 172  77
  CDC5L MUTATED CDC5L WILD-TYPE 
             12             249 
  CDC5L MUTATED CDC5L WILD-TYPE 
              3              77 
$`CDC5L MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6801 TCGA-BR-7707 TCGA-BR-7851 
        6.97        30.90        34.68        21.11        23.93        12.43 
TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-A4MI TCGA-FP-A4BE TCGA-HU-A4H8 TCGA-IN-7808 
        1.12        15.81         0.10        11.08         8.88         3.45 

$`CDC5L WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 
       25.61        18.05        19.89         8.98        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 
       32.94        12.82         9.21        24.76        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
        5.03        13.58         0.56         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
       19.36        23.84        12.30         9.67        27.42        21.21 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  CDC5L MUTATED CDC5L WILD-TYPE 
            0.1             0.0 
  CDC5L MUTATED CDC5L WILD-TYPE 
          34.68          105.07 
  CDC5L MUTATED CDC5L WILD-TYPE 
         11.755          12.660 
[1] "0.1 - 34.7 (11.8)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.3"
D644V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDC5L MUTATED         0        0        2        0         4         1
  CDC5L WILD-TYPE       1        9       25       26        27        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDC5L MUTATED           1          2          1          0        1
  CDC5L WILD-TYPE         2         47         35         24       23
D644V3, multiclass
            clus
vv           CDC5L MUTATED CDC5L WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              4              27
  STAGE IIB              1              43
  STAGE III              1               2
  STAGE IIIA             2              47
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDC5L MUTATED     1   2   8   3
  CDC5L WILD-TYPE  10  70 114  72
D644V4, multiclass
    clus
vv   CDC5L MUTATED CDC5L WILD-TYPE
  T1             1              10
  T2             2              70
  T3             8             114
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CDC5L MUTATED    7  4  1  1
  CDC5L WILD-TYPE 86 77 49 52
D644V5, multiclass
    clus
vv   CDC5L MUTATED CDC5L WILD-TYPE
  N0             7              86
  N1             4              77
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D644V6, binary
                 cls
clus                0   1
  CDC5L MUTATED    11   2
  CDC5L WILD-TYPE 246  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC5L MUTATED     11    2
  CDC5L WILD-TYPE  246   16
   clus
vv  CDC5L MUTATED CDC5L WILD-TYPE
  0            11             246
  1             2              16
[1] 2 2
[1] FALSE
D644V7, binary
                 cls
clus                0   1
  CDC5L MUTATED     6   9
  CDC5L WILD-TYPE 104 170
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC5L MUTATED      6    9
  CDC5L WILD-TYPE  104  170
        clus
vv       CDC5L MUTATED CDC5L WILD-TYPE
  FEMALE             6             104
  MALE               9             170
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CDC5L MUTATED                                       1
  CDC5L WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CDC5L MUTATED                                                       11
  CDC5L WILD-TYPE                                                    124
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CDC5L MUTATED                                                                   1
  CDC5L WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CDC5L MUTATED                                                  2
  CDC5L WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CDC5L MUTATED                                                          0
  CDC5L WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CDC5L MUTATED                                                           0
  CDC5L WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CDC5L MUTATED                                          0
  CDC5L WILD-TYPE                                        3
D644V8, multiclass
                                                                   clus
vv                                                                  CDC5L MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  CDC5L WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D644V9, binary
                 cls
clus                0   1
  CDC5L MUTATED     0  15
  CDC5L WILD-TYPE   5 269
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC5L MUTATED      0   15
  CDC5L WILD-TYPE    5  269
     clus
vv    CDC5L MUTATED CDC5L WILD-TYPE
  NO              0               5
  YES            15             269
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDC5L MUTATED     8   0   0   5
  CDC5L WILD-TYPE 219  10  10  19
D644V10, multiclass
    clus
vv   CDC5L MUTATED CDC5L WILD-TYPE
  R0             8             219
  R1             0              10
  R2             0              10
  RX             5              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D644V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDC5L MUTATED       3                         1    11
  CDC5L WILD-TYPE    73                         3   157
D644V12, multiclass
                           clus
vv                          CDC5L MUTATED CDC5L WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                11             157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(645) Variable = COL20A1 MUTATION ANALYSIS
D645V1, survival
                   sevent
clus2                 0   1
  COL20A1 MUTATED    14   3
  COL20A1 WILD-TYPE 167  77
  COL20A1 MUTATED COL20A1 WILD-TYPE 
               17               244 
  COL20A1 MUTATED COL20A1 WILD-TYPE 
                3                77 
$`COL20A1 MUTATED`
TCGA-BR-6452 TCGA-BR-6563 TCGA-BR-7707 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8680 
       34.68        39.12        23.93        19.50         1.12        15.81 
TCGA-BR-8683 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MI 
        9.86        11.57         0.10         9.34         6.58         0.10 
TCGA-CG-4305 TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-6822 TCGA-HU-A4GY 
       15.95       105.07        21.07        12.33         0.26 

$`COL20A1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        19.33        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
        0.49        11.54        16.44        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         0.13         3.42        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       12.20        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         6.02         0.99        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        10.55        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.25        10.19         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  COL20A1 MUTATED COL20A1 WILD-TYPE 
              0.1               0.0 
  COL20A1 MUTATED COL20A1 WILD-TYPE 
           105.07             79.07 
  COL20A1 MUTATED COL20A1 WILD-TYPE 
            12.33             12.64 
[1] "0.1 - 105.1 (12.3)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "2.4"
D645V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  COL20A1 MUTATED         0        0        3        3         3         2
  COL20A1 WILD-TYPE       1        9       24       23        28        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COL20A1 MUTATED           0          2          3          1        1
  COL20A1 WILD-TYPE         3         47         33         23       23
D645V3, multiclass
            clus
vv           COL20A1 MUTATED COL20A1 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 3                24
  STAGE II                 3                23
  STAGE IIA                3                28
  STAGE IIB                2                42
  STAGE III                0                 3
  STAGE IIIA               2                47
  STAGE IIIB               3                33
  STAGE IIIC               1                23
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  COL20A1 MUTATED     0   6   8   4
  COL20A1 WILD-TYPE  11  66 114  71
D645V4, multiclass
    clus
vv   COL20A1 MUTATED COL20A1 WILD-TYPE
  T1               0                11
  T2               6                66
  T3               8               114
  T4               4                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  COL20A1 MUTATED    7  6  4  1
  COL20A1 WILD-TYPE 86 75 46 52
D645V5, multiclass
    clus
vv   COL20A1 MUTATED COL20A1 WILD-TYPE
  N0               7                86
  N1               6                75
  N2               4                46
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D645V6, binary
                   cls
clus                  0   1
  COL20A1 MUTATED    17   1
  COL20A1 WILD-TYPE 240  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL20A1 MUTATED     17    1
  COL20A1 WILD-TYPE  240   17
   clus
vv  COL20A1 MUTATED COL20A1 WILD-TYPE
  0              17               240
  1               1                17
[1] 2 2
[1] FALSE
D645V7, binary
                   cls
clus                  0   1
  COL20A1 MUTATED     7  11
  COL20A1 WILD-TYPE 103 168
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL20A1 MUTATED      7   11
  COL20A1 WILD-TYPE  103  168
        clus
vv       COL20A1 MUTATED COL20A1 WILD-TYPE
  FEMALE               7               103
  MALE                11               168
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  COL20A1 MUTATED                                       3
  COL20A1 WILD-TYPE                                    47
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  COL20A1 MUTATED                                                       10
  COL20A1 WILD-TYPE                                                    125
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  COL20A1 MUTATED                                                                   2
  COL20A1 WILD-TYPE                                                                38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  COL20A1 MUTATED                                                  3
  COL20A1 WILD-TYPE                                               35
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  COL20A1 MUTATED                                                          0
  COL20A1 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  COL20A1 MUTATED                                                           0
  COL20A1 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  COL20A1 MUTATED                                          0
  COL20A1 WILD-TYPE                                        3
D645V8, multiclass
                                                                   clus
vv                                                                  COL20A1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  COL20A1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D645V9, binary
                   cls
clus                  0   1
  COL20A1 MUTATED     0  18
  COL20A1 WILD-TYPE   5 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL20A1 MUTATED      0   18
  COL20A1 WILD-TYPE    5  266
     clus
vv    COL20A1 MUTATED COL20A1 WILD-TYPE
  NO                0                 5
  YES              18               266
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  COL20A1 MUTATED    16   0   0   0
  COL20A1 WILD-TYPE 211  10  10  24
D645V10, multiclass
    clus
vv   COL20A1 MUTATED COL20A1 WILD-TYPE
  R0              16               211
  R1               0                10
  R2               0                10
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D645V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  COL20A1 MUTATED       7                         0     7
  COL20A1 WILD-TYPE    69                         4   161
D645V12, multiclass
                           clus
vv                          COL20A1 MUTATED COL20A1 WILD-TYPE
  ASIAN                                   7                69
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   7               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(646) Variable = AP3M2 MUTATION ANALYSIS
D646V1, survival
                 sevent
clus2               0   1
  AP3M2 MUTATED     6   4
  AP3M2 WILD-TYPE 175  76
  AP3M2 MUTATED AP3M2 WILD-TYPE 
             10             251 
  AP3M2 MUTATED AP3M2 WILD-TYPE 
              4              76 
$`AP3M2 MUTATED`
TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-7717 TCGA-BR-8589 TCGA-CG-4305 
       30.90         9.57        34.68        18.15        15.81        15.95 
TCGA-CG-5734 TCGA-HU-A4G9 TCGA-HU-A4GT TCGA-HU-A4GX 
        7.99        24.20         6.51        10.19 

$`AP3M2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       18.35         6.18         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       15.42        28.01        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       11.84         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10         6.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  AP3M2 MUTATED AP3M2 WILD-TYPE 
           6.51            0.00 
  AP3M2 MUTATED AP3M2 WILD-TYPE 
          34.68          105.07 
  AP3M2 MUTATED AP3M2 WILD-TYPE 
          15.88           12.59 
[1] "6.5 - 34.7 (15.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1"  
D646V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AP3M2 MUTATED         0        1        0        2         2         0
  AP3M2 WILD-TYPE       1        8       27       24        29        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AP3M2 MUTATED           0          1          1          1        1
  AP3M2 WILD-TYPE         3         48         35         23       23
D646V3, multiclass
            clus
vv           AP3M2 MUTATED AP3M2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               2              24
  STAGE IIA              2              29
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AP3M2 MUTATED     1   3   3   3
  AP3M2 WILD-TYPE  10  69 119  72
D646V4, multiclass
    clus
vv   AP3M2 MUTATED AP3M2 WILD-TYPE
  T1             1              10
  T2             3              69
  T3             3             119
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  AP3M2 MUTATED    3  5  1  0
  AP3M2 WILD-TYPE 90 76 49 53
D646V5, multiclass
    clus
vv   AP3M2 MUTATED AP3M2 WILD-TYPE
  N0             3              90
  N1             5              76
  N2             1              49
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D646V6, binary
                 cls
clus                0   1
  AP3M2 MUTATED    10   0
  AP3M2 WILD-TYPE 247  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3M2 MUTATED     10    0
  AP3M2 WILD-TYPE  247   18
   clus
vv  AP3M2 MUTATED AP3M2 WILD-TYPE
  0            10             247
  1             0              18
[1] 2 2
[1] FALSE
D646V7, binary
                 cls
clus                0   1
  AP3M2 MUTATED     5   5
  AP3M2 WILD-TYPE 105 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3M2 MUTATED      5    5
  AP3M2 WILD-TYPE  105  174
        clus
vv       AP3M2 MUTATED AP3M2 WILD-TYPE
  FEMALE             5             105
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AP3M2 MUTATED                                       1
  AP3M2 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AP3M2 MUTATED                                                        6
  AP3M2 WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AP3M2 MUTATED                                                                   1
  AP3M2 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AP3M2 MUTATED                                                  2
  AP3M2 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AP3M2 MUTATED                                                          0
  AP3M2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AP3M2 MUTATED                                                           0
  AP3M2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AP3M2 MUTATED                                          0
  AP3M2 WILD-TYPE                                        3
D646V8, multiclass
                                                                   clus
vv                                                                  AP3M2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  AP3M2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D646V9, binary
                 cls
clus                0   1
  AP3M2 MUTATED     0  10
  AP3M2 WILD-TYPE   5 274
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3M2 MUTATED      0   10
  AP3M2 WILD-TYPE    5  274
     clus
vv    AP3M2 MUTATED AP3M2 WILD-TYPE
  NO              0               5
  YES            10             274
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AP3M2 MUTATED     8   0   0   2
  AP3M2 WILD-TYPE 219  10  10  22
D646V10, multiclass
    clus
vv   AP3M2 MUTATED AP3M2 WILD-TYPE
  R0             8             219
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D646V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AP3M2 MUTATED       3                         0     5
  AP3M2 WILD-TYPE    73                         4   163
D646V12, multiclass
                           clus
vv                          AP3M2 MUTATED AP3M2 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(647) Variable = NAA16 MUTATION ANALYSIS
D647V1, survival
                 sevent
clus2               0   1
  NAA16 MUTATED     6   1
  NAA16 WILD-TYPE 175  79
  NAA16 MUTATED NAA16 WILD-TYPE 
              7             254 
  NAA16 MUTATED NAA16 WILD-TYPE 
              1              79 
$`NAA16 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-4306 TCGA-CG-4449 
       26.70        34.68        15.81        11.57         1.02        19.07 
TCGA-CG-5723 
      105.07 

$`NAA16 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        47.05        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         6.02         0.99        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  NAA16 MUTATED NAA16 WILD-TYPE 
           1.02            0.00 
  NAA16 MUTATED NAA16 WILD-TYPE 
         105.07           79.07 
  NAA16 MUTATED NAA16 WILD-TYPE 
         19.070          12.575 
[1] "1.0 - 105.1 (19.1)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "4.6"
D647V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NAA16 MUTATED         0        0        0        2         1         1
  NAA16 WILD-TYPE       1        9       27       24        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NAA16 MUTATED           0          0          1          0        2
  NAA16 WILD-TYPE         3         49         35         24       22
D647V3, multiclass
            clus
vv           NAA16 MUTATED NAA16 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               2              24
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NAA16 MUTATED     0   2   3   2
  NAA16 WILD-TYPE  11  70 119  73
D647V4, multiclass
    clus
vv   NAA16 MUTATED NAA16 WILD-TYPE
  T1             0              11
  T2             2              70
  T3             3             119
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  NAA16 MUTATED    2  2  2  1
  NAA16 WILD-TYPE 91 79 48 52
D647V5, multiclass
    clus
vv   NAA16 MUTATED NAA16 WILD-TYPE
  N0             2              91
  N1             2              79
  N2             2              48
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D647V6, binary
                 cls
clus                0   1
  NAA16 MUTATED     6   2
  NAA16 WILD-TYPE 251  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA16 MUTATED      6    2
  NAA16 WILD-TYPE  251   16
   clus
vv  NAA16 MUTATED NAA16 WILD-TYPE
  0             6             251
  1             2              16
[1] 2 2
[1] FALSE
D647V7, binary
                 cls
clus                0   1
  NAA16 MUTATED     4   4
  NAA16 WILD-TYPE 106 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA16 MUTATED      4    4
  NAA16 WILD-TYPE  106  175
        clus
vv       NAA16 MUTATED NAA16 WILD-TYPE
  FEMALE             4             106
  MALE               4             175
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NAA16 MUTATED                                       1
  NAA16 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NAA16 MUTATED                                                        5
  NAA16 WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NAA16 MUTATED                                                                   0
  NAA16 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NAA16 MUTATED                                                  1
  NAA16 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NAA16 MUTATED                                                          1
  NAA16 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NAA16 MUTATED                                                           0
  NAA16 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NAA16 MUTATED                                          0
  NAA16 WILD-TYPE                                        3
D647V8, multiclass
                                                                   clus
vv                                                                  NAA16 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  NAA16 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D647V9, binary
                 cls
clus                0   1
  NAA16 MUTATED     0   8
  NAA16 WILD-TYPE   5 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA16 MUTATED      0    8
  NAA16 WILD-TYPE    5  276
     clus
vv    NAA16 MUTATED NAA16 WILD-TYPE
  NO              0               5
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NAA16 MUTATED     6   0   1   1
  NAA16 WILD-TYPE 221  10   9  23
D647V10, multiclass
    clus
vv   NAA16 MUTATED NAA16 WILD-TYPE
  R0             6             221
  R1             0              10
  R2             1               9
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D647V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NAA16 MUTATED       1                         0     4
  NAA16 WILD-TYPE    75                         4   164
D647V12, multiclass
                           clus
vv                          NAA16 MUTATED NAA16 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(648) Variable = NPR3 MUTATION ANALYSIS
D648V1, survival
                sevent
clus2              0   1
  NPR3 MUTATED     8   1
  NPR3 WILD-TYPE 173  79
  NPR3 MUTATED NPR3 WILD-TYPE 
             9            252 
  NPR3 MUTATED NPR3 WILD-TYPE 
             1             79 
$`NPR3 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-8081 TCGA-BR-8680 TCGA-BR-A4J8 TCGA-CG-4305 
       26.70         6.97        20.55        15.81        13.51        15.95 
TCGA-CG-5721 TCGA-CG-5723 TCGA-HU-A4G8 
        6.02       105.07        11.84 

$`NPR3 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69        12.26         9.60         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        1.02         0.99         0.99        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  NPR3 MUTATED NPR3 WILD-TYPE 
          6.02           0.00 
  NPR3 MUTATED NPR3 WILD-TYPE 
        105.07          79.07 
  NPR3 MUTATED NPR3 WILD-TYPE 
        15.810         12.575 
[1] "6.0 - 105.1 (15.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "4.6"
D648V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NPR3 MUTATED         0        0        0        2         0         3
  NPR3 WILD-TYPE       1        9       27       24        31        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NPR3 MUTATED           0          2          1          1        2
  NPR3 WILD-TYPE         3         47         35         23       22
D648V3, multiclass
            clus
vv           NPR3 MUTATED NPR3 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              2             24
  STAGE IIA             0             31
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            1             35
  STAGE IIIC            1             23
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NPR3 MUTATED     0   2   3   6
  NPR3 WILD-TYPE  11  70 119  69
D648V4, multiclass
    clus
vv   NPR3 MUTATED NPR3 WILD-TYPE
  T1            0             11
  T2            2             70
  T3            3            119
  T4            6             69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  NPR3 MUTATED    3  5  1  2
  NPR3 WILD-TYPE 90 76 49 51
D648V5, multiclass
    clus
vv   NPR3 MUTATED NPR3 WILD-TYPE
  N0            3             90
  N1            5             76
  N2            1             49
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D648V6, binary
                cls
clus               0   1
  NPR3 MUTATED     9   1
  NPR3 WILD-TYPE 248  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPR3 MUTATED      9    1
  NPR3 WILD-TYPE  248   17
   clus
vv  NPR3 MUTATED NPR3 WILD-TYPE
  0            9            248
  1            1             17
[1] 2 2
[1] FALSE
D648V7, binary
                cls
clus               0   1
  NPR3 MUTATED     6   5
  NPR3 WILD-TYPE 104 174
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPR3 MUTATED      6    5
  NPR3 WILD-TYPE  104  174
        clus
vv       NPR3 MUTATED NPR3 WILD-TYPE
  FEMALE            6            104
  MALE              5            174
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NPR3 MUTATED                                       2
  NPR3 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NPR3 MUTATED                                                        7
  NPR3 WILD-TYPE                                                    128
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NPR3 MUTATED                                                                   1
  NPR3 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NPR3 MUTATED                                                  1
  NPR3 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NPR3 MUTATED                                                          0
  NPR3 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NPR3 MUTATED                                                           0
  NPR3 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NPR3 MUTATED                                          0
  NPR3 WILD-TYPE                                        3
D648V8, multiclass
                                                                   clus
vv                                                                  NPR3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  NPR3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D648V9, binary
                cls
clus               0   1
  NPR3 MUTATED     0  11
  NPR3 WILD-TYPE   5 273
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPR3 MUTATED      0   11
  NPR3 WILD-TYPE    5  273
     clus
vv    NPR3 MUTATED NPR3 WILD-TYPE
  NO             0              5
  YES           11            273
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NPR3 MUTATED     8   0   0   2
  NPR3 WILD-TYPE 219  10  10  22
D648V10, multiclass
    clus
vv   NPR3 MUTATED NPR3 WILD-TYPE
  R0            8            219
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D648V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NPR3 MUTATED       2                         0     6
  NPR3 WILD-TYPE    74                         4   162
D648V12, multiclass
                           clus
vv                          NPR3 MUTATED NPR3 WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                6            162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(649) Variable = COX8C MUTATION ANALYSIS
D649V1, survival
                 sevent
clus2               0   1
  COX8C MUTATED     2   1
  COX8C WILD-TYPE 179  79
  COX8C MUTATED COX8C WILD-TYPE 
              3             258 
  COX8C MUTATED COX8C WILD-TYPE 
              1              79 
$`COX8C MUTATED`
TCGA-BR-8078 TCGA-BR-8591 TCGA-HU-A4GQ 
       12.26        13.45         0.10 

$`COX8C WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  COX8C MUTATED COX8C WILD-TYPE 
            0.1             0.0 
  COX8C MUTATED COX8C WILD-TYPE 
          13.45          105.07 
  COX8C MUTATED COX8C WILD-TYPE 
          12.26           12.64 
[1] "0.1 - 13.4 (12.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.9"
D649V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  COX8C MUTATED         0        0        0        0         0         1
  COX8C WILD-TYPE       1        9       27       26        31        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COX8C MUTATED           0          0          0          2        0
  COX8C WILD-TYPE         3         49         36         22       24
D649V3, multiclass
            clus
vv           COX8C MUTATED COX8C WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              0              31
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             2              22
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  COX8C MUTATED     0   0   0   3
  COX8C WILD-TYPE  11  72 122  72
D649V4, multiclass
    clus
vv   COX8C MUTATED COX8C WILD-TYPE
  T1             0              11
  T2             0              72
  T3             0             122
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  COX8C MUTATED    1  1  1  1
  COX8C WILD-TYPE 92 80 49 52
D649V5, multiclass
    clus
vv   COX8C MUTATED COX8C WILD-TYPE
  N0             1              92
  N1             1              80
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D649V6, binary
                 cls
clus                0   1
  COX8C MUTATED     4   0
  COX8C WILD-TYPE 253  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  COX8C MUTATED      4    0
  COX8C WILD-TYPE  253   18
   clus
vv  COX8C MUTATED COX8C WILD-TYPE
  0             4             253
  1             0              18
[1] 2 2
[1] FALSE
D649V7, binary
                 cls
clus                0   1
  COX8C MUTATED     2   2
  COX8C WILD-TYPE 108 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  COX8C MUTATED      2    2
  COX8C WILD-TYPE  108  177
        clus
vv       COX8C MUTATED COX8C WILD-TYPE
  FEMALE             2             108
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  COX8C MUTATED                                       0
  COX8C WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  COX8C MUTATED                                                        3
  COX8C WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  COX8C MUTATED                                                                   0
  COX8C WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  COX8C MUTATED                                                  1
  COX8C WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  COX8C MUTATED                                                          0
  COX8C WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  COX8C MUTATED                                                           0
  COX8C WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  COX8C MUTATED                                          0
  COX8C WILD-TYPE                                        3
D649V8, multiclass
                                                                   clus
vv                                                                  COX8C MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  COX8C WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D649V9, binary
                 cls
clus                0   1
  COX8C MUTATED     0   4
  COX8C WILD-TYPE   5 280
[1] "tbl2"
                 cls
clus              [,1] [,2]
  COX8C MUTATED      0    4
  COX8C WILD-TYPE    5  280
     clus
vv    COX8C MUTATED COX8C WILD-TYPE
  NO              0               5
  YES             4             280
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  COX8C MUTATED     3   0   0   1
  COX8C WILD-TYPE 224  10  10  23
D649V10, multiclass
    clus
vv   COX8C MUTATED COX8C WILD-TYPE
  R0             3             224
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D649V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  COX8C MUTATED       1                         0     3
  COX8C WILD-TYPE    75                         4   165
D649V12, multiclass
                           clus
vv                          COX8C MUTATED COX8C WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(650) Variable = KLHDC8B MUTATION ANALYSIS
D650V1, survival
                   sevent
clus2                 0   1
  KLHDC8B MUTATED     5   2
  KLHDC8B WILD-TYPE 176  78
  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
                7               254 
  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
                2                78 
$`KLHDC8B MUTATED`
TCGA-BR-8081 TCGA-BR-8363 TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-5728 TCGA-HJ-7597 
       20.55         0.26         0.10         0.10        65.10        26.47 
TCGA-HU-A4GU 
        6.25 

$`KLHDC8B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        19.50        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        28.96        79.07         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56        11.08         5.52         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       11.77        29.98         8.98         0.10         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
              0.1               0.0 
  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
            65.10            105.07 
  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
             6.25             12.64 
[1] "0.1 - 65.1 (6.2)"   "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D650V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KLHDC8B MUTATED         0        0        3        1         0         2
  KLHDC8B WILD-TYPE       1        9       24       25        31        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KLHDC8B MUTATED           0          0          1          0        0
  KLHDC8B WILD-TYPE         3         49         35         24       24
D650V3, multiclass
            clus
vv           KLHDC8B MUTATED KLHDC8B WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 3                24
  STAGE II                 1                25
  STAGE IIA                0                31
  STAGE IIB                2                42
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               1                35
  STAGE IIIC               0                24
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  KLHDC8B MUTATED     0   3   3   1
  KLHDC8B WILD-TYPE  11  69 119  74
D650V4, multiclass
    clus
vv   KLHDC8B MUTATED KLHDC8B WILD-TYPE
  T1               0                11
  T2               3                69
  T3               3               119
  T4               1                74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  KLHDC8B MUTATED    5  2  0  0
  KLHDC8B WILD-TYPE 88 79 50 53
D650V5, multiclass
    clus
vv   KLHDC8B MUTATED KLHDC8B WILD-TYPE
  N0               5                88
  N1               2                79
  N2               0                50
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D650V6, binary
                   cls
clus                  0   1
  KLHDC8B MUTATED     7   0
  KLHDC8B WILD-TYPE 250  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KLHDC8B MUTATED      7    0
  KLHDC8B WILD-TYPE  250   18
   clus
vv  KLHDC8B MUTATED KLHDC8B WILD-TYPE
  0               7               250
  1               0                18
[1] 2 2
[1] FALSE
D650V7, binary
                   cls
clus                  0   1
  KLHDC8B MUTATED     4   4
  KLHDC8B WILD-TYPE 106 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KLHDC8B MUTATED      4    4
  KLHDC8B WILD-TYPE  106  175
        clus
vv       KLHDC8B MUTATED KLHDC8B WILD-TYPE
  FEMALE               4               106
  MALE                 4               175
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KLHDC8B MUTATED                                       1
  KLHDC8B WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KLHDC8B MUTATED                                                        5
  KLHDC8B WILD-TYPE                                                    130
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KLHDC8B MUTATED                                                                   1
  KLHDC8B WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KLHDC8B MUTATED                                                  0
  KLHDC8B WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KLHDC8B MUTATED                                                          0
  KLHDC8B WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KLHDC8B MUTATED                                                           0
  KLHDC8B WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KLHDC8B MUTATED                                          1
  KLHDC8B WILD-TYPE                                        2
D650V8, multiclass
                                                                   clus
vv                                                                  KLHDC8B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  KLHDC8B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D650V9, binary
                   cls
clus                  0   1
  KLHDC8B MUTATED     0   8
  KLHDC8B WILD-TYPE   5 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KLHDC8B MUTATED      0    8
  KLHDC8B WILD-TYPE    5  276
     clus
vv    KLHDC8B MUTATED KLHDC8B WILD-TYPE
  NO                0                 5
  YES               8               276
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  KLHDC8B MUTATED     6   0   0   1
  KLHDC8B WILD-TYPE 221  10  10  23
D650V10, multiclass
    clus
vv   KLHDC8B MUTATED KLHDC8B WILD-TYPE
  R0               6               221
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D650V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KLHDC8B MUTATED       3                         0     4
  KLHDC8B WILD-TYPE    73                         4   164
D650V12, multiclass
                           clus
vv                          KLHDC8B MUTATED KLHDC8B WILD-TYPE
  ASIAN                                   3                73
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   4               164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(651) Variable = ZBTB40 MUTATION ANALYSIS
D651V1, survival
                  sevent
clus2                0   1
  ZBTB40 MUTATED     6   3
  ZBTB40 WILD-TYPE 175  77
  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
               9              252 
  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
               3               77 
$`ZBTB40 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8370 TCGA-BR-8676 TCGA-CD-A48C TCGA-CG-5733 
       30.90        34.68         3.32         7.53        11.61        21.07 
TCGA-F1-A448 TCGA-HU-A4GH TCGA-HU-A4GU 
       21.27        11.77         6.25 

$`ZBTB40 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       18.35         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31        14.04        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG 
        0.10         3.42         9.34        11.31        12.43         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        72.23         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN 
       11.84        24.20         3.25        22.75        25.81        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
            3.32             0.00 
  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
           34.68           105.07 
  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
           11.77            12.64 
[1] "3.3 - 34.7 (11.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D651V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZBTB40 MUTATED         0        1        0        1         1         2
  ZBTB40 WILD-TYPE       1        8       27       25        30        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB40 MUTATED           0          1          3          0        0
  ZBTB40 WILD-TYPE         3         48         33         24       24
D651V3, multiclass
            clus
vv           ZBTB40 MUTATED ZBTB40 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                0               27
  STAGE II                1               25
  STAGE IIA               1               30
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              3               33
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZBTB40 MUTATED     1   3   6   0
  ZBTB40 WILD-TYPE  10  69 116  75
D651V4, multiclass
    clus
vv   ZBTB40 MUTATED ZBTB40 WILD-TYPE
  T1              1               10
  T2              3               69
  T3              6              116
  T4              0               75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZBTB40 MUTATED    2  3  1  3
  ZBTB40 WILD-TYPE 91 78 49 50
D651V5, multiclass
    clus
vv   ZBTB40 MUTATED ZBTB40 WILD-TYPE
  N0              2               91
  N1              3               78
  N2              1               49
  N3              3               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D651V6, binary
                  cls
clus                 0   1
  ZBTB40 MUTATED    10   0
  ZBTB40 WILD-TYPE 247  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB40 MUTATED     10    0
  ZBTB40 WILD-TYPE  247   18
   clus
vv  ZBTB40 MUTATED ZBTB40 WILD-TYPE
  0             10              247
  1              0               18
[1] 2 2
[1] FALSE
D651V7, binary
                  cls
clus                 0   1
  ZBTB40 MUTATED     4   6
  ZBTB40 WILD-TYPE 106 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB40 MUTATED      4    6
  ZBTB40 WILD-TYPE  106  173
        clus
vv       ZBTB40 MUTATED ZBTB40 WILD-TYPE
  FEMALE              4              106
  MALE                6              173
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZBTB40 MUTATED                                       2
  ZBTB40 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZBTB40 MUTATED                                                        3
  ZBTB40 WILD-TYPE                                                    132
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZBTB40 MUTATED                                                                   2
  ZBTB40 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZBTB40 MUTATED                                                  1
  ZBTB40 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZBTB40 MUTATED                                                          2
  ZBTB40 WILD-TYPE                                                       14
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZBTB40 MUTATED                                                           0
  ZBTB40 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZBTB40 MUTATED                                          0
  ZBTB40 WILD-TYPE                                        3
D651V8, multiclass
                                                                   clus
vv                                                                  ZBTB40 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ZBTB40 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D651V9, binary
                  cls
clus                 0   1
  ZBTB40 MUTATED     1   9
  ZBTB40 WILD-TYPE   4 275
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB40 MUTATED      1    9
  ZBTB40 WILD-TYPE    4  275
     clus
vv    ZBTB40 MUTATED ZBTB40 WILD-TYPE
  NO               1                4
  YES              9              275
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZBTB40 MUTATED     8   0   0   1
  ZBTB40 WILD-TYPE 219  10  10  23
D651V10, multiclass
    clus
vv   ZBTB40 MUTATED ZBTB40 WILD-TYPE
  R0              8              219
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D651V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZBTB40 MUTATED       3                         0     5
  ZBTB40 WILD-TYPE    73                         4   163
D651V12, multiclass
                           clus
vv                          ZBTB40 MUTATED ZBTB40 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  5              163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(652) Variable = FOLH1 MUTATION ANALYSIS
D652V1, survival
                 sevent
clus2               0   1
  FOLH1 MUTATED     7   3
  FOLH1 WILD-TYPE 174  77
  FOLH1 MUTATED FOLH1 WILD-TYPE 
             10             251 
  FOLH1 MUTATED FOLH1 WILD-TYPE 
              3              77 
$`FOLH1 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8284 TCGA-BR-8370 TCGA-BR-A4PD TCGA-CD-A487 
        6.97        34.68         8.05         3.32        20.65         9.34 
TCGA-CG-5721 TCGA-CG-5728 TCGA-F1-6874 TCGA-HU-A4GQ 
        6.02        65.10        14.47         0.10 

$`FOLH1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8286 
       14.43         0.69        12.26         9.60        20.55        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        3.42        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 
       14.76         0.62         7.99        16.24        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  FOLH1 MUTATED FOLH1 WILD-TYPE 
            0.1             0.0 
  FOLH1 MUTATED FOLH1 WILD-TYPE 
          65.10          105.07 
  FOLH1 MUTATED FOLH1 WILD-TYPE 
          8.695          12.660 
[1] "0.1 - 65.1 (8.7)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.1"
D652V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FOLH1 MUTATED         0        0        3        0         1         2
  FOLH1 WILD-TYPE       1        9       24       26        30        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FOLH1 MUTATED           0          1          1          2        1
  FOLH1 WILD-TYPE         3         48         35         22       23
D652V3, multiclass
            clus
vv           FOLH1 MUTATED FOLH1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               3              24
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             2              22
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FOLH1 MUTATED     0   3   4   4
  FOLH1 WILD-TYPE  11  69 118  71
D652V4, multiclass
    clus
vv   FOLH1 MUTATED FOLH1 WILD-TYPE
  T1             0              11
  T2             3              69
  T3             4             118
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  FOLH1 MUTATED    5  3  1  2
  FOLH1 WILD-TYPE 88 78 49 51
D652V5, multiclass
    clus
vv   FOLH1 MUTATED FOLH1 WILD-TYPE
  N0             5              88
  N1             3              78
  N2             1              49
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D652V6, binary
                 cls
clus                0   1
  FOLH1 MUTATED    10   0
  FOLH1 WILD-TYPE 247  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOLH1 MUTATED     10    0
  FOLH1 WILD-TYPE  247   18
   clus
vv  FOLH1 MUTATED FOLH1 WILD-TYPE
  0            10             247
  1             0              18
[1] 2 2
[1] FALSE
D652V7, binary
                 cls
clus                0   1
  FOLH1 MUTATED     4   7
  FOLH1 WILD-TYPE 106 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOLH1 MUTATED      4    7
  FOLH1 WILD-TYPE  106  172
        clus
vv       FOLH1 MUTATED FOLH1 WILD-TYPE
  FEMALE             4             106
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FOLH1 MUTATED                                       2
  FOLH1 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FOLH1 MUTATED                                                        3
  FOLH1 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FOLH1 MUTATED                                                                   5
  FOLH1 WILD-TYPE                                                                35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FOLH1 MUTATED                                                  1
  FOLH1 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FOLH1 MUTATED                                                          0
  FOLH1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FOLH1 MUTATED                                                           0
  FOLH1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FOLH1 MUTATED                                          0
  FOLH1 WILD-TYPE                                        3
D652V8, multiclass
                                                                   clus
vv                                                                  FOLH1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  FOLH1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D652V9, binary
                 cls
clus                0   1
  FOLH1 MUTATED     0  11
  FOLH1 WILD-TYPE   5 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOLH1 MUTATED      0   11
  FOLH1 WILD-TYPE    5  273
     clus
vv    FOLH1 MUTATED FOLH1 WILD-TYPE
  NO              0               5
  YES            11             273
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FOLH1 MUTATED    10   0   0   1
  FOLH1 WILD-TYPE 217  10  10  23
D652V10, multiclass
    clus
vv   FOLH1 MUTATED FOLH1 WILD-TYPE
  R0            10             217
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D652V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FOLH1 MUTATED       2                         0     6
  FOLH1 WILD-TYPE    74                         4   162
D652V12, multiclass
                           clus
vv                          FOLH1 MUTATED FOLH1 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(653) Variable = TXLNG MUTATION ANALYSIS
D653V1, survival
                 sevent
clus2               0   1
  TXLNG MUTATED     3   3
  TXLNG WILD-TYPE 178  77
  TXLNG MUTATED TXLNG WILD-TYPE 
              6             255 
  TXLNG MUTATED TXLNG WILD-TYPE 
              3              77 
$`TXLNG MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-D7-A4YV 
        6.97        34.68        12.26        11.57         6.58         5.92 

$`TXLNG WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  TXLNG MUTATED TXLNG WILD-TYPE 
           5.92            0.00 
  TXLNG MUTATED TXLNG WILD-TYPE 
          34.68          105.07 
  TXLNG MUTATED TXLNG WILD-TYPE 
           9.27           12.76 
[1] "5.9 - 34.7 (9.3)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.9"
D653V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TXLNG MUTATED         0        0        0        0         2         2
  TXLNG WILD-TYPE       1        9       27       26        29        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TXLNG MUTATED           0          2          1          0        0
  TXLNG WILD-TYPE         3         47         35         24       24
D653V3, multiclass
            clus
vv           TXLNG MUTATED TXLNG WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TXLNG MUTATED     0   0   5   2
  TXLNG WILD-TYPE  11  72 117  73
D653V4, multiclass
    clus
vv   TXLNG MUTATED TXLNG WILD-TYPE
  T1             0              11
  T2             0              72
  T3             5             117
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  TXLNG MUTATED    4  2  0  1
  TXLNG WILD-TYPE 89 79 50 52
D653V5, multiclass
    clus
vv   TXLNG MUTATED TXLNG WILD-TYPE
  N0             4              89
  N1             2              79
  N2             0              50
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D653V6, binary
                 cls
clus                0   1
  TXLNG MUTATED     6   0
  TXLNG WILD-TYPE 251  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXLNG MUTATED      6    0
  TXLNG WILD-TYPE  251   18
   clus
vv  TXLNG MUTATED TXLNG WILD-TYPE
  0             6             251
  1             0              18
[1] 2 2
[1] FALSE
D653V7, binary
                 cls
clus                0   1
  TXLNG MUTATED     5   2
  TXLNG WILD-TYPE 105 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXLNG MUTATED      5    2
  TXLNG WILD-TYPE  105  177
        clus
vv       TXLNG MUTATED TXLNG WILD-TYPE
  FEMALE             5             105
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TXLNG MUTATED                                       1
  TXLNG WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TXLNG MUTATED                                                        5
  TXLNG WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TXLNG MUTATED                                                                   0
  TXLNG WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TXLNG MUTATED                                                  1
  TXLNG WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TXLNG MUTATED                                                          0
  TXLNG WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TXLNG MUTATED                                                           0
  TXLNG WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TXLNG MUTATED                                          0
  TXLNG WILD-TYPE                                        3
D653V8, multiclass
                                                                   clus
vv                                                                  TXLNG MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  TXLNG WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D653V9, binary
                 cls
clus                0   1
  TXLNG MUTATED     0   7
  TXLNG WILD-TYPE   5 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXLNG MUTATED      0    7
  TXLNG WILD-TYPE    5  277
     clus
vv    TXLNG MUTATED TXLNG WILD-TYPE
  NO              0               5
  YES             7             277
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TXLNG MUTATED     4   0   0   2
  TXLNG WILD-TYPE 223  10  10  22
D653V10, multiclass
    clus
vv   TXLNG MUTATED TXLNG WILD-TYPE
  R0             4             223
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D653V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TXLNG MUTATED       1                         0     6
  TXLNG WILD-TYPE    75                         4   162
D653V12, multiclass
                           clus
vv                          TXLNG MUTATED TXLNG WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(654) Variable = SFTPC MUTATION ANALYSIS
D654V1, survival
                 sevent
clus2               0   1
  SFTPC MUTATED     1   1
  SFTPC WILD-TYPE 180  79
  SFTPC MUTATED SFTPC WILD-TYPE 
              2             259 
  SFTPC MUTATED SFTPC WILD-TYPE 
              1              79 
$`SFTPC MUTATED`
TCGA-BR-6452 TCGA-CG-5726 
       34.68        28.96 

$`SFTPC WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 
        0.99         6.02         0.99       105.07        12.03        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  SFTPC MUTATED SFTPC WILD-TYPE 
          28.96            0.00 
  SFTPC MUTATED SFTPC WILD-TYPE 
          34.68          105.07 
  SFTPC MUTATED SFTPC WILD-TYPE 
          31.82           12.59 
[1] "29.0 - 34.7 (31.8)" "0.0 - 105.1 (12.6)"
[1] "Remove cluster labels:" "SFTPC MUTATED"         
D654V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SFTPC MUTATED         1        1        0        0         1         0
  SFTPC WILD-TYPE       0        8       27       26        30        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SFTPC MUTATED           0          0          0          0        0
  SFTPC WILD-TYPE         3         49         36         24       24
D654V3, multiclass
            clus
vv           SFTPC MUTATED SFTPC WILD-TYPE
  STAGE I                1               0
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SFTPC MUTATED     2   0   1   0
  SFTPC WILD-TYPE   9  72 121  75
D654V4, multiclass
    clus
vv   SFTPC MUTATED SFTPC WILD-TYPE
  T1             2               9
  T2             0              72
  T3             1             121
  T4             0              75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  SFTPC MUTATED    2  1  0  0
  SFTPC WILD-TYPE 91 80 50 53
D654V5, multiclass
    clus
vv   SFTPC MUTATED SFTPC WILD-TYPE
  N0             2              91
  N1             1              80
  N2             0              50
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D654V6, binary
                 cls
clus                0   1
  SFTPC MUTATED     2   0
  SFTPC WILD-TYPE 255  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFTPC MUTATED      2    0
  SFTPC WILD-TYPE  255   18
   clus
vv  SFTPC MUTATED SFTPC WILD-TYPE
  0             2             255
  1             0              18
[1] 2 2
[1] FALSE
D654V7, binary
                 cls
clus                0   1
  SFTPC MUTATED     1   2
  SFTPC WILD-TYPE 109 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFTPC MUTATED      1    2
  SFTPC WILD-TYPE  109  177
        clus
vv       SFTPC MUTATED SFTPC WILD-TYPE
  FEMALE             1             109
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SFTPC MUTATED                                       0
  SFTPC WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SFTPC MUTATED                                                        2
  SFTPC WILD-TYPE                                                    133
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SFTPC MUTATED                                                                   1
  SFTPC WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SFTPC MUTATED                                                  0
  SFTPC WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SFTPC MUTATED                                                          0
  SFTPC WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SFTPC MUTATED                                                           0
  SFTPC WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SFTPC MUTATED                                          0
  SFTPC WILD-TYPE                                        3
D654V8, multiclass
                                                                   clus
vv                                                                  SFTPC MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  SFTPC WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D654V9, binary
                 cls
clus                0   1
  SFTPC MUTATED     0   3
  SFTPC WILD-TYPE   5 281
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFTPC MUTATED      0    3
  SFTPC WILD-TYPE    5  281
     clus
vv    SFTPC MUTATED SFTPC WILD-TYPE
  NO              0               5
  YES             3             281
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SFTPC MUTATED     3   0   0   0
  SFTPC WILD-TYPE 224  10  10  24
D654V10, multiclass
    clus
vv   SFTPC MUTATED SFTPC WILD-TYPE
  R0             3             224
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D654V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SFTPC MUTATED       0                         1     1
  SFTPC WILD-TYPE    76                         3   167
D654V12, multiclass
[1] "Remove cluster labels:" "SFTPC MUTATED"         
clus
  SFTPC MUTATED SFTPC WILD-TYPE 
              2             246 
     TCGA-B7-5816      TCGA-B7-5818      TCGA-BR-4183      TCGA-BR-4184 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-4187      TCGA-BR-4188      TCGA-BR-4191      TCGA-BR-4201 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256      TCGA-BR-4257 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4292 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-4294      TCGA-BR-4357      TCGA-BR-4361      TCGA-BR-4362 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-4363      TCGA-BR-4366      TCGA-BR-4368      TCGA-BR-4369 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-4370      TCGA-BR-4371      TCGA-BR-6453      TCGA-BR-6454 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457      TCGA-BR-6458 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565      TCGA-BR-6566 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707      TCGA-BR-6710 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803      TCGA-BR-6852 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703      TCGA-BR-7707 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-7715      TCGA-BR-7716      TCGA-BR-7717      TCGA-BR-7722 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-7723      TCGA-BR-7851      TCGA-BR-7901      TCGA-BR-7957 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-7958      TCGA-BR-7959      TCGA-BR-8058      TCGA-BR-8059 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-8077      TCGA-BR-8078      TCGA-BR-8080      TCGA-BR-8081 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-8284      TCGA-BR-8286      TCGA-BR-8289      TCGA-BR-8291 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-8295      TCGA-BR-8296      TCGA-BR-8297      TCGA-BR-8360 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-8361      TCGA-BR-8363      TCGA-BR-8364      TCGA-BR-8365 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-8366      TCGA-BR-8367      TCGA-BR-8368      TCGA-BR-8369 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-8370      TCGA-BR-8371      TCGA-BR-8372      TCGA-BR-8373 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-8380      TCGA-BR-8381      TCGA-BR-8382      TCGA-BR-8384 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-8483      TCGA-BR-8484      TCGA-BR-8485      TCGA-BR-8486 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-8487      TCGA-BR-8588      TCGA-BR-8589      TCGA-BR-8590 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-8591      TCGA-BR-8592      TCGA-BR-8676      TCGA-BR-8677 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-8678      TCGA-BR-8679      TCGA-BR-8680      TCGA-BR-8682 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-8683      TCGA-BR-8686      TCGA-BR-8687      TCGA-BR-8690 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-A44T      TCGA-BR-A44U      TCGA-BR-A452      TCGA-BR-A453 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-A4CQ      TCGA-BR-A4CR      TCGA-BR-A4CS      TCGA-BR-A4IU 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-A4IV      TCGA-BR-A4IY      TCGA-BR-A4IZ      TCGA-BR-A4J1 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-A4J2      TCGA-BR-A4J4      TCGA-BR-A4J6      TCGA-BR-A4J7 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-A4J8      TCGA-BR-A4PD      TCGA-BR-A4PE      TCGA-BR-A4PF 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-BR-A4QI      TCGA-BR-A4QL      TCGA-BR-A4QM      TCGA-CD-5798 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-CD-5799      TCGA-CD-5800      TCGA-CD-5801      TCGA-CD-5802 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-CD-5803      TCGA-CD-5804      TCGA-CD-5813      TCGA-CD-8524 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-CD-8525      TCGA-CD-8526      TCGA-CD-8527      TCGA-CD-8528 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-CD-8529      TCGA-CD-8530      TCGA-CD-8531      TCGA-CD-8532 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-CD-8534      TCGA-CD-8535      TCGA-CD-8536      TCGA-CD-A486 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-CD-A487      TCGA-CD-A489      TCGA-CD-A48A      TCGA-CD-A48C 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-CD-A4MG      TCGA-CD-A4MH      TCGA-CD-A4MI      TCGA-CD-A4MJ 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-D7-5577      TCGA-D7-5578      TCGA-D7-5579      TCGA-D7-6518 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-D7-6519      TCGA-D7-6520      TCGA-D7-6521      TCGA-D7-6522 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-D7-6524      TCGA-D7-6525      TCGA-D7-6526      TCGA-D7-6527 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-D7-6528      TCGA-D7-6815      TCGA-D7-6817      TCGA-D7-6818 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-D7-6820      TCGA-D7-6822      TCGA-D7-8570      TCGA-D7-8572 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-D7-8573      TCGA-D7-8574      TCGA-D7-8575      TCGA-D7-8576 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-D7-8578      TCGA-D7-8579      TCGA-D7-A4YT      TCGA-D7-A4YU 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-D7-A4YV      TCGA-D7-A4YX      TCGA-D7-A4YY      TCGA-D7-A4Z0 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-EQ-5647      TCGA-EQ-8122      TCGA-EQ-A4SO      TCGA-F1-6874 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-F1-6875      TCGA-F1-A448      TCGA-FP-7735      TCGA-FP-7829 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-FP-7916      TCGA-FP-7998      TCGA-FP-8099      TCGA-FP-8209 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-FP-8210      TCGA-FP-8211      TCGA-FP-8631      TCGA-FP-A4BE 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-FP-A4BF      TCGA-HJ-7597      TCGA-HU-8243      TCGA-HU-8245 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-HU-8249      TCGA-HU-8602      TCGA-HU-8604      TCGA-HU-8608 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-HU-8610      TCGA-HU-A4G2      TCGA-HU-A4G3      TCGA-HU-A4G6 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-HU-A4G8      TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-HU-A4GF      TCGA-HU-A4GH      TCGA-HU-A4GN      TCGA-HU-A4GP 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-HU-A4GQ      TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-HU-A4GY      TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-HU-A4H4      TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-HU-A4HD      TCGA-IN-7806      TCGA-IN-7808      TCGA-IN-8462 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 
     TCGA-IN-8663      TCGA-IP-7968 
"SFTPC WILD-TYPE" "SFTPC WILD-TYPE" 

Clustering(655) Variable = P2RX1 MUTATION ANALYSIS
D655V1, survival
                 sevent
clus2               0   1
  P2RX1 MUTATED     3   0
  P2RX1 WILD-TYPE 178  80
  P2RX1 MUTATED P2RX1 WILD-TYPE 
              3             258 
  P2RX1 MUTATED P2RX1 WILD-TYPE 
              0              80 
$`P2RX1 MUTATED`
TCGA-CG-5728 TCGA-HU-8602 TCGA-HU-A4G8 
       65.10        11.41        11.84 

$`P2RX1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        5.52        26.47         5.92        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  P2RX1 MUTATED P2RX1 WILD-TYPE 
          11.41            0.00 
  P2RX1 MUTATED P2RX1 WILD-TYPE 
          65.10          105.07 
  P2RX1 MUTATED P2RX1 WILD-TYPE 
          11.84           12.64 
[1] "11.4 - 65.1 (11.8)" "0.0 - 105.1 (12.6)"
[1] "hr="     "9500000"
D655V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  P2RX1 MUTATED         0        0        1        0         0         2
  P2RX1 WILD-TYPE       1        9       26       26        31        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  P2RX1 MUTATED           0          0          0          0        0
  P2RX1 WILD-TYPE         3         49         36         24       24
D655V3, multiclass
            clus
vv           P2RX1 MUTATED P2RX1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              0              31
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  P2RX1 MUTATED     0   1   1   1
  P2RX1 WILD-TYPE  11  71 121  74
D655V4, multiclass
    clus
vv   P2RX1 MUTATED P2RX1 WILD-TYPE
  T1             0              11
  T2             1              71
  T3             1             121
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  P2RX1 MUTATED    2  1  0  0
  P2RX1 WILD-TYPE 91 80 50 53
D655V5, multiclass
    clus
vv   P2RX1 MUTATED P2RX1 WILD-TYPE
  N0             2              91
  N1             1              80
  N2             0              50
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D655V6, binary
                 cls
clus                0   1
  P2RX1 MUTATED     3   0
  P2RX1 WILD-TYPE 254  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RX1 MUTATED      3    0
  P2RX1 WILD-TYPE  254   18
   clus
vv  P2RX1 MUTATED P2RX1 WILD-TYPE
  0             3             254
  1             0              18
[1] 2 2
[1] FALSE
D655V7, binary
                 cls
clus                0   1
  P2RX1 MUTATED     3   0
  P2RX1 WILD-TYPE 107 179
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RX1 MUTATED      3    0
  P2RX1 WILD-TYPE  107  179
        clus
vv       P2RX1 MUTATED P2RX1 WILD-TYPE
  FEMALE             3             107
  MALE               0             179
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  P2RX1 MUTATED                                       2
  P2RX1 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  P2RX1 MUTATED                                                        0
  P2RX1 WILD-TYPE                                                    135
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  P2RX1 MUTATED                                                                   1
  P2RX1 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  P2RX1 MUTATED                                                  0
  P2RX1 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  P2RX1 MUTATED                                                          0
  P2RX1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  P2RX1 MUTATED                                                           0
  P2RX1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  P2RX1 MUTATED                                          0
  P2RX1 WILD-TYPE                                        3
D655V8, multiclass
                                                                   clus
vv                                                                  P2RX1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        0
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  P2RX1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        135
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D655V9, binary
                 cls
clus                0   1
  P2RX1 MUTATED     0   3
  P2RX1 WILD-TYPE   5 281
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RX1 MUTATED      0    3
  P2RX1 WILD-TYPE    5  281
     clus
vv    P2RX1 MUTATED P2RX1 WILD-TYPE
  NO              0               5
  YES             3             281
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  P2RX1 MUTATED     2   0   0   0
  P2RX1 WILD-TYPE 225  10  10  24
D655V10, multiclass
[1] "Remove cluster labels:" "P2RX1 MUTATED"         
clus
  P2RX1 MUTATED P2RX1 WILD-TYPE 
              2             269 
     TCGA-B7-5816      TCGA-B7-5818      TCGA-BR-4183      TCGA-BR-4184 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-4187      TCGA-BR-4188      TCGA-BR-4191      TCGA-BR-4201 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256      TCGA-BR-4257 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4292 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-4294      TCGA-BR-4357      TCGA-BR-4361      TCGA-BR-4362 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-4363      TCGA-BR-4366      TCGA-BR-4368      TCGA-BR-4369 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-4370      TCGA-BR-4371      TCGA-BR-6452      TCGA-BR-6453 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-6852      TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-7707      TCGA-BR-7715      TCGA-BR-7716      TCGA-BR-7717 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-7722      TCGA-BR-7723      TCGA-BR-7851      TCGA-BR-7901 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-7957      TCGA-BR-7958      TCGA-BR-7959      TCGA-BR-8058 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8059      TCGA-BR-8077      TCGA-BR-8078      TCGA-BR-8080 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8081      TCGA-BR-8284      TCGA-BR-8286      TCGA-BR-8289 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8291      TCGA-BR-8295      TCGA-BR-8296      TCGA-BR-8297 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8360      TCGA-BR-8361      TCGA-BR-8363      TCGA-BR-8364 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8365      TCGA-BR-8366      TCGA-BR-8367      TCGA-BR-8368 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8369      TCGA-BR-8370      TCGA-BR-8371      TCGA-BR-8372 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8373      TCGA-BR-8380      TCGA-BR-8381      TCGA-BR-8382 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8384      TCGA-BR-8483      TCGA-BR-8484      TCGA-BR-8485 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8486      TCGA-BR-8487      TCGA-BR-8588      TCGA-BR-8589 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8590      TCGA-BR-8591      TCGA-BR-8592      TCGA-BR-8676 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8677      TCGA-BR-8678      TCGA-BR-8679      TCGA-BR-8680 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8682      TCGA-BR-8683      TCGA-BR-8686      TCGA-BR-8687 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8690      TCGA-BR-A44T      TCGA-BR-A44U      TCGA-BR-A452 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-A453      TCGA-BR-A4CQ      TCGA-BR-A4CR      TCGA-BR-A4CS 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-A4IU      TCGA-BR-A4IV      TCGA-BR-A4IY      TCGA-BR-A4IZ 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-A4J1      TCGA-BR-A4J2      TCGA-BR-A4J4      TCGA-BR-A4J6 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-A4J7      TCGA-BR-A4J8      TCGA-BR-A4PD      TCGA-BR-A4PE 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-A4PF      TCGA-BR-A4QI      TCGA-BR-A4QL      TCGA-BR-A4QM 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CD-5800      TCGA-CD-5801      TCGA-CD-5804      TCGA-CD-8524 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CD-8525      TCGA-CD-8526      TCGA-CD-8527      TCGA-CD-8528 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CD-8529      TCGA-CD-8530      TCGA-CD-8531      TCGA-CD-8532 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CD-8534      TCGA-CD-8535      TCGA-CD-8536      TCGA-CD-A487 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CG-4300      TCGA-CG-4301      TCGA-CG-4304      TCGA-CG-4305 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CG-4306      TCGA-CG-4436      TCGA-CG-4437      TCGA-CG-4438 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CG-4440      TCGA-CG-4441      TCGA-CG-4442      TCGA-CG-4443 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CG-4444      TCGA-CG-4449      TCGA-CG-4455      TCGA-CG-4462 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CG-4465      TCGA-CG-4466      TCGA-CG-4469      TCGA-CG-4474 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CG-4475      TCGA-CG-4476      TCGA-CG-4477      TCGA-CG-5717 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CG-5718      TCGA-CG-5719      TCGA-CG-5720      TCGA-CG-5721 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CG-5722      TCGA-CG-5723      TCGA-CG-5724      TCGA-CG-5726 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CG-5727      TCGA-CG-5730      TCGA-CG-5732      TCGA-CG-5733 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CG-5734      TCGA-D7-5577      TCGA-D7-5578      TCGA-D7-5579 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-D7-6518      TCGA-D7-6519      TCGA-D7-6520      TCGA-D7-6521 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-D7-6522      TCGA-D7-6524      TCGA-D7-6525      TCGA-D7-6526 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-D7-6527      TCGA-D7-6528      TCGA-D7-6815      TCGA-D7-6817 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-D7-6818      TCGA-D7-6820      TCGA-D7-6822      TCGA-D7-8570 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-D7-8572      TCGA-D7-8573      TCGA-D7-8574      TCGA-D7-8575 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-D7-8576      TCGA-D7-8578      TCGA-D7-8579      TCGA-D7-A4YT 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-D7-A4YU      TCGA-D7-A4YV      TCGA-D7-A4YX      TCGA-D7-A4YY 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-D7-A4Z0      TCGA-EQ-5647      TCGA-EQ-A4SO      TCGA-F1-6177 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-F1-6874      TCGA-F1-6875      TCGA-F1-A448      TCGA-FP-7735 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-FP-7829      TCGA-FP-7998      TCGA-FP-8099      TCGA-FP-8209 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-FP-8211      TCGA-FP-8631      TCGA-FP-A4BE      TCGA-FP-A4BF 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-HF-7132      TCGA-HF-7133      TCGA-HF-7136      TCGA-HJ-7597 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-HU-8243      TCGA-HU-8245      TCGA-HU-8249      TCGA-HU-8604 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-HU-8608      TCGA-HU-8610      TCGA-HU-A4G2      TCGA-HU-A4G3 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-HU-A4G6      TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-HU-A4GF      TCGA-HU-A4GH      TCGA-HU-A4GN      TCGA-HU-A4GP 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-HU-A4GQ      TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-HU-A4GY      TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-HU-A4H4      TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-HU-A4HD      TCGA-IN-7806      TCGA-IN-8462      TCGA-IN-8663 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-IP-7968 
"P2RX1 WILD-TYPE" 
D655V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  P2RX1 MUTATED       2                         0     0
  P2RX1 WILD-TYPE    74                         4   168
D655V12, multiclass
[1] "Remove cluster labels:" "P2RX1 MUTATED"         
clus
  P2RX1 MUTATED P2RX1 WILD-TYPE 
              2             246 
     TCGA-B7-5816      TCGA-B7-5818      TCGA-BR-4183      TCGA-BR-4184 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-4187      TCGA-BR-4188      TCGA-BR-4191      TCGA-BR-4201 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256      TCGA-BR-4257 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4292 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-4294      TCGA-BR-4357      TCGA-BR-4361      TCGA-BR-4362 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-4363      TCGA-BR-4366      TCGA-BR-4368      TCGA-BR-4369 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-4370      TCGA-BR-4371      TCGA-BR-6452      TCGA-BR-6453 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-6852      TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-7707      TCGA-BR-7715      TCGA-BR-7716      TCGA-BR-7717 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-7722      TCGA-BR-7723      TCGA-BR-7851      TCGA-BR-7901 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-7957      TCGA-BR-7958      TCGA-BR-7959      TCGA-BR-8058 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8059      TCGA-BR-8077      TCGA-BR-8078      TCGA-BR-8080 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8081      TCGA-BR-8284      TCGA-BR-8286      TCGA-BR-8289 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8291      TCGA-BR-8295      TCGA-BR-8296      TCGA-BR-8297 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8360      TCGA-BR-8361      TCGA-BR-8363      TCGA-BR-8364 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8365      TCGA-BR-8366      TCGA-BR-8367      TCGA-BR-8368 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8369      TCGA-BR-8370      TCGA-BR-8371      TCGA-BR-8372 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8373      TCGA-BR-8380      TCGA-BR-8381      TCGA-BR-8382 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8384      TCGA-BR-8483      TCGA-BR-8484      TCGA-BR-8485 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8486      TCGA-BR-8487      TCGA-BR-8588      TCGA-BR-8589 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8590      TCGA-BR-8591      TCGA-BR-8592      TCGA-BR-8676 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8677      TCGA-BR-8678      TCGA-BR-8679      TCGA-BR-8680 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8682      TCGA-BR-8683      TCGA-BR-8686      TCGA-BR-8687 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-8690      TCGA-BR-A44T      TCGA-BR-A44U      TCGA-BR-A452 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-A453      TCGA-BR-A4CQ      TCGA-BR-A4CR      TCGA-BR-A4CS 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-A4IU      TCGA-BR-A4IV      TCGA-BR-A4IY      TCGA-BR-A4IZ 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-A4J1      TCGA-BR-A4J2      TCGA-BR-A4J4      TCGA-BR-A4J6 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-A4J7      TCGA-BR-A4J8      TCGA-BR-A4PD      TCGA-BR-A4PE 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-BR-A4PF      TCGA-BR-A4QI      TCGA-BR-A4QL      TCGA-BR-A4QM 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CD-5798      TCGA-CD-5799      TCGA-CD-5800      TCGA-CD-5801 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CD-5802      TCGA-CD-5803      TCGA-CD-5804      TCGA-CD-5813 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CD-8524      TCGA-CD-8525      TCGA-CD-8526      TCGA-CD-8527 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CD-8528      TCGA-CD-8529      TCGA-CD-8530      TCGA-CD-8531 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CD-8532      TCGA-CD-8534      TCGA-CD-8535      TCGA-CD-8536 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CD-A486      TCGA-CD-A487      TCGA-CD-A489      TCGA-CD-A48A 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CD-A48C      TCGA-CD-A4MG      TCGA-CD-A4MH      TCGA-CD-A4MI 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-CD-A4MJ      TCGA-D7-5577      TCGA-D7-5578      TCGA-D7-5579 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-D7-6518      TCGA-D7-6519      TCGA-D7-6520      TCGA-D7-6521 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-D7-6522      TCGA-D7-6524      TCGA-D7-6525      TCGA-D7-6526 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-D7-6527      TCGA-D7-6528      TCGA-D7-6815      TCGA-D7-6817 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-D7-6818      TCGA-D7-6820      TCGA-D7-6822      TCGA-D7-8570 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-D7-8572      TCGA-D7-8573      TCGA-D7-8574      TCGA-D7-8575 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-D7-8576      TCGA-D7-8578      TCGA-D7-8579      TCGA-D7-A4YT 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-D7-A4YU      TCGA-D7-A4YV      TCGA-D7-A4YX      TCGA-D7-A4YY 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-D7-A4Z0      TCGA-EQ-5647      TCGA-EQ-8122      TCGA-EQ-A4SO 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-F1-6177      TCGA-F1-6874      TCGA-F1-6875      TCGA-F1-A448 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-FP-7735      TCGA-FP-7829      TCGA-FP-7916      TCGA-FP-7998 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-FP-8099      TCGA-FP-8209      TCGA-FP-8210      TCGA-FP-8211 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-FP-8631      TCGA-FP-A4BE      TCGA-FP-A4BF      TCGA-HJ-7597 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-HU-8243      TCGA-HU-8245      TCGA-HU-8249      TCGA-HU-8604 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-HU-8608      TCGA-HU-8610      TCGA-HU-A4G2      TCGA-HU-A4G3 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-HU-A4G6      TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-HU-A4GF      TCGA-HU-A4GH      TCGA-HU-A4GN      TCGA-HU-A4GP 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-HU-A4GQ      TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-HU-A4GY      TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-HU-A4H4      TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-HU-A4HD      TCGA-IN-7806      TCGA-IN-7808      TCGA-IN-8462 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 
     TCGA-IN-8663      TCGA-IP-7968 
"P2RX1 WILD-TYPE" "P2RX1 WILD-TYPE" 

Clustering(656) Variable = CORIN MUTATION ANALYSIS
D656V1, survival
                 sevent
clus2               0   1
  CORIN MUTATED     5   3
  CORIN WILD-TYPE 176  77
  CORIN MUTATED CORIN WILD-TYPE 
              8             253 
  CORIN MUTATED CORIN WILD-TYPE 
              3              77 
$`CORIN MUTATED`
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8361 TCGA-BR-8680 TCGA-D7-6527 
        6.61        34.68        32.94        19.50        15.81        10.26 
TCGA-HU-A4GQ TCGA-HU-A4H3 
        0.10        19.36 

$`CORIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
       18.35        30.90         6.18         9.57        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  CORIN MUTATED CORIN WILD-TYPE 
            0.1             0.0 
  CORIN MUTATED CORIN WILD-TYPE 
          34.68          105.07 
  CORIN MUTATED CORIN WILD-TYPE 
         17.585          12.590 
[1] "0.1 - 34.7 (17.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D656V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CORIN MUTATED         1        0        0        1         2         0
  CORIN WILD-TYPE       0        9       27       25        29        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CORIN MUTATED           1          0          0          3        1
  CORIN WILD-TYPE         2         49         36         21       23
D656V3, multiclass
            clus
vv           CORIN MUTATED CORIN WILD-TYPE
  STAGE I                1               0
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              2              29
  STAGE IIB              0              44
  STAGE III              1               2
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             3              21
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CORIN MUTATED     1   2   2   4
  CORIN WILD-TYPE  10  70 120  71
D656V4, multiclass
    clus
vv   CORIN MUTATED CORIN WILD-TYPE
  T1             1              10
  T2             2              70
  T3             2             120
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CORIN MUTATED    2  3  3  1
  CORIN WILD-TYPE 91 78 47 52
D656V5, multiclass
    clus
vv   CORIN MUTATED CORIN WILD-TYPE
  N0             2              91
  N1             3              78
  N2             3              47
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D656V6, binary
                 cls
clus                0   1
  CORIN MUTATED     8   1
  CORIN WILD-TYPE 249  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CORIN MUTATED      8    1
  CORIN WILD-TYPE  249   17
   clus
vv  CORIN MUTATED CORIN WILD-TYPE
  0             8             249
  1             1              17
[1] 2 2
[1] FALSE
D656V7, binary
                 cls
clus                0   1
  CORIN MUTATED     5   5
  CORIN WILD-TYPE 105 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CORIN MUTATED      5    5
  CORIN WILD-TYPE  105  174
        clus
vv       CORIN MUTATED CORIN WILD-TYPE
  FEMALE             5             105
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CORIN MUTATED                                       1
  CORIN WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CORIN MUTATED                                                        6
  CORIN WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CORIN MUTATED                                                                   0
  CORIN WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CORIN MUTATED                                                  2
  CORIN WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CORIN MUTATED                                                          0
  CORIN WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CORIN MUTATED                                                           1
  CORIN WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CORIN MUTATED                                          0
  CORIN WILD-TYPE                                        3
D656V8, multiclass
                                                                   clus
vv                                                                  CORIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  CORIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D656V9, binary
                 cls
clus                0   1
  CORIN MUTATED     0  10
  CORIN WILD-TYPE   5 274
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CORIN MUTATED      0   10
  CORIN WILD-TYPE    5  274
     clus
vv    CORIN MUTATED CORIN WILD-TYPE
  NO              0               5
  YES            10             274
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CORIN MUTATED     8   0   0   2
  CORIN WILD-TYPE 219  10  10  22
D656V10, multiclass
    clus
vv   CORIN MUTATED CORIN WILD-TYPE
  R0             8             219
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D656V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CORIN MUTATED       3                         1     6
  CORIN WILD-TYPE    73                         3   162
D656V12, multiclass
                           clus
vv                          CORIN MUTATED CORIN WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(657) Variable = ACSS2 MUTATION ANALYSIS
D657V1, survival
                 sevent
clus2               0   1
  ACSS2 MUTATED     6   1
  ACSS2 WILD-TYPE 175  79
  ACSS2 MUTATED ACSS2 WILD-TYPE 
              7             254 
  ACSS2 MUTATED ACSS2 WILD-TYPE 
              1              79 
$`ACSS2 MUTATED`
TCGA-BR-6452 TCGA-BR-8372 TCGA-BR-A4J2 TCGA-CD-8536 TCGA-CD-A4MI TCGA-HU-A4GQ 
       34.68        19.17        14.17         0.10         0.10         0.10 
TCGA-HU-A4GX 
       10.19 

$`ACSS2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 
       13.51        12.89         8.98         0.72         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         6.51         6.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  ACSS2 MUTATED ACSS2 WILD-TYPE 
            0.1             0.0 
  ACSS2 MUTATED ACSS2 WILD-TYPE 
          34.68          105.07 
  ACSS2 MUTATED ACSS2 WILD-TYPE 
          10.19           12.64 
[1] "0.1 - 34.7 (10.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.8"
D657V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ACSS2 MUTATED         0        0        1        1         1         1
  ACSS2 WILD-TYPE       1        9       26       25        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACSS2 MUTATED           0          0          1          3        1
  ACSS2 WILD-TYPE         3         49         35         21       23
D657V3, multiclass
            clus
vv           ACSS2 MUTATED ACSS2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             3              21
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ACSS2 MUTATED     0   1   3   5
  ACSS2 WILD-TYPE  11  71 119  70
D657V4, multiclass
    clus
vv   ACSS2 MUTATED ACSS2 WILD-TYPE
  T1             0              11
  T2             1              71
  T3             3             119
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ACSS2 MUTATED    4  1  3  1
  ACSS2 WILD-TYPE 89 80 47 52
D657V5, multiclass
    clus
vv   ACSS2 MUTATED ACSS2 WILD-TYPE
  N0             4              89
  N1             1              80
  N2             3              47
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D657V6, binary
                 cls
clus                0   1
  ACSS2 MUTATED     8   1
  ACSS2 WILD-TYPE 249  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACSS2 MUTATED      8    1
  ACSS2 WILD-TYPE  249   17
   clus
vv  ACSS2 MUTATED ACSS2 WILD-TYPE
  0             8             249
  1             1              17
[1] 2 2
[1] FALSE
D657V7, binary
                 cls
clus                0   1
  ACSS2 MUTATED     3   6
  ACSS2 WILD-TYPE 107 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACSS2 MUTATED      3    6
  ACSS2 WILD-TYPE  107  173
        clus
vv       ACSS2 MUTATED ACSS2 WILD-TYPE
  FEMALE             3             107
  MALE               6             173
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ACSS2 MUTATED                                       3
  ACSS2 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ACSS2 MUTATED                                                        4
  ACSS2 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ACSS2 MUTATED                                                                   1
  ACSS2 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ACSS2 MUTATED                                                  1
  ACSS2 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ACSS2 MUTATED                                                          0
  ACSS2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ACSS2 MUTATED                                                           0
  ACSS2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ACSS2 MUTATED                                          0
  ACSS2 WILD-TYPE                                        3
D657V8, multiclass
                                                                   clus
vv                                                                  ACSS2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ACSS2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D657V9, binary
                 cls
clus                0   1
  ACSS2 MUTATED     0   9
  ACSS2 WILD-TYPE   5 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACSS2 MUTATED      0    9
  ACSS2 WILD-TYPE    5  275
     clus
vv    ACSS2 MUTATED ACSS2 WILD-TYPE
  NO              0               5
  YES             9             275
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ACSS2 MUTATED     7   0   1   0
  ACSS2 WILD-TYPE 220  10   9  24
D657V10, multiclass
    clus
vv   ACSS2 MUTATED ACSS2 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             1               9
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D657V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACSS2 MUTATED       5                         0     2
  ACSS2 WILD-TYPE    71                         4   166
D657V12, multiclass
                           clus
vv                          ACSS2 MUTATED ACSS2 WILD-TYPE
  ASIAN                                 5              71
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 2             166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(658) Variable = CD1E MUTATION ANALYSIS
D658V1, survival
                sevent
clus2              0   1
  CD1E MUTATED     4   1
  CD1E WILD-TYPE 177  79
  CD1E MUTATED CD1E WILD-TYPE 
             5            256 
  CD1E MUTATED CD1E WILD-TYPE 
             1             79 
$`CD1E MUTATED`
TCGA-BR-6453 TCGA-BR-7723 TCGA-D7-6518 TCGA-D7-6822 TCGA-HU-A4GU 
       15.95        28.73        19.13        12.33         6.25 

$`CD1E WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        11.93        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        10.55        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  CD1E MUTATED CD1E WILD-TYPE 
          6.25           0.00 
  CD1E MUTATED CD1E WILD-TYPE 
         28.73         105.07 
  CD1E MUTATED CD1E WILD-TYPE 
        15.950         12.605 
[1] "6.2 - 28.7 (15.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.9"
D658V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CD1E MUTATED         0        0        2        0         1         1
  CD1E WILD-TYPE       1        9       25       26        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CD1E MUTATED           0          1          1          0        0
  CD1E WILD-TYPE         3         48         35         24       24
D658V3, multiclass
            clus
vv           CD1E MUTATED CD1E WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              0             26
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CD1E MUTATED     0   4   2   0
  CD1E WILD-TYPE  11  68 120  75
D658V4, multiclass
    clus
vv   CD1E MUTATED CD1E WILD-TYPE
  T1            0             11
  T2            4             68
  T3            2            120
  T4            0             75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  CD1E MUTATED    2  2  0  2
  CD1E WILD-TYPE 91 79 50 51
D658V5, multiclass
    clus
vv   CD1E MUTATED CD1E WILD-TYPE
  N0            2             91
  N1            2             79
  N2            0             50
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D658V6, binary
                cls
clus               0   1
  CD1E MUTATED     7   0
  CD1E WILD-TYPE 250  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD1E MUTATED      7    0
  CD1E WILD-TYPE  250   18
   clus
vv  CD1E MUTATED CD1E WILD-TYPE
  0            7            250
  1            0             18
[1] 2 2
[1] FALSE
D658V7, binary
                cls
clus               0   1
  CD1E MUTATED     0   7
  CD1E WILD-TYPE 110 172
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD1E MUTATED      0    7
  CD1E WILD-TYPE  110  172
        clus
vv       CD1E MUTATED CD1E WILD-TYPE
  FEMALE            0            110
  MALE              7            172
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CD1E MUTATED                                       2
  CD1E WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CD1E MUTATED                                                        3
  CD1E WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CD1E MUTATED                                                                   1
  CD1E WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CD1E MUTATED                                                  1
  CD1E WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CD1E MUTATED                                                          0
  CD1E WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CD1E MUTATED                                                           0
  CD1E WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CD1E MUTATED                                          0
  CD1E WILD-TYPE                                        3
D658V8, multiclass
                                                                   clus
vv                                                                  CD1E MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  CD1E WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D658V9, binary
                cls
clus               0   1
  CD1E MUTATED     0   7
  CD1E WILD-TYPE   5 277
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD1E MUTATED      0    7
  CD1E WILD-TYPE    5  277
     clus
vv    CD1E MUTATED CD1E WILD-TYPE
  NO             0              5
  YES            7            277
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CD1E MUTATED     5   1   0   1
  CD1E WILD-TYPE 222   9  10  23
D658V10, multiclass
    clus
vv   CD1E MUTATED CD1E WILD-TYPE
  R0            5            222
  R1            1              9
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D658V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD1E MUTATED       1                         0     5
  CD1E WILD-TYPE    75                         4   163
D658V12, multiclass
                           clus
vv                          CD1E MUTATED CD1E WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                5            163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(659) Variable = SCN10A MUTATION ANALYSIS
D659V1, survival
                  sevent
clus2                0   1
  SCN10A MUTATED    18   7
  SCN10A WILD-TYPE 163  73
  SCN10A MUTATED SCN10A WILD-TYPE 
              25              236 
  SCN10A MUTATED SCN10A WILD-TYPE 
               7               73 
$`SCN10A MUTATED`
TCGA-BR-6566 TCGA-BR-6801 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8367 
       32.78        21.11        32.94        12.26         0.26        26.33 
TCGA-BR-8368 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8678 TCGA-CD-A48A 
        4.31        15.81         9.34        13.45        11.54        12.43 
TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-8578 
        1.02         4.01         6.02       105.07        65.10        21.14 
TCGA-D7-A4Z0 TCGA-FP-8631 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H4 
       14.76         0.56        29.98         0.10        10.19        23.84 
TCGA-IN-8663 
        3.39 

$`SCN10A WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        25.61        18.05        19.89         8.98 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       22.19        17.52         0.95        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8592 
       25.18         9.21        20.22         1.12        12.79         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        3.42         9.34        11.31        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        7.99         8.05        54.08        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
        0.99        12.03        28.96        79.07         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        14.66        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       15.16        13.78         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BE TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       24.20         3.25        22.75        25.81        11.77         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.25         0.26         2.10        12.95        19.36 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IP-7968 
       18.81         2.53 

  SCN10A MUTATED SCN10A WILD-TYPE 
             0.1              0.0 
  SCN10A MUTATED SCN10A WILD-TYPE 
          105.07            79.07 
  SCN10A MUTATED SCN10A WILD-TYPE 
           12.43            12.64 
[1] "0.1 - 105.1 (12.4)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.5"
D659V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SCN10A MUTATED         0        0        5        1         5         4
  SCN10A WILD-TYPE       1        9       22       25        26        40
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SCN10A MUTATED           0          2          2          5        4
  SCN10A WILD-TYPE         3         47         34         19       20
D659V3, multiclass
            clus
vv           SCN10A MUTATED SCN10A WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                5               22
  STAGE II                1               25
  STAGE IIA               5               26
  STAGE IIB               4               40
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              2               34
  STAGE IIIC              5               19
  STAGE IV                4               20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SCN10A MUTATED     0  10   8  10
  SCN10A WILD-TYPE  11  62 114  65
D659V4, multiclass
    clus
vv   SCN10A MUTATED SCN10A WILD-TYPE
  T1              0               11
  T2             10               62
  T3              8              114
  T4             10               65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  SCN10A MUTATED   11  4  9  4
  SCN10A WILD-TYPE 82 77 41 49
D659V5, multiclass
    clus
vv   SCN10A MUTATED SCN10A WILD-TYPE
  N0             11               82
  N1              4               77
  N2              9               41
  N3              4               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D659V6, binary
                  cls
clus                 0   1
  SCN10A MUTATED    25   2
  SCN10A WILD-TYPE 232  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCN10A MUTATED     25    2
  SCN10A WILD-TYPE  232   16
   clus
vv  SCN10A MUTATED SCN10A WILD-TYPE
  0             25              232
  1              2               16
[1] 2 2
[1] FALSE
D659V7, binary
                  cls
clus                 0   1
  SCN10A MUTATED    13  15
  SCN10A WILD-TYPE  97 164
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCN10A MUTATED     13   15
  SCN10A WILD-TYPE   97  164
        clus
vv       SCN10A MUTATED SCN10A WILD-TYPE
  FEMALE             13               97
  MALE               15              164
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SCN10A MUTATED                                       1
  SCN10A WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SCN10A MUTATED                                                       19
  SCN10A WILD-TYPE                                                    116
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SCN10A MUTATED                                                                   4
  SCN10A WILD-TYPE                                                                36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SCN10A MUTATED                                                  3
  SCN10A WILD-TYPE                                               35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SCN10A MUTATED                                                          1
  SCN10A WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SCN10A MUTATED                                                           0
  SCN10A WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SCN10A MUTATED                                          0
  SCN10A WILD-TYPE                                        3
D659V8, multiclass
                                                                   clus
vv                                                                  SCN10A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        19
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  SCN10A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         116
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D659V9, binary
                  cls
clus                 0   1
  SCN10A MUTATED     0  28
  SCN10A WILD-TYPE   5 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCN10A MUTATED      0   28
  SCN10A WILD-TYPE    5  256
     clus
vv    SCN10A MUTATED SCN10A WILD-TYPE
  NO               0                5
  YES             28              256
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SCN10A MUTATED    23   0   2   2
  SCN10A WILD-TYPE 204  10   8  22
D659V10, multiclass
    clus
vv   SCN10A MUTATED SCN10A WILD-TYPE
  R0             23              204
  R1              0               10
  R2              2                8
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D659V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SCN10A MUTATED       5                         0    18
  SCN10A WILD-TYPE    71                         4   150
D659V12, multiclass
                           clus
vv                          SCN10A MUTATED SCN10A WILD-TYPE
  ASIAN                                  5               71
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                 18              150
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(660) Variable = CBLN3 MUTATION ANALYSIS
D660V1, survival
                 sevent
clus2               0   1
  CBLN3 MUTATED     2   2
  CBLN3 WILD-TYPE 179  78
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              4             257 
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              2              78 
$`CBLN3 MUTATED`
TCGA-BR-8368 TCGA-BR-A4QL TCGA-CG-5726 TCGA-D7-8576 
        4.31        11.57        28.96        14.66 

$`CBLN3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        18.21        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  CBLN3 MUTATED CBLN3 WILD-TYPE 
           4.31            0.00 
  CBLN3 MUTATED CBLN3 WILD-TYPE 
          28.96          105.07 
  CBLN3 MUTATED CBLN3 WILD-TYPE 
         13.115          12.620 
[1] "4.3 - 29.0 (13.1)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D660V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CBLN3 MUTATED         0        1        2        0         0         0
  CBLN3 WILD-TYPE       1        8       25       26        31        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CBLN3 MUTATED           0          0          2          0        0
  CBLN3 WILD-TYPE         3         49         34         24       24
D660V3, multiclass
            clus
vv           CBLN3 MUTATED CBLN3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              0              31
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             2              34
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CBLN3 MUTATED     1   2   2   0
  CBLN3 WILD-TYPE  10  70 120  75
D660V4, multiclass
    clus
vv   CBLN3 MUTATED CBLN3 WILD-TYPE
  T1             1              10
  T2             2              70
  T3             2             120
  T4             0              75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CBLN3 MUTATED    3  0  0  2
  CBLN3 WILD-TYPE 90 81 50 51
D660V5, multiclass
    clus
vv   CBLN3 MUTATED CBLN3 WILD-TYPE
  N0             3              90
  N1             0              81
  N2             0              50
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D660V6, binary
                 cls
clus                0   1
  CBLN3 MUTATED     5   0
  CBLN3 WILD-TYPE 252  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLN3 MUTATED      5    0
  CBLN3 WILD-TYPE  252   18
   clus
vv  CBLN3 MUTATED CBLN3 WILD-TYPE
  0             5             252
  1             0              18
[1] 2 2
[1] FALSE
D660V7, binary
                 cls
clus                0   1
  CBLN3 MUTATED     3   2
  CBLN3 WILD-TYPE 107 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLN3 MUTATED      3    2
  CBLN3 WILD-TYPE  107  177
        clus
vv       CBLN3 MUTATED CBLN3 WILD-TYPE
  FEMALE             3             107
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CBLN3 MUTATED                                       0
  CBLN3 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CBLN3 MUTATED                                                        2
  CBLN3 WILD-TYPE                                                    133
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CBLN3 MUTATED                                                                   2
  CBLN3 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CBLN3 MUTATED                                                  1
  CBLN3 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CBLN3 MUTATED                                                          0
  CBLN3 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CBLN3 MUTATED                                                           0
  CBLN3 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CBLN3 MUTATED                                          0
  CBLN3 WILD-TYPE                                        3
D660V8, multiclass
                                                                   clus
vv                                                                  CBLN3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  CBLN3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D660V9, binary
                 cls
clus                0   1
  CBLN3 MUTATED     0   5
  CBLN3 WILD-TYPE   5 279
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLN3 MUTATED      0    5
  CBLN3 WILD-TYPE    5  279
     clus
vv    CBLN3 MUTATED CBLN3 WILD-TYPE
  NO              0               5
  YES             5             279
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CBLN3 MUTATED     5   0   0   0
  CBLN3 WILD-TYPE 222  10  10  24
D660V10, multiclass
    clus
vv   CBLN3 MUTATED CBLN3 WILD-TYPE
  R0             5             222
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D660V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CBLN3 MUTATED       0                         0     3
  CBLN3 WILD-TYPE    76                         4   165
D660V12, multiclass
                           clus
vv                          CBLN3 MUTATED CBLN3 WILD-TYPE
  ASIAN                                 0              76
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(661) Variable = DGKD MUTATION ANALYSIS
D661V1, survival
                sevent
clus2              0   1
  DGKD MUTATED     4   2
  DGKD WILD-TYPE 177  78
  DGKD MUTATED DGKD WILD-TYPE 
             6            255 
  DGKD MUTATED DGKD WILD-TYPE 
             2             78 
$`DGKD MUTATED`
TCGA-BR-4201 TCGA-BR-8368 TCGA-BR-8487 TCGA-CD-8525 TCGA-HU-8602 TCGA-HU-A4GQ 
       30.90         4.31         1.12         0.07        11.41         0.10 

$`DGKD WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  DGKD MUTATED DGKD WILD-TYPE 
          0.07           0.00 
  DGKD MUTATED DGKD WILD-TYPE 
         30.90         105.07 
  DGKD MUTATED DGKD WILD-TYPE 
         2.715         12.760 
[1] "0.1 - 30.9 (2.7)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.7"
D661V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DGKD MUTATED         0        0        1        0         1         1
  DGKD WILD-TYPE       1        9       26       26        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DGKD MUTATED           0          1          0          1        0
  DGKD WILD-TYPE         3         48         36         23       24
D661V3, multiclass
            clus
vv           DGKD MUTATED DGKD WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            1             23
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DGKD MUTATED     0   2   2   2
  DGKD WILD-TYPE  11  70 120  73
D661V4, multiclass
    clus
vv   DGKD MUTATED DGKD WILD-TYPE
  T1            0             11
  T2            2             70
  T3            2            120
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  DGKD MUTATED    3  1  1  0
  DGKD WILD-TYPE 90 80 49 53
D661V5, multiclass
    clus
vv   DGKD MUTATED DGKD WILD-TYPE
  N0            3             90
  N1            1             80
  N2            1             49
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D661V6, binary
                cls
clus               0   1
  DGKD MUTATED     6   0
  DGKD WILD-TYPE 251  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKD MUTATED      6    0
  DGKD WILD-TYPE  251   18
   clus
vv  DGKD MUTATED DGKD WILD-TYPE
  0            6            251
  1            0             18
[1] 2 2
[1] FALSE
D661V7, binary
                cls
clus               0   1
  DGKD MUTATED     5   1
  DGKD WILD-TYPE 105 178
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKD MUTATED      5    1
  DGKD WILD-TYPE  105  178
        clus
vv       DGKD MUTATED DGKD WILD-TYPE
  FEMALE            5            105
  MALE              1            178
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DGKD MUTATED                                       1
  DGKD WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DGKD MUTATED                                                        3
  DGKD WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DGKD MUTATED                                                                   0
  DGKD WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DGKD MUTATED                                                  1
  DGKD WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DGKD MUTATED                                                          1
  DGKD WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DGKD MUTATED                                                           0
  DGKD WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DGKD MUTATED                                          0
  DGKD WILD-TYPE                                        3
D661V8, multiclass
                                                                   clus
vv                                                                  DGKD MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  DGKD WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D661V9, binary
                cls
clus               0   1
  DGKD MUTATED     0   6
  DGKD WILD-TYPE   5 278
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKD MUTATED      0    6
  DGKD WILD-TYPE    5  278
     clus
vv    DGKD MUTATED DGKD WILD-TYPE
  NO             0              5
  YES            6            278
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DGKD MUTATED     5   0   0   1
  DGKD WILD-TYPE 222  10  10  23
D661V10, multiclass
    clus
vv   DGKD MUTATED DGKD WILD-TYPE
  R0            5            222
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D661V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DGKD MUTATED       3                         0     3
  DGKD WILD-TYPE    73                         4   165
D661V12, multiclass
                           clus
vv                          DGKD MUTATED DGKD WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                3            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(662) Variable = MAGI2 MUTATION ANALYSIS
D662V1, survival
                 sevent
clus2               0   1
  MAGI2 MUTATED    14   7
  MAGI2 WILD-TYPE 167  73
  MAGI2 MUTATED MAGI2 WILD-TYPE 
             21             240 
  MAGI2 MUTATED MAGI2 WILD-TYPE 
              7              73 
$`MAGI2 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-8363 
        6.97        34.68        24.76        23.93        15.32         0.26 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-8535 TCGA-CD-A48A TCGA-CG-5721 
        9.21         1.12        15.81         0.13        12.43         6.02 
TCGA-D7-6822 TCGA-HJ-7597 TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       12.33        26.47         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-IN-7808 TCGA-IN-8663 
       10.19         3.45         3.39 

$`MAGI2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7715 
       30.90        31.20        32.94        12.82         9.21        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       28.01        18.15        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        20.55         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
        2.20        15.58         7.40         6.18        19.50        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        5.39        25.18        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         3.42         9.34        11.31        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.52         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IP-7968 
        9.67         8.88        27.42        21.21        18.81         2.53 

  MAGI2 MUTATED MAGI2 WILD-TYPE 
            0.1             0.0 
  MAGI2 MUTATED MAGI2 WILD-TYPE 
          34.68          105.07 
  MAGI2 MUTATED MAGI2 WILD-TYPE 
          8.980          12.805 
[1] "0.1 - 34.7 (9.0)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.5"
D662V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAGI2 MUTATED         0        1        4        1         6         3
  MAGI2 WILD-TYPE       1        8       23       25        25        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAGI2 MUTATED           1          3          0          4        3
  MAGI2 WILD-TYPE         2         46         36         20       21
D662V3, multiclass
            clus
vv           MAGI2 MUTATED MAGI2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               4              23
  STAGE II               1              25
  STAGE IIA              6              25
  STAGE IIB              3              41
  STAGE III              1               2
  STAGE IIIA             3              46
  STAGE IIIB             0              36
  STAGE IIIC             4              20
  STAGE IV               3              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MAGI2 MUTATED     1   7  11   7
  MAGI2 WILD-TYPE  10  65 111  68
D662V4, multiclass
    clus
vv   MAGI2 MUTATED MAGI2 WILD-TYPE
  T1             1              10
  T2             7              65
  T3            11             111
  T4             7              68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  MAGI2 MUTATED   10  9  5  3
  MAGI2 WILD-TYPE 83 72 45 50
D662V5, multiclass
    clus
vv   MAGI2 MUTATED MAGI2 WILD-TYPE
  N0            10              83
  N1             9              72
  N2             5              45
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D662V6, binary
                 cls
clus                0   1
  MAGI2 MUTATED    24   2
  MAGI2 WILD-TYPE 233  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAGI2 MUTATED     24    2
  MAGI2 WILD-TYPE  233   16
   clus
vv  MAGI2 MUTATED MAGI2 WILD-TYPE
  0            24             233
  1             2              16
[1] 2 2
[1] FALSE
D662V7, binary
                 cls
clus                0   1
  MAGI2 MUTATED    13  15
  MAGI2 WILD-TYPE  97 164
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAGI2 MUTATED     13   15
  MAGI2 WILD-TYPE   97  164
        clus
vv       MAGI2 MUTATED MAGI2 WILD-TYPE
  FEMALE            13              97
  MALE              15             164
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MAGI2 MUTATED                                       5
  MAGI2 WILD-TYPE                                    45
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MAGI2 MUTATED                                                       15
  MAGI2 WILD-TYPE                                                    120
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MAGI2 MUTATED                                                                   1
  MAGI2 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MAGI2 MUTATED                                                  4
  MAGI2 WILD-TYPE                                               34
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MAGI2 MUTATED                                                          1
  MAGI2 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MAGI2 MUTATED                                                           1
  MAGI2 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MAGI2 MUTATED                                          1
  MAGI2 WILD-TYPE                                        2
D662V8, multiclass
                                                                   clus
vv                                                                  MAGI2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       15
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  MAGI2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        120
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D662V9, binary
                 cls
clus                0   1
  MAGI2 MUTATED     1  27
  MAGI2 WILD-TYPE   4 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAGI2 MUTATED      1   27
  MAGI2 WILD-TYPE    4  257
     clus
vv    MAGI2 MUTATED MAGI2 WILD-TYPE
  NO              1               4
  YES            27             257
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MAGI2 MUTATED    21   0   0   5
  MAGI2 WILD-TYPE 206  10  10  19
D662V10, multiclass
    clus
vv   MAGI2 MUTATED MAGI2 WILD-TYPE
  R0            21             206
  R1             0              10
  R2             0              10
  RX             5              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D662V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAGI2 MUTATED       8                         0    17
  MAGI2 WILD-TYPE    68                         4   151
D662V12, multiclass
                           clus
vv                          MAGI2 MUTATED MAGI2 WILD-TYPE
  ASIAN                                 8              68
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                17             151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(663) Variable = FIGNL1 MUTATION ANALYSIS
D663V1, survival
                  sevent
clus2                0   1
  FIGNL1 MUTATED     6   2
  FIGNL1 WILD-TYPE 175  78
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
               8              253 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
               2               78 
$`FIGNL1 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6802 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8682 
       26.70         6.97        30.90        19.50         1.12        16.44 
TCGA-CD-A4MG TCGA-HU-8602 
        6.58        11.41 

$`FIGNL1 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        15.81         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        5.52        26.47         5.92        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
            1.12             0.00 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
           30.90           105.07 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
          13.925           12.620 
[1] "1.1 - 30.9 (13.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D663V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FIGNL1 MUTATED         0        0        0        0         2         3
  FIGNL1 WILD-TYPE       1        9       27       26        29        41
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FIGNL1 MUTATED           0          3          0          1        0
  FIGNL1 WILD-TYPE         3         46         36         23       24
D663V3, multiclass
            clus
vv           FIGNL1 MUTATED FIGNL1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               2               29
  STAGE IIB               3               41
  STAGE III               0                3
  STAGE IIIA              3               46
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FIGNL1 MUTATED     0   0   4   5
  FIGNL1 WILD-TYPE  11  72 118  70
D663V4, multiclass
    clus
vv   FIGNL1 MUTATED FIGNL1 WILD-TYPE
  T1              0               11
  T2              0               72
  T3              4              118
  T4              5               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  FIGNL1 MUTATED    6  1  2  0
  FIGNL1 WILD-TYPE 87 80 48 53
D663V5, multiclass
    clus
vv   FIGNL1 MUTATED FIGNL1 WILD-TYPE
  N0              6               87
  N1              1               80
  N2              2               48
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D663V6, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED     8   0
  FIGNL1 WILD-TYPE 249  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED      8    0
  FIGNL1 WILD-TYPE  249   18
   clus
vv  FIGNL1 MUTATED FIGNL1 WILD-TYPE
  0              8              249
  1              0               18
[1] 2 2
[1] FALSE
D663V7, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED     5   4
  FIGNL1 WILD-TYPE 105 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED      5    4
  FIGNL1 WILD-TYPE  105  175
        clus
vv       FIGNL1 MUTATED FIGNL1 WILD-TYPE
  FEMALE              5              105
  MALE                4              175
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FIGNL1 MUTATED                                       3
  FIGNL1 WILD-TYPE                                    47
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FIGNL1 MUTATED                                                        5
  FIGNL1 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FIGNL1 MUTATED                                                                   0
  FIGNL1 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FIGNL1 MUTATED                                                  0
  FIGNL1 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FIGNL1 MUTATED                                                          1
  FIGNL1 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FIGNL1 MUTATED                                                           0
  FIGNL1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FIGNL1 MUTATED                                          0
  FIGNL1 WILD-TYPE                                        3
D663V8, multiclass
                                                                   clus
vv                                                                  FIGNL1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  FIGNL1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D663V9, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED     0   9
  FIGNL1 WILD-TYPE   5 275
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED      0    9
  FIGNL1 WILD-TYPE    5  275
     clus
vv    FIGNL1 MUTATED FIGNL1 WILD-TYPE
  NO               0                5
  YES              9              275
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FIGNL1 MUTATED     6   0   0   2
  FIGNL1 WILD-TYPE 221  10  10  22
D663V10, multiclass
    clus
vv   FIGNL1 MUTATED FIGNL1 WILD-TYPE
  R0              6              221
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D663V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FIGNL1 MUTATED       3                         0     6
  FIGNL1 WILD-TYPE    73                         4   162
D663V12, multiclass
                           clus
vv                          FIGNL1 MUTATED FIGNL1 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(664) Variable = STK36 MUTATION ANALYSIS
D664V1, survival
                 sevent
clus2               0   1
  STK36 MUTATED     6   1
  STK36 WILD-TYPE 175  79
  STK36 MUTATED STK36 WILD-TYPE 
              7             254 
  STK36 MUTATED STK36 WILD-TYPE 
              1              79 
$`STK36 MUTATED`
TCGA-BR-6452 TCGA-BR-7851 TCGA-BR-8680 TCGA-CD-A486 TCGA-CG-5717 TCGA-CG-5721 
       34.68        12.43        15.81         3.42         6.97         6.02 
TCGA-FP-8099 
       17.06 

$`STK36 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         0.10         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       22.29        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  STK36 MUTATED STK36 WILD-TYPE 
           3.42            0.00 
  STK36 MUTATED STK36 WILD-TYPE 
          34.68          105.07 
  STK36 MUTATED STK36 WILD-TYPE 
          12.43           12.64 
[1] "3.4 - 34.7 (12.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.1"
D664V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  STK36 MUTATED         0        0        1        1         3         1
  STK36 WILD-TYPE       1        9       26       25        28        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STK36 MUTATED           0          0          0          0        3
  STK36 WILD-TYPE         3         49         36         24       21
D664V3, multiclass
            clus
vv           STK36 MUTATED STK36 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              3              28
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               3              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STK36 MUTATED     1   2   3   4
  STK36 WILD-TYPE  10  70 119  71
D664V4, multiclass
    clus
vv   STK36 MUTATED STK36 WILD-TYPE
  T1             1              10
  T2             2              70
  T3             3             119
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  STK36 MUTATED    5  2  2  0
  STK36 WILD-TYPE 88 79 48 53
D664V5, multiclass
    clus
vv   STK36 MUTATED STK36 WILD-TYPE
  N0             5              88
  N1             2              79
  N2             2              48
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D664V6, binary
                 cls
clus                0   1
  STK36 MUTATED     8   1
  STK36 WILD-TYPE 249  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK36 MUTATED      8    1
  STK36 WILD-TYPE  249   17
   clus
vv  STK36 MUTATED STK36 WILD-TYPE
  0             8             249
  1             1              17
[1] 2 2
[1] FALSE
D664V7, binary
                 cls
clus                0   1
  STK36 MUTATED     3   7
  STK36 WILD-TYPE 107 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK36 MUTATED      3    7
  STK36 WILD-TYPE  107  172
        clus
vv       STK36 MUTATED STK36 WILD-TYPE
  FEMALE             3             107
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  STK36 MUTATED                                       0
  STK36 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  STK36 MUTATED                                                        6
  STK36 WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  STK36 MUTATED                                                                   3
  STK36 WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  STK36 MUTATED                                                  1
  STK36 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  STK36 MUTATED                                                          0
  STK36 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  STK36 MUTATED                                                           0
  STK36 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  STK36 MUTATED                                          0
  STK36 WILD-TYPE                                        3
D664V8, multiclass
                                                                   clus
vv                                                                  STK36 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  STK36 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D664V9, binary
                 cls
clus                0   1
  STK36 MUTATED     0  10
  STK36 WILD-TYPE   5 274
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK36 MUTATED      0   10
  STK36 WILD-TYPE    5  274
     clus
vv    STK36 MUTATED STK36 WILD-TYPE
  NO              0               5
  YES            10             274
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  STK36 MUTATED     7   0   0   2
  STK36 WILD-TYPE 220  10  10  22
D664V10, multiclass
    clus
vv   STK36 MUTATED STK36 WILD-TYPE
  R0             7             220
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D664V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STK36 MUTATED       2                         0     5
  STK36 WILD-TYPE    74                         4   163
D664V12, multiclass
                           clus
vv                          STK36 MUTATED STK36 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(665) Variable = USP13 MUTATION ANALYSIS
D665V1, survival
                 sevent
clus2               0   1
  USP13 MUTATED     5   5
  USP13 WILD-TYPE 176  75
  USP13 MUTATED USP13 WILD-TYPE 
             10             251 
  USP13 MUTATED USP13 WILD-TYPE 
              5              75 
$`USP13 MUTATED`
TCGA-BR-4184 TCGA-BR-7723 TCGA-BR-8078 TCGA-BR-8382 TCGA-BR-8591 TCGA-CD-5801 
        6.97        28.73        12.26        15.85        13.45        13.18 
TCGA-CD-8527 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4469 
        0.07        15.95         1.02         7.07 

$`USP13 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        0.26         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        15.81         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        2.83         3.25        13.15         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 
       12.62        20.02         3.02        27.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 
       12.03         0.00         9.01        18.97        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  USP13 MUTATED USP13 WILD-TYPE 
           0.07            0.00 
  USP13 MUTATED USP13 WILD-TYPE 
          28.73          105.07 
  USP13 MUTATED USP13 WILD-TYPE 
          12.72           12.62 
[1] "0.1 - 28.7 (12.7)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.1"
D665V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  USP13 MUTATED         0        0        1        2         0         1
  USP13 WILD-TYPE       1        9       26       24        31        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  USP13 MUTATED           0          2          1          2        2
  USP13 WILD-TYPE         3         47         35         22       22
D665V3, multiclass
            clus
vv           USP13 MUTATED USP13 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               2              24
  STAGE IIA              0              31
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             1              35
  STAGE IIIC             2              22
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP13 MUTATED     0   3   5   3
  USP13 WILD-TYPE  11  69 117  72
D665V4, multiclass
    clus
vv   USP13 MUTATED USP13 WILD-TYPE
  T1             0              11
  T2             3              69
  T3             5             117
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  USP13 MUTATED    2  4  1  4
  USP13 WILD-TYPE 91 77 49 49
D665V5, multiclass
    clus
vv   USP13 MUTATED USP13 WILD-TYPE
  N0             2              91
  N1             4              77
  N2             1              49
  N3             4              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D665V6, binary
                 cls
clus                0   1
  USP13 MUTATED     9   1
  USP13 WILD-TYPE 248  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP13 MUTATED      9    1
  USP13 WILD-TYPE  248   17
   clus
vv  USP13 MUTATED USP13 WILD-TYPE
  0             9             248
  1             1              17
[1] 2 2
[1] FALSE
D665V7, binary
                 cls
clus                0   1
  USP13 MUTATED     3   8
  USP13 WILD-TYPE 107 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP13 MUTATED      3    8
  USP13 WILD-TYPE  107  171
        clus
vv       USP13 MUTATED USP13 WILD-TYPE
  FEMALE             3             107
  MALE               8             171
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  USP13 MUTATED                                       0
  USP13 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  USP13 MUTATED                                                        8
  USP13 WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  USP13 MUTATED                                                                   3
  USP13 WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  USP13 MUTATED                                                  0
  USP13 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  USP13 MUTATED                                                          0
  USP13 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  USP13 MUTATED                                                           0
  USP13 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  USP13 MUTATED                                          0
  USP13 WILD-TYPE                                        3
D665V8, multiclass
                                                                   clus
vv                                                                  USP13 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  USP13 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D665V9, binary
                 cls
clus                0   1
  USP13 MUTATED     0  11
  USP13 WILD-TYPE   5 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP13 MUTATED      0   11
  USP13 WILD-TYPE    5  273
     clus
vv    USP13 MUTATED USP13 WILD-TYPE
  NO              0               5
  YES            11             273
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USP13 MUTATED     8   1   1   1
  USP13 WILD-TYPE 219   9   9  23
D665V10, multiclass
    clus
vv   USP13 MUTATED USP13 WILD-TYPE
  R0             8             219
  R1             1               9
  R2             1               9
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D665V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  USP13 MUTATED       2                         0     5
  USP13 WILD-TYPE    74                         4   163
D665V12, multiclass
                           clus
vv                          USP13 MUTATED USP13 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(666) Variable = CALCRL MUTATION ANALYSIS
D666V1, survival
                  sevent
clus2                0   1
  CALCRL MUTATED     4   3
  CALCRL WILD-TYPE 177  77
  CALCRL MUTATED CALCRL WILD-TYPE 
               7              254 
  CALCRL MUTATED CALCRL WILD-TYPE 
               3               77 
$`CALCRL MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8683 TCGA-CG-4305 
       26.70         6.97        19.50        14.04         9.86        15.95 
TCGA-CG-5724 
       12.03 

$`CALCRL WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
        7.53         0.49        11.54        15.81        16.44        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 
        1.02         0.99         6.02         0.99       105.07        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  CALCRL MUTATED CALCRL WILD-TYPE 
            6.97             0.00 
  CALCRL MUTATED CALCRL WILD-TYPE 
           26.70           105.07 
  CALCRL MUTATED CALCRL WILD-TYPE 
          14.040           12.605 
[1] "7.0 - 26.7 (14.0)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D666V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CALCRL MUTATED         0        0        0        1         0         1
  CALCRL WILD-TYPE       1        9       27       25        31        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CALCRL MUTATED           0          1          2          1        1
  CALCRL WILD-TYPE         3         48         34         23       23
D666V3, multiclass
            clus
vv           CALCRL MUTATED CALCRL WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                1               25
  STAGE IIA               0               31
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              2               34
  STAGE IIIC              1               23
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CALCRL MUTATED     0   1   4   3
  CALCRL WILD-TYPE  11  71 118  72
D666V4, multiclass
    clus
vv   CALCRL MUTATED CALCRL WILD-TYPE
  T1              0               11
  T2              1               71
  T3              4              118
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CALCRL MUTATED    1  2  2  2
  CALCRL WILD-TYPE 92 79 48 51
D666V5, multiclass
    clus
vv   CALCRL MUTATED CALCRL WILD-TYPE
  N0              1               92
  N1              2               79
  N2              2               48
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D666V6, binary
                  cls
clus                 0   1
  CALCRL MUTATED     5   1
  CALCRL WILD-TYPE 252  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CALCRL MUTATED      5    1
  CALCRL WILD-TYPE  252   17
   clus
vv  CALCRL MUTATED CALCRL WILD-TYPE
  0              5              252
  1              1               17
[1] 2 2
[1] FALSE
D666V7, binary
                  cls
clus                 0   1
  CALCRL MUTATED     4   4
  CALCRL WILD-TYPE 106 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CALCRL MUTATED      4    4
  CALCRL WILD-TYPE  106  175
        clus
vv       CALCRL MUTATED CALCRL WILD-TYPE
  FEMALE              4              106
  MALE                4              175
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CALCRL MUTATED                                       2
  CALCRL WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CALCRL MUTATED                                                        5
  CALCRL WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CALCRL MUTATED                                                                   0
  CALCRL WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CALCRL MUTATED                                                  1
  CALCRL WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CALCRL MUTATED                                                          0
  CALCRL WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CALCRL MUTATED                                                           0
  CALCRL WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CALCRL MUTATED                                          0
  CALCRL WILD-TYPE                                        3
D666V8, multiclass
                                                                   clus
vv                                                                  CALCRL MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  CALCRL WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D666V9, binary
                  cls
clus                 0   1
  CALCRL MUTATED     0   8
  CALCRL WILD-TYPE   5 276
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CALCRL MUTATED      0    8
  CALCRL WILD-TYPE    5  276
     clus
vv    CALCRL MUTATED CALCRL WILD-TYPE
  NO               0                5
  YES              8              276
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CALCRL MUTATED     5   0   1   2
  CALCRL WILD-TYPE 222  10   9  22
D666V10, multiclass
    clus
vv   CALCRL MUTATED CALCRL WILD-TYPE
  R0              5              222
  R1              0               10
  R2              1                9
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D666V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CALCRL MUTATED       1                         0     5
  CALCRL WILD-TYPE    75                         4   163
D666V12, multiclass
                           clus
vv                          CALCRL MUTATED CALCRL WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  5              163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(667) Variable = AFP MUTATION ANALYSIS
D667V1, survival
               sevent
clus2             0   1
  AFP MUTATED     2   1
  AFP WILD-TYPE 179  79
  AFP MUTATED AFP WILD-TYPE 
            3           258 
  AFP MUTATED AFP WILD-TYPE 
            1            79 
$`AFP MUTATED`
TCGA-BR-4184 TCGA-BR-7851 TCGA-CD-A4MI 
        6.97        12.43         0.10 

$`AFP WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  AFP MUTATED AFP WILD-TYPE 
          0.1           0.0 
  AFP MUTATED AFP WILD-TYPE 
        12.43        105.07 
  AFP MUTATED AFP WILD-TYPE 
         6.97         12.71 
[1] "0.1 - 12.4 (7.0)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "2.6"
D667V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AFP MUTATED         0        0        0        0         0         1
  AFP WILD-TYPE       1        9       27       26        31        43
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AFP MUTATED           0          1          1          0        0
  AFP WILD-TYPE         3         48         35         24       24
D667V3, multiclass
            clus
vv           AFP MUTATED AFP WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             9
  STAGE IB             0            27
  STAGE II             0            26
  STAGE IIA            0            31
  STAGE IIB            1            43
  STAGE III            0             3
  STAGE IIIA           1            48
  STAGE IIIB           1            35
  STAGE IIIC           0            24
  STAGE IV             0            24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  AFP MUTATED     0   0   2   1
  AFP WILD-TYPE  11  72 120  74
D667V4, multiclass
    clus
vv   AFP MUTATED AFP WILD-TYPE
  T1           0            11
  T2           0            72
  T3           2           120
  T4           1            74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  AFP MUTATED    1  2  0  0
  AFP WILD-TYPE 92 79 50 53
D667V5, multiclass
    clus
vv   AFP MUTATED AFP WILD-TYPE
  N0           1            92
  N1           2            79
  N2           0            50
  N3           0            53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D667V6, binary
               cls
clus              0   1
  AFP MUTATED     2   0
  AFP WILD-TYPE 255  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  AFP MUTATED      2    0
  AFP WILD-TYPE  255   18
   clus
vv  AFP MUTATED AFP WILD-TYPE
  0           2           255
  1           0            18
[1] 2 2
[1] FALSE
D667V7, binary
               cls
clus              0   1
  AFP MUTATED     0   3
  AFP WILD-TYPE 110 176
[1] "tbl2"
               cls
clus            [,1] [,2]
  AFP MUTATED      0    3
  AFP WILD-TYPE  110  176
        clus
vv       AFP MUTATED AFP WILD-TYPE
  FEMALE           0           110
  MALE             3           176
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AFP MUTATED                                       0
  AFP WILD-TYPE                                    50
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AFP MUTATED                                                        2
  AFP WILD-TYPE                                                    133
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AFP MUTATED                                                                   1
  AFP WILD-TYPE                                                                39
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AFP MUTATED                                                  0
  AFP WILD-TYPE                                               38
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AFP MUTATED                                                          0
  AFP WILD-TYPE                                                       16
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AFP MUTATED                                                           0
  AFP WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AFP MUTATED                                          0
  AFP WILD-TYPE                                        3
D667V8, multiclass
                                                                   clus
vv                                                                  AFP MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  AFP WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D667V9, binary
               cls
clus              0   1
  AFP MUTATED     0   3
  AFP WILD-TYPE   5 281
[1] "tbl2"
               cls
clus            [,1] [,2]
  AFP MUTATED      0    3
  AFP WILD-TYPE    5  281
     clus
vv    AFP MUTATED AFP WILD-TYPE
  NO            0             5
  YES           3           281
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  AFP MUTATED     1   0   0   1
  AFP WILD-TYPE 226  10  10  23
D667V10, multiclass
[1] "Remove cluster labels:" "AFP MUTATED"           
clus
  AFP MUTATED AFP WILD-TYPE 
            2           269 
   TCGA-B7-5816    TCGA-B7-5818    TCGA-BR-4183    TCGA-BR-4187    TCGA-BR-4188 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-4191    TCGA-BR-4201    TCGA-BR-4253    TCGA-BR-4255    TCGA-BR-4256 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-4257    TCGA-BR-4267    TCGA-BR-4279    TCGA-BR-4280    TCGA-BR-4292 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-4294    TCGA-BR-4357    TCGA-BR-4361    TCGA-BR-4362    TCGA-BR-4363 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-4366    TCGA-BR-4368    TCGA-BR-4369    TCGA-BR-4370    TCGA-BR-4371 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-6452    TCGA-BR-6453    TCGA-BR-6454    TCGA-BR-6455    TCGA-BR-6456 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-6457    TCGA-BR-6458    TCGA-BR-6563    TCGA-BR-6564    TCGA-BR-6565 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-6566    TCGA-BR-6705    TCGA-BR-6706    TCGA-BR-6707    TCGA-BR-6710 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-6801    TCGA-BR-6802    TCGA-BR-6803    TCGA-BR-6852    TCGA-BR-7196 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-7197    TCGA-BR-7703    TCGA-BR-7707    TCGA-BR-7715    TCGA-BR-7716 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-7717    TCGA-BR-7722    TCGA-BR-7723    TCGA-BR-7901    TCGA-BR-7957 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-7958    TCGA-BR-7959    TCGA-BR-8058    TCGA-BR-8059    TCGA-BR-8077 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8078    TCGA-BR-8080    TCGA-BR-8081    TCGA-BR-8284    TCGA-BR-8286 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8289    TCGA-BR-8291    TCGA-BR-8295    TCGA-BR-8296    TCGA-BR-8297 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8360    TCGA-BR-8361    TCGA-BR-8363    TCGA-BR-8364    TCGA-BR-8365 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8366    TCGA-BR-8367    TCGA-BR-8368    TCGA-BR-8369    TCGA-BR-8370 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8371    TCGA-BR-8372    TCGA-BR-8373    TCGA-BR-8380    TCGA-BR-8381 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8382    TCGA-BR-8384    TCGA-BR-8483    TCGA-BR-8484    TCGA-BR-8485 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8486    TCGA-BR-8487    TCGA-BR-8588    TCGA-BR-8589    TCGA-BR-8590 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8591    TCGA-BR-8592    TCGA-BR-8676    TCGA-BR-8677    TCGA-BR-8678 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8679    TCGA-BR-8680    TCGA-BR-8682    TCGA-BR-8683    TCGA-BR-8686 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8687    TCGA-BR-8690    TCGA-BR-A44T    TCGA-BR-A44U    TCGA-BR-A452 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-A453    TCGA-BR-A4CQ    TCGA-BR-A4CR    TCGA-BR-A4CS    TCGA-BR-A4IU 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-A4IV    TCGA-BR-A4IY    TCGA-BR-A4IZ    TCGA-BR-A4J1    TCGA-BR-A4J2 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-A4J4    TCGA-BR-A4J6    TCGA-BR-A4J7    TCGA-BR-A4J8    TCGA-BR-A4PD 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-A4PE    TCGA-BR-A4PF    TCGA-BR-A4QI    TCGA-BR-A4QL    TCGA-BR-A4QM 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CD-5800    TCGA-CD-5801    TCGA-CD-5804    TCGA-CD-8524    TCGA-CD-8525 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CD-8526    TCGA-CD-8527    TCGA-CD-8528    TCGA-CD-8529    TCGA-CD-8530 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CD-8531    TCGA-CD-8532    TCGA-CD-8534    TCGA-CD-8535    TCGA-CD-8536 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CD-A487    TCGA-CG-4300    TCGA-CG-4301    TCGA-CG-4304    TCGA-CG-4305 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-4306    TCGA-CG-4436    TCGA-CG-4437    TCGA-CG-4438    TCGA-CG-4440 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-4441    TCGA-CG-4442    TCGA-CG-4443    TCGA-CG-4444    TCGA-CG-4449 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-4455    TCGA-CG-4462    TCGA-CG-4465    TCGA-CG-4466    TCGA-CG-4469 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-4474    TCGA-CG-4475    TCGA-CG-4476    TCGA-CG-4477    TCGA-CG-5717 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-5718    TCGA-CG-5719    TCGA-CG-5720    TCGA-CG-5721    TCGA-CG-5722 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-5723    TCGA-CG-5724    TCGA-CG-5726    TCGA-CG-5727    TCGA-CG-5728 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-5730    TCGA-CG-5732    TCGA-CG-5733    TCGA-CG-5734    TCGA-D7-5577 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-5578    TCGA-D7-5579    TCGA-D7-6518    TCGA-D7-6519    TCGA-D7-6520 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-6521    TCGA-D7-6522    TCGA-D7-6524    TCGA-D7-6525    TCGA-D7-6526 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-6527    TCGA-D7-6528    TCGA-D7-6815    TCGA-D7-6817    TCGA-D7-6818 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-6820    TCGA-D7-6822    TCGA-D7-8570    TCGA-D7-8572    TCGA-D7-8573 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-8574    TCGA-D7-8575    TCGA-D7-8576    TCGA-D7-8578    TCGA-D7-8579 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-A4YT    TCGA-D7-A4YU    TCGA-D7-A4YV    TCGA-D7-A4YX    TCGA-D7-A4YY 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-A4Z0    TCGA-EQ-5647    TCGA-EQ-A4SO    TCGA-F1-6177    TCGA-F1-6874 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-F1-6875    TCGA-F1-A448    TCGA-FP-7735    TCGA-FP-7829    TCGA-FP-7998 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-FP-8099    TCGA-FP-8209    TCGA-FP-8211    TCGA-FP-8631    TCGA-FP-A4BE 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-FP-A4BF    TCGA-HF-7132    TCGA-HF-7133    TCGA-HF-7136    TCGA-HJ-7597 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-8243    TCGA-HU-8245    TCGA-HU-8249    TCGA-HU-8602    TCGA-HU-8604 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-8608    TCGA-HU-8610    TCGA-HU-A4G2    TCGA-HU-A4G3    TCGA-HU-A4G6 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-A4G9    TCGA-HU-A4GC    TCGA-HU-A4GD    TCGA-HU-A4GF    TCGA-HU-A4GH 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-A4GN    TCGA-HU-A4GP    TCGA-HU-A4GQ    TCGA-HU-A4GT    TCGA-HU-A4GU 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-A4GX    TCGA-HU-A4GY    TCGA-HU-A4H0    TCGA-HU-A4H2    TCGA-HU-A4H3 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-A4H4    TCGA-HU-A4H5    TCGA-HU-A4H6    TCGA-HU-A4H8    TCGA-HU-A4HD 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-IN-7806    TCGA-IN-8462    TCGA-IN-8663    TCGA-IP-7968 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
D667V11, continuous
[1] "Remove cluster labels:" "AFP MUTATED"           
clus
  AFP MUTATED AFP WILD-TYPE 
            2           249 
   TCGA-B7-5816    TCGA-BR-4183    TCGA-BR-4188    TCGA-BR-4191    TCGA-BR-4253 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-4255    TCGA-BR-4256    TCGA-BR-4267    TCGA-BR-4279    TCGA-BR-4280 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-4361    TCGA-BR-4362    TCGA-BR-4368    TCGA-BR-6452    TCGA-BR-6453 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-6454    TCGA-BR-6455    TCGA-BR-6456    TCGA-BR-6457    TCGA-BR-6458 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-6563    TCGA-BR-6564    TCGA-BR-6565    TCGA-BR-6566    TCGA-BR-6705 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-6706    TCGA-BR-6707    TCGA-BR-6710    TCGA-BR-6801    TCGA-BR-6802 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-6803    TCGA-BR-6852    TCGA-BR-7196    TCGA-BR-7197    TCGA-BR-7703 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-7707    TCGA-BR-7715    TCGA-BR-7716    TCGA-BR-7717    TCGA-BR-7722 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-7723    TCGA-BR-7901    TCGA-BR-7957    TCGA-BR-7958    TCGA-BR-7959 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8058    TCGA-BR-8059    TCGA-BR-8077    TCGA-BR-8078    TCGA-BR-8080 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8081    TCGA-BR-8284    TCGA-BR-8286    TCGA-BR-8289    TCGA-BR-8291 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8295    TCGA-BR-8296    TCGA-BR-8297    TCGA-BR-8360    TCGA-BR-8361 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8363    TCGA-BR-8364    TCGA-BR-8365    TCGA-BR-8366    TCGA-BR-8367 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8368    TCGA-BR-8369    TCGA-BR-8370    TCGA-BR-8371    TCGA-BR-8372 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8373    TCGA-BR-8380    TCGA-BR-8381    TCGA-BR-8382    TCGA-BR-8384 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8483    TCGA-BR-8484    TCGA-BR-8485    TCGA-BR-8486    TCGA-BR-8487 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8588    TCGA-BR-8589    TCGA-BR-8590    TCGA-BR-8591    TCGA-BR-8592 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8676    TCGA-BR-8677    TCGA-BR-8678    TCGA-BR-8679    TCGA-BR-8680 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8682    TCGA-BR-8683    TCGA-BR-8686    TCGA-BR-8687    TCGA-BR-8690 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-A44T    TCGA-BR-A44U    TCGA-BR-A452    TCGA-BR-A453    TCGA-BR-A4CQ 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-A4CR    TCGA-BR-A4CS    TCGA-BR-A4IU    TCGA-BR-A4IV    TCGA-BR-A4IY 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-A4IZ    TCGA-BR-A4J1    TCGA-BR-A4J2    TCGA-BR-A4J4    TCGA-BR-A4J6 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-A4J8    TCGA-BR-A4PD    TCGA-BR-A4PE    TCGA-BR-A4PF    TCGA-BR-A4QI 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-A4QL    TCGA-BR-A4QM    TCGA-CD-5804    TCGA-CD-8525    TCGA-CD-8526 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CD-8531    TCGA-CD-8535    TCGA-CD-A487    TCGA-CG-4301    TCGA-CG-4304 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-4305    TCGA-CG-4436    TCGA-CG-4437    TCGA-CG-4438    TCGA-CG-4440 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-4441    TCGA-CG-4442    TCGA-CG-4443    TCGA-CG-4444    TCGA-CG-4449 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-4455    TCGA-CG-4462    TCGA-CG-4465    TCGA-CG-4466    TCGA-CG-4469 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-4474    TCGA-CG-4475    TCGA-CG-4476    TCGA-CG-4477    TCGA-CG-5717 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-5718    TCGA-CG-5719    TCGA-CG-5720    TCGA-CG-5721    TCGA-CG-5722 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-5723    TCGA-CG-5724    TCGA-CG-5726    TCGA-CG-5727    TCGA-CG-5728 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-5730    TCGA-CG-5732    TCGA-CG-5733    TCGA-CG-5734    TCGA-D7-5577 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-5578    TCGA-D7-5579    TCGA-D7-6518    TCGA-D7-6519    TCGA-D7-6520 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-6521    TCGA-D7-6522    TCGA-D7-6524    TCGA-D7-6525    TCGA-D7-6526 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-6527    TCGA-D7-6528    TCGA-D7-6815    TCGA-D7-6817    TCGA-D7-6818 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-6820    TCGA-D7-6822    TCGA-D7-8570    TCGA-D7-8572    TCGA-D7-8573 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-8574    TCGA-D7-8575    TCGA-D7-8576    TCGA-D7-8578    TCGA-D7-8579 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-A4YT    TCGA-D7-A4YU    TCGA-D7-A4YV    TCGA-D7-A4YX    TCGA-D7-A4YY 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-A4Z0    TCGA-EQ-5647    TCGA-EQ-8122    TCGA-EQ-A4SO    TCGA-F1-6177 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-F1-6874    TCGA-F1-6875    TCGA-F1-A448    TCGA-FP-7735    TCGA-FP-7829 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-FP-7916    TCGA-FP-7998    TCGA-FP-8099    TCGA-FP-8209    TCGA-FP-8210 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-FP-8211    TCGA-FP-8631    TCGA-FP-A4BE    TCGA-FP-A4BF    TCGA-HF-7132 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HF-7133    TCGA-HF-7136    TCGA-HJ-7597    TCGA-HU-8243    TCGA-HU-8245 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-8249    TCGA-HU-8602    TCGA-HU-8604    TCGA-HU-8608    TCGA-HU-8610 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-A4G2    TCGA-HU-A4G3    TCGA-HU-A4G6    TCGA-HU-A4G8    TCGA-HU-A4G9 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-A4GC    TCGA-HU-A4GD    TCGA-HU-A4GF    TCGA-HU-A4GH    TCGA-HU-A4GN 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-A4GP    TCGA-HU-A4GQ    TCGA-HU-A4GT    TCGA-HU-A4GU    TCGA-HU-A4GX 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-A4GY    TCGA-HU-A4H0    TCGA-HU-A4H2    TCGA-HU-A4H3    TCGA-HU-A4H4 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-A4H5    TCGA-HU-A4H6    TCGA-HU-A4H8    TCGA-HU-A4HD    TCGA-IN-7806 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-IN-7808    TCGA-IN-8462    TCGA-IN-8663    TCGA-IP-7968 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AFP MUTATED       1                         0     2
  AFP WILD-TYPE    75                         4   166
D667V12, multiclass
                           clus
vv                          AFP MUTATED AFP WILD-TYPE
  ASIAN                               1            75
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                               2           166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(668) Variable = DISP2 MUTATION ANALYSIS
D668V1, survival
                 sevent
clus2               0   1
  DISP2 MUTATED    12   2
  DISP2 WILD-TYPE 169  78
  DISP2 MUTATED DISP2 WILD-TYPE 
             14             247 
  DISP2 MUTATED DISP2 WILD-TYPE 
              2              78 
$`DISP2 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7851 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8487 
       34.68        32.94        12.43        19.50         0.26         1.12 
TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-A4MJ TCGA-CG-4437 TCGA-CG-5733 TCGA-FP-8099 
       13.45        11.57        12.62         8.05        21.07        17.06 
TCGA-FP-A4BE TCGA-HU-A4G3 
       11.08         5.59 

$`DISP2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       15.81         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 
       12.43        11.61         6.58        12.20         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       14.07        22.29        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 
       12.10        10.62         0.76        24.30        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  DISP2 MUTATED DISP2 WILD-TYPE 
           0.26            0.00 
  DISP2 MUTATED DISP2 WILD-TYPE 
          34.68          105.07 
  DISP2 MUTATED DISP2 WILD-TYPE 
         12.525          12.660 
[1] "0.3 - 34.7 (12.5)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "2.3"
D668V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DISP2 MUTATED         0        0        2        1         5         2
  DISP2 WILD-TYPE       1        9       25       25        26        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DISP2 MUTATED           0          1          1          2        1
  DISP2 WILD-TYPE         3         48         35         22       23
D668V3, multiclass
            clus
vv           DISP2 MUTATED DISP2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               1              25
  STAGE IIA              5              26
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             2              22
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DISP2 MUTATED     0   5   6   4
  DISP2 WILD-TYPE  11  67 116  71
D668V4, multiclass
    clus
vv   DISP2 MUTATED DISP2 WILD-TYPE
  T1             0              11
  T2             5              67
  T3             6             116
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  DISP2 MUTATED    8  1  4  2
  DISP2 WILD-TYPE 85 80 46 51
D668V5, multiclass
    clus
vv   DISP2 MUTATED DISP2 WILD-TYPE
  N0             8              85
  N1             1              80
  N2             4              46
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D668V6, binary
                 cls
clus                0   1
  DISP2 MUTATED    14   0
  DISP2 WILD-TYPE 243  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DISP2 MUTATED     14    0
  DISP2 WILD-TYPE  243   18
   clus
vv  DISP2 MUTATED DISP2 WILD-TYPE
  0            14             243
  1             0              18
[1] 2 2
[1] FALSE
D668V7, binary
                 cls
clus                0   1
  DISP2 MUTATED     8   7
  DISP2 WILD-TYPE 102 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DISP2 MUTATED      8    7
  DISP2 WILD-TYPE  102  172
        clus
vv       DISP2 MUTATED DISP2 WILD-TYPE
  FEMALE             8             102
  MALE               7             172
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DISP2 MUTATED                                       0
  DISP2 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DISP2 MUTATED                                                       11
  DISP2 WILD-TYPE                                                    124
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DISP2 MUTATED                                                                   3
  DISP2 WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DISP2 MUTATED                                                  1
  DISP2 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DISP2 MUTATED                                                          0
  DISP2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DISP2 MUTATED                                                           0
  DISP2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DISP2 MUTATED                                          0
  DISP2 WILD-TYPE                                        3
D668V8, multiclass
                                                                   clus
vv                                                                  DISP2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  DISP2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D668V9, binary
                 cls
clus                0   1
  DISP2 MUTATED     0  15
  DISP2 WILD-TYPE   5 269
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DISP2 MUTATED      0   15
  DISP2 WILD-TYPE    5  269
     clus
vv    DISP2 MUTATED DISP2 WILD-TYPE
  NO              0               5
  YES            15             269
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  DISP2 MUTATED    13   0   0   1
  DISP2 WILD-TYPE 214  10  10  23
D668V10, multiclass
    clus
vv   DISP2 MUTATED DISP2 WILD-TYPE
  R0            13             214
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D668V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DISP2 MUTATED       2                         1    10
  DISP2 WILD-TYPE    74                         3   158
D668V12, multiclass
                           clus
vv                          DISP2 MUTATED DISP2 WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                10             158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(669) Variable = MGA MUTATION ANALYSIS
D669V1, survival
               sevent
clus2             0   1
  MGA MUTATED    17   7
  MGA WILD-TYPE 164  73
  MGA MUTATED MGA WILD-TYPE 
           24           237 
  MGA MUTATED MGA WILD-TYPE 
            7            73 
$`MGA MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8360 
       11.70         6.97        30.90        34.68        32.94         6.18 
TCGA-BR-8361 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-5801 TCGA-CD-8531 
       19.50        15.81        13.45        15.81        13.18         0.10 
TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-A4YY TCGA-F1-6874 
        9.01        30.97         6.02        28.96        13.78        14.47 
TCGA-F1-A448 TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-A4GQ TCGA-HU-A4H3 TCGA-HU-A4H8 
       21.27        11.08        26.47         0.10        19.36         8.88 

$`MGA WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 
       26.70         6.61         4.64         7.43        18.35         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       12.82         9.21        24.76        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        20.55         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20        15.58         7.40         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 
       25.18         9.21        20.22         1.12        12.79         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.15         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.13         0.16         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
       29.98        47.05        19.07        12.03         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        22.98         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       16.44         5.92        15.16        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       16.24        72.23         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        12.30         9.67        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  MGA MUTATED MGA WILD-TYPE 
          0.1           0.0 
  MGA MUTATED MGA WILD-TYPE 
        34.68        105.07 
  MGA MUTATED MGA WILD-TYPE 
       14.125        12.430 
[1] "0.1 - 34.7 (14.1)"  "0.0 - 105.1 (12.4)"
[1] "hr=" "1.3"
D669V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MGA MUTATED         0        1        5        0         4         0
  MGA WILD-TYPE       1        8       22       26        27        44
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MGA MUTATED           0          3          3          4        3
  MGA WILD-TYPE         3         46         33         20       21
D669V3, multiclass
            clus
vv           MGA MUTATED MGA WILD-TYPE
  STAGE I              0             1
  STAGE IA             1             8
  STAGE IB             5            22
  STAGE II             0            26
  STAGE IIA            4            27
  STAGE IIB            0            44
  STAGE III            0             3
  STAGE IIIA           3            46
  STAGE IIIB           3            33
  STAGE IIIC           4            20
  STAGE IV             3            21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MGA MUTATED     2   5   9   8
  MGA WILD-TYPE   9  67 113  67
D669V4, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  T1           2             9
  T2           5            67
  T3           9           113
  T4           8            67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  MGA MUTATED    9  7  3  5
  MGA WILD-TYPE 84 74 47 48
D669V5, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  N0           9            84
  N1           7            74
  N2           3            47
  N3           5            48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D669V6, binary
               cls
clus              0   1
  MGA MUTATED    21   2
  MGA WILD-TYPE 236  16
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     21    2
  MGA WILD-TYPE  236   16
   clus
vv  MGA MUTATED MGA WILD-TYPE
  0          21           236
  1           2            16
[1] 2 2
[1] FALSE
D669V7, binary
               cls
clus              0   1
  MGA MUTATED    10  15
  MGA WILD-TYPE 100 164
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     10   15
  MGA WILD-TYPE  100  164
        clus
vv       MGA MUTATED MGA WILD-TYPE
  FEMALE          10           100
  MALE            15           164
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MGA MUTATED                                       4
  MGA WILD-TYPE                                    46
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MGA MUTATED                                                       11
  MGA WILD-TYPE                                                    124
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MGA MUTATED                                                                   5
  MGA WILD-TYPE                                                                35
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MGA MUTATED                                                  3
  MGA WILD-TYPE                                               35
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MGA MUTATED                                                          1
  MGA WILD-TYPE                                                       15
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MGA MUTATED                                                           0
  MGA WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MGA MUTATED                                          1
  MGA WILD-TYPE                                        2
D669V8, multiclass
                                                                   clus
vv                                                                  MGA MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                     11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    1
                                                                   clus
vv                                                                  MGA WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D669V9, binary
               cls
clus              0   1
  MGA MUTATED     0  25
  MGA WILD-TYPE   5 259
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED      0   25
  MGA WILD-TYPE    5  259
     clus
vv    MGA MUTATED MGA WILD-TYPE
  NO            0             5
  YES          25           259
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  MGA MUTATED    21   0   1   3
  MGA WILD-TYPE 206  10   9  21
D669V10, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  R0          21           206
  R1           0            10
  R2           1             9
  RX           3            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D669V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MGA MUTATED       6                         1    14
  MGA WILD-TYPE    70                         3   154
D669V12, multiclass
                           clus
vv                          MGA MUTATED MGA WILD-TYPE
  ASIAN                               6            70
  BLACK OR AFRICAN AMERICAN           1             3
  WHITE                              14           154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(670) Variable = PPP1R12C MUTATION ANALYSIS
D670V1, survival
                    sevent
clus2                  0   1
  PPP1R12C MUTATED     5   0
  PPP1R12C WILD-TYPE 176  80
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
                 5                256 
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
                 0                 80 
$`PPP1R12C MUTATED`
TCGA-BR-7703 TCGA-BR-7851 TCGA-BR-8487 TCGA-BR-8680 TCGA-HU-A4G8 
       24.76        12.43         1.12        15.81        11.84 

$`PPP1R12C WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
              1.12               0.00 
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
             24.76             105.07 
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
             12.43              12.64 
[1] "1.1 - 24.8 (12.4)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "9200000"
D670V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPP1R12C MUTATED         0        1        0        0         1         2
  PPP1R12C WILD-TYPE       1        8       27       26        30        42
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP1R12C MUTATED           0          0          0          0        1
  PPP1R12C WILD-TYPE         3         49         36         24       23
D670V3, multiclass
            clus
vv           PPP1R12C MUTATED PPP1R12C WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  1                  8
  STAGE IB                  0                 27
  STAGE II                  0                 26
  STAGE IIA                 1                 30
  STAGE IIB                 2                 42
  STAGE III                 0                  3
  STAGE IIIA                0                 49
  STAGE IIIB                0                 36
  STAGE IIIC                0                 24
  STAGE IV                  1                 23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  PPP1R12C MUTATED     1   0   2   2
  PPP1R12C WILD-TYPE  10  72 120  73
D670V4, multiclass
    clus
vv   PPP1R12C MUTATED PPP1R12C WILD-TYPE
  T1                1                 10
  T2                0                 72
  T3                2                120
  T4                2                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  PPP1R12C MUTATED    3  1  1  0
  PPP1R12C WILD-TYPE 90 80 49 53
D670V5, multiclass
    clus
vv   PPP1R12C MUTATED PPP1R12C WILD-TYPE
  N0                3                 90
  N1                1                 80
  N2                1                 49
  N3                0                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D670V6, binary
                    cls
clus                   0   1
  PPP1R12C MUTATED     4   1
  PPP1R12C WILD-TYPE 253  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12C MUTATED      4    1
  PPP1R12C WILD-TYPE  253   17
   clus
vv  PPP1R12C MUTATED PPP1R12C WILD-TYPE
  0                4                253
  1                1                 17
[1] 2 2
[1] FALSE
D670V7, binary
                    cls
clus                   0   1
  PPP1R12C MUTATED     2   3
  PPP1R12C WILD-TYPE 108 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12C MUTATED      2    3
  PPP1R12C WILD-TYPE  108  176
        clus
vv       PPP1R12C MUTATED PPP1R12C WILD-TYPE
  FEMALE                2                108
  MALE                  3                176
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PPP1R12C MUTATED                                       1
  PPP1R12C WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PPP1R12C MUTATED                                                        1
  PPP1R12C WILD-TYPE                                                    134
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PPP1R12C MUTATED                                                                   1
  PPP1R12C WILD-TYPE                                                                39
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PPP1R12C MUTATED                                                  1
  PPP1R12C WILD-TYPE                                               37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PPP1R12C MUTATED                                                          0
  PPP1R12C WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PPP1R12C MUTATED                                                           1
  PPP1R12C WILD-TYPE                                                         5
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PPP1R12C MUTATED                                          0
  PPP1R12C WILD-TYPE                                        3
D670V8, multiclass
                                                                   clus
vv                                                                  PPP1R12C MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           1
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  PPP1R12C WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D670V9, binary
                    cls
clus                   0   1
  PPP1R12C MUTATED     0   5
  PPP1R12C WILD-TYPE   5 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12C MUTATED      0    5
  PPP1R12C WILD-TYPE    5  279
     clus
vv    PPP1R12C MUTATED PPP1R12C WILD-TYPE
  NO                 0                  5
  YES                5                279
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  PPP1R12C MUTATED     4   0   0   0
  PPP1R12C WILD-TYPE 223  10  10  24
D670V10, multiclass
    clus
vv   PPP1R12C MUTATED PPP1R12C WILD-TYPE
  R0                4                223
  R1                0                 10
  R2                0                 10
  RX                0                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D670V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPP1R12C MUTATED       2                         0     3
  PPP1R12C WILD-TYPE    74                         4   165
D670V12, multiclass
                           clus
vv                          PPP1R12C MUTATED PPP1R12C WILD-TYPE
  ASIAN                                    2                 74
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    3                165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(671) Variable = UNC50 MUTATION ANALYSIS
D671V1, survival
                 sevent
clus2               0   1
  UNC50 MUTATED     2   0
  UNC50 WILD-TYPE 179  80
  UNC50 MUTATED UNC50 WILD-TYPE 
              2             259 
  UNC50 MUTATED UNC50 WILD-TYPE 
              0              80 
$`UNC50 MUTATED`
TCGA-BR-8368 TCGA-FP-A4BE 
        4.31        11.08 

$`UNC50 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  UNC50 MUTATED UNC50 WILD-TYPE 
           4.31            0.00 
  UNC50 MUTATED UNC50 WILD-TYPE 
          11.08          105.07 
  UNC50 MUTATED UNC50 WILD-TYPE 
          7.695          12.660 
[1] "4.3 - 11.1 (7.7)"   "0.0 - 105.1 (12.7)"
[1] "Remove cluster labels:" "UNC50 MUTATED"         
D671V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UNC50 MUTATED         0        0        2        0         1         0
  UNC50 WILD-TYPE       1        9       25       26        30        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UNC50 MUTATED           0          0          0          0        0
  UNC50 WILD-TYPE         3         49         36         24       24
D671V3, multiclass
            clus
vv           UNC50 MUTATED UNC50 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  UNC50 MUTATED     0   2   1   0
  UNC50 WILD-TYPE  11  70 121  75
D671V4, multiclass
    clus
vv   UNC50 MUTATED UNC50 WILD-TYPE
  T1             0              11
  T2             2              70
  T3             1             121
  T4             0              75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  UNC50 MUTATED    3  0  0  0
  UNC50 WILD-TYPE 90 81 50 53
D671V5, multiclass
    clus
vv   UNC50 MUTATED UNC50 WILD-TYPE
  N0             3              90
  N1             0              81
  N2             0              50
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D671V6, binary
                 cls
clus                0   1
  UNC50 MUTATED     3   0
  UNC50 WILD-TYPE 254  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC50 MUTATED      3    0
  UNC50 WILD-TYPE  254   18
   clus
vv  UNC50 MUTATED UNC50 WILD-TYPE
  0             3             254
  1             0              18
[1] 2 2
[1] FALSE
D671V7, binary
                 cls
clus                0   1
  UNC50 MUTATED     1   2
  UNC50 WILD-TYPE 109 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC50 MUTATED      1    2
  UNC50 WILD-TYPE  109  177
        clus
vv       UNC50 MUTATED UNC50 WILD-TYPE
  FEMALE             1             109
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  UNC50 MUTATED                                       0
  UNC50 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  UNC50 MUTATED                                                        2
  UNC50 WILD-TYPE                                                    133
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  UNC50 MUTATED                                                                   1
  UNC50 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  UNC50 MUTATED                                                  0
  UNC50 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  UNC50 MUTATED                                                          0
  UNC50 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  UNC50 MUTATED                                                           0
  UNC50 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  UNC50 MUTATED                                          0
  UNC50 WILD-TYPE                                        3
D671V8, multiclass
                                                                   clus
vv                                                                  UNC50 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  UNC50 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D671V9, binary
                 cls
clus                0   1
  UNC50 MUTATED     0   3
  UNC50 WILD-TYPE   5 281
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC50 MUTATED      0    3
  UNC50 WILD-TYPE    5  281
     clus
vv    UNC50 MUTATED UNC50 WILD-TYPE
  NO              0               5
  YES             3             281
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  UNC50 MUTATED     3   0   0   0
  UNC50 WILD-TYPE 224  10  10  24
D671V10, multiclass
    clus
vv   UNC50 MUTATED UNC50 WILD-TYPE
  R0             3             224
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D671V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UNC50 MUTATED       0                         1     1
  UNC50 WILD-TYPE    76                         3   167
D671V12, multiclass
[1] "Remove cluster labels:" "UNC50 MUTATED"         
clus
  UNC50 MUTATED UNC50 WILD-TYPE 
              2             246 
     TCGA-B7-5816      TCGA-B7-5818      TCGA-BR-4183      TCGA-BR-4184 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-4187      TCGA-BR-4188      TCGA-BR-4191      TCGA-BR-4201 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256      TCGA-BR-4257 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4292 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-4294      TCGA-BR-4357      TCGA-BR-4361      TCGA-BR-4362 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-4363      TCGA-BR-4366      TCGA-BR-4368      TCGA-BR-4369 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-4370      TCGA-BR-4371      TCGA-BR-6452      TCGA-BR-6453 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-6852      TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-7707      TCGA-BR-7715      TCGA-BR-7716      TCGA-BR-7717 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-7722      TCGA-BR-7723      TCGA-BR-7851      TCGA-BR-7901 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-7957      TCGA-BR-7958      TCGA-BR-7959      TCGA-BR-8058 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-8059      TCGA-BR-8077      TCGA-BR-8078      TCGA-BR-8080 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-8081      TCGA-BR-8284      TCGA-BR-8286      TCGA-BR-8289 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-8291      TCGA-BR-8295      TCGA-BR-8296      TCGA-BR-8297 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-8360      TCGA-BR-8361      TCGA-BR-8363      TCGA-BR-8364 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-8365      TCGA-BR-8366      TCGA-BR-8367      TCGA-BR-8369 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-8370      TCGA-BR-8371      TCGA-BR-8372      TCGA-BR-8373 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-8380      TCGA-BR-8381      TCGA-BR-8382      TCGA-BR-8384 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-8483      TCGA-BR-8484      TCGA-BR-8485      TCGA-BR-8486 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-8487      TCGA-BR-8588      TCGA-BR-8589      TCGA-BR-8590 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-8591      TCGA-BR-8592      TCGA-BR-8676      TCGA-BR-8677 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-8678      TCGA-BR-8679      TCGA-BR-8680      TCGA-BR-8682 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-8683      TCGA-BR-8686      TCGA-BR-8687      TCGA-BR-8690 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-A44T      TCGA-BR-A44U      TCGA-BR-A452      TCGA-BR-A453 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-A4CQ      TCGA-BR-A4CR      TCGA-BR-A4CS      TCGA-BR-A4IU 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-A4IV      TCGA-BR-A4IY      TCGA-BR-A4IZ      TCGA-BR-A4J1 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-A4J2      TCGA-BR-A4J4      TCGA-BR-A4J6      TCGA-BR-A4J7 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-A4J8      TCGA-BR-A4PD      TCGA-BR-A4PE      TCGA-BR-A4PF 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-BR-A4QI      TCGA-BR-A4QL      TCGA-BR-A4QM      TCGA-CD-5798 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-CD-5799      TCGA-CD-5800      TCGA-CD-5801      TCGA-CD-5802 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-CD-5803      TCGA-CD-5804      TCGA-CD-5813      TCGA-CD-8524 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-CD-8525      TCGA-CD-8526      TCGA-CD-8527      TCGA-CD-8528 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-CD-8529      TCGA-CD-8530      TCGA-CD-8531      TCGA-CD-8532 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-CD-8534      TCGA-CD-8535      TCGA-CD-8536      TCGA-CD-A486 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-CD-A487      TCGA-CD-A489      TCGA-CD-A48A      TCGA-CD-A48C 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-CD-A4MG      TCGA-CD-A4MH      TCGA-CD-A4MI      TCGA-CD-A4MJ 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-D7-5577      TCGA-D7-5578      TCGA-D7-5579      TCGA-D7-6518 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-D7-6519      TCGA-D7-6520      TCGA-D7-6521      TCGA-D7-6522 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-D7-6524      TCGA-D7-6525      TCGA-D7-6526      TCGA-D7-6527 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-D7-6528      TCGA-D7-6815      TCGA-D7-6817      TCGA-D7-6818 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-D7-6820      TCGA-D7-6822      TCGA-D7-8570      TCGA-D7-8572 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-D7-8573      TCGA-D7-8574      TCGA-D7-8575      TCGA-D7-8576 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-D7-8578      TCGA-D7-8579      TCGA-D7-A4YT      TCGA-D7-A4YU 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-D7-A4YV      TCGA-D7-A4YX      TCGA-D7-A4YY      TCGA-D7-A4Z0 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-EQ-5647      TCGA-EQ-8122      TCGA-EQ-A4SO      TCGA-F1-6177 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-F1-6874      TCGA-F1-6875      TCGA-F1-A448      TCGA-FP-7735 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-FP-7829      TCGA-FP-7916      TCGA-FP-7998      TCGA-FP-8099 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-FP-8209      TCGA-FP-8210      TCGA-FP-8211      TCGA-FP-8631 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-FP-A4BF      TCGA-HJ-7597      TCGA-HU-8243      TCGA-HU-8245 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-HU-8249      TCGA-HU-8602      TCGA-HU-8604      TCGA-HU-8608 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-HU-8610      TCGA-HU-A4G2      TCGA-HU-A4G3      TCGA-HU-A4G6 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-HU-A4G8      TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-HU-A4GF      TCGA-HU-A4GH      TCGA-HU-A4GN      TCGA-HU-A4GP 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-HU-A4GQ      TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-HU-A4GY      TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-HU-A4H4      TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-HU-A4HD      TCGA-IN-7806      TCGA-IN-7808      TCGA-IN-8462 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 
     TCGA-IN-8663      TCGA-IP-7968 
"UNC50 WILD-TYPE" "UNC50 WILD-TYPE" 

Clustering(672) Variable = CNGA4 MUTATION ANALYSIS
D672V1, survival
                 sevent
clus2               0   1
  CNGA4 MUTATED    13   3
  CNGA4 WILD-TYPE 168  77
  CNGA4 MUTATED CNGA4 WILD-TYPE 
             16             245 
  CNGA4 MUTATED CNGA4 WILD-TYPE 
              3              77 
$`CNGA4 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-7197 TCGA-BR-8361 TCGA-BR-8382 TCGA-BR-8680 
       26.70         6.97         9.21        19.50        15.85        15.81 
TCGA-BR-A4IY TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-5579 
       12.89        11.57         6.58         6.02        65.10        11.93 
TCGA-D7-6818 TCGA-D7-A4YV TCGA-FP-8631 TCGA-HU-A4GN 
       10.55         5.92         0.56        29.98 

$`CNGA4 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        32.94        12.82        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        1.48        13.41        13.51         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        28.96        79.07         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        12.36        12.66        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.22        15.98        12.79        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
       59.54         5.03        13.58        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        11.77         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  CNGA4 MUTATED CNGA4 WILD-TYPE 
           0.56            0.00 
  CNGA4 MUTATED CNGA4 WILD-TYPE 
          65.10          105.07 
  CNGA4 MUTATED CNGA4 WILD-TYPE 
          11.75           12.66 
[1] "0.6 - 65.1 (11.8)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.8"
D672V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CNGA4 MUTATED         0        0        1        1         2         3
  CNGA4 WILD-TYPE       1        9       26       25        29        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNGA4 MUTATED           0          4          1          2        2
  CNGA4 WILD-TYPE         3         45         35         22       22
D672V3, multiclass
            clus
vv           CNGA4 MUTATED CNGA4 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               1              25
  STAGE IIA              2              29
  STAGE IIB              3              41
  STAGE III              0               3
  STAGE IIIA             4              45
  STAGE IIIB             1              35
  STAGE IIIC             2              22
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CNGA4 MUTATED     0   3   8   6
  CNGA4 WILD-TYPE  11  69 114  69
D672V4, multiclass
    clus
vv   CNGA4 MUTATED CNGA4 WILD-TYPE
  T1             0              11
  T2             3              69
  T3             8             114
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CNGA4 MUTATED    5  5  4  3
  CNGA4 WILD-TYPE 88 76 46 50
D672V5, multiclass
    clus
vv   CNGA4 MUTATED CNGA4 WILD-TYPE
  N0             5              88
  N1             5              76
  N2             4              46
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D672V6, binary
                 cls
clus                0   1
  CNGA4 MUTATED    14   1
  CNGA4 WILD-TYPE 243  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNGA4 MUTATED     14    1
  CNGA4 WILD-TYPE  243   17
   clus
vv  CNGA4 MUTATED CNGA4 WILD-TYPE
  0            14             243
  1             1              17
[1] 2 2
[1] FALSE
D672V7, binary
                 cls
clus                0   1
  CNGA4 MUTATED     8  10
  CNGA4 WILD-TYPE 102 169
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNGA4 MUTATED      8   10
  CNGA4 WILD-TYPE  102  169
        clus
vv       CNGA4 MUTATED CNGA4 WILD-TYPE
  FEMALE             8             102
  MALE              10             169
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CNGA4 MUTATED                                       3
  CNGA4 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CNGA4 MUTATED                                                        8
  CNGA4 WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CNGA4 MUTATED                                                                   3
  CNGA4 WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CNGA4 MUTATED                                                  3
  CNGA4 WILD-TYPE                                               35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CNGA4 MUTATED                                                          1
  CNGA4 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CNGA4 MUTATED                                                           0
  CNGA4 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CNGA4 MUTATED                                          0
  CNGA4 WILD-TYPE                                        3
D672V8, multiclass
                                                                   clus
vv                                                                  CNGA4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  CNGA4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D672V9, binary
                 cls
clus                0   1
  CNGA4 MUTATED     1  17
  CNGA4 WILD-TYPE   4 267
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNGA4 MUTATED      1   17
  CNGA4 WILD-TYPE    4  267
     clus
vv    CNGA4 MUTATED CNGA4 WILD-TYPE
  NO              1               4
  YES            17             267
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CNGA4 MUTATED    13   1   0   3
  CNGA4 WILD-TYPE 214   9  10  21
D672V10, multiclass
    clus
vv   CNGA4 MUTATED CNGA4 WILD-TYPE
  R0            13             214
  R1             1               9
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D672V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CNGA4 MUTATED       4                         0    12
  CNGA4 WILD-TYPE    72                         4   156
D672V12, multiclass
                           clus
vv                          CNGA4 MUTATED CNGA4 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                12             156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(673) Variable = C3 MUTATION ANALYSIS
D673V1, survival
              sevent
clus2            0   1
  C3 MUTATED    18   6
  C3 WILD-TYPE 163  74
  C3 MUTATED C3 WILD-TYPE 
          24          237 
  C3 MUTATED C3 WILD-TYPE 
           6           74 
$`C3 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6564 TCGA-BR-6852 TCGA-BR-7958 
       26.70         6.97        34.68        26.10        32.94        12.76 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8289 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8370 
       20.55         8.05         2.66         6.18         0.26         3.32 
TCGA-BR-8680 TCGA-CD-5799 TCGA-CD-5800 TCGA-CG-5721 TCGA-CG-5727 TCGA-CG-5728 
       15.81         3.25        13.15         6.02        79.07        65.10 
TCGA-D7-A4YU TCGA-F1-6874 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4GX 
       16.44        14.47        11.41        11.84         0.10        10.19 

$`C3 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        19.33        39.12         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       12.82         9.21        24.76        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
       12.95        16.31         2.20        15.58         7.40        19.50 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 
        1.15        13.64        11.57         5.13         2.83        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
      105.07        12.03        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
       13.78        14.76         0.62         7.99        16.24        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       26.47         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        11.77        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  C3 MUTATED C3 WILD-TYPE 
         0.1          0.0 
  C3 MUTATED C3 WILD-TYPE 
       79.07       105.07 
  C3 MUTATED C3 WILD-TYPE 
       12.30        12.62 
[1] "0.1 - 79.1 (12.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.6"
D673V2, continuous
              vv
clus           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  C3 MUTATED         0        0        3        3         3         4         0
  C3 WILD-TYPE       1        9       24       23        28        40         3
              vv
clus           STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C3 MUTATED            3          3          3        3
  C3 WILD-TYPE         46         33         21       21
D673V3, multiclass
            clus
vv           C3 MUTATED C3 WILD-TYPE
  STAGE I             0            1
  STAGE IA            0            9
  STAGE IB            3           24
  STAGE II            3           23
  STAGE IIA           3           28
  STAGE IIB           4           40
  STAGE III           0            3
  STAGE IIIA          3           46
  STAGE IIIB          3           33
  STAGE IIIC          3           21
  STAGE IV            3           21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            T1  T2  T3  T4
  C3 MUTATED     0   4  10  11
  C3 WILD-TYPE  11  68 112  64
D673V4, multiclass
    clus
vv   C3 MUTATED C3 WILD-TYPE
  T1          0           11
  T2          4           68
  T3         10          112
  T4         11           64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           N0 N1 N2 N3
  C3 MUTATED   13  4  4  4
  C3 WILD-TYPE 80 77 46 49
D673V5, multiclass
    clus
vv   C3 MUTATED C3 WILD-TYPE
  N0         13           80
  N1          4           77
  N2          4           46
  N3          4           49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D673V6, binary
              cls
clus             0   1
  C3 MUTATED    22   2
  C3 WILD-TYPE 235  16
[1] "tbl2"
              cls
clus           [,1] [,2]
  C3 MUTATED     22    2
  C3 WILD-TYPE  235   16
   clus
vv  C3 MUTATED C3 WILD-TYPE
  0         22          235
  1          2           16
[1] 2 2
[1] FALSE
D673V7, binary
              cls
clus             0   1
  C3 MUTATED    13  12
  C3 WILD-TYPE  97 167
[1] "tbl2"
              cls
clus           [,1] [,2]
  C3 MUTATED     13   12
  C3 WILD-TYPE   97  167
        clus
vv       C3 MUTATED C3 WILD-TYPE
  FEMALE         13           97
  MALE           12          167
[1] 2 2
[1] FALSE
              vv
clus           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C3 MUTATED                                       6
  C3 WILD-TYPE                                    44
              vv
clus           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C3 MUTATED                                                        7
  C3 WILD-TYPE                                                    128
              vv
clus           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C3 MUTATED                                                                   8
  C3 WILD-TYPE                                                                32
              vv
clus           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C3 MUTATED                                                  3
  C3 WILD-TYPE                                               35
              vv
clus           STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C3 MUTATED                                                          0
  C3 WILD-TYPE                                                       16
              vv
clus           STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C3 MUTATED                                                           1
  C3 WILD-TYPE                                                         5
              vv
clus           STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C3 MUTATED                                          0
  C3 WILD-TYPE                                        3
D673V8, multiclass
                                                                   clus
vv                                                                  C3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                      6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                     7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)          8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                           3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                  1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                   0
                                                                   clus
vv                                                                  C3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       44
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                     128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D673V9, binary
              cls
clus             0   1
  C3 MUTATED     0  25
  C3 WILD-TYPE   5 259
[1] "tbl2"
              cls
clus           [,1] [,2]
  C3 MUTATED      0   25
  C3 WILD-TYPE    5  259
     clus
vv    C3 MUTATED C3 WILD-TYPE
  NO           0            5
  YES         25          259
[1] 2 2
[1] FALSE
              vv
clus            R0  R1  R2  RX
  C3 MUTATED    21   0   0   2
  C3 WILD-TYPE 206  10  10  22
D673V10, multiclass
    clus
vv   C3 MUTATED C3 WILD-TYPE
  R0         21          206
  R1          0           10
  R2          0           10
  RX          2           22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D673V11, continuous
              vv
clus           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C3 MUTATED       7                         0    15
  C3 WILD-TYPE    69                         4   153
D673V12, multiclass
                           clus
vv                          C3 MUTATED C3 WILD-TYPE
  ASIAN                              7           69
  BLACK OR AFRICAN AMERICAN          0            4
  WHITE                             15          153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(674) Variable = GPX6 MUTATION ANALYSIS
D674V1, survival
                sevent
clus2              0   1
  GPX6 MUTATED     4   0
  GPX6 WILD-TYPE 177  80
  GPX6 MUTATED GPX6 WILD-TYPE 
             4            257 
  GPX6 MUTATED GPX6 WILD-TYPE 
             0             80 
$`GPX6 MUTATED`
TCGA-BR-7707 TCGA-BR-A4IY TCGA-CD-A48A TCGA-CG-4437 
       23.93        12.89        12.43         8.05 

$`GPX6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  GPX6 MUTATED GPX6 WILD-TYPE 
          8.05           0.00 
  GPX6 MUTATED GPX6 WILD-TYPE 
         23.93         105.07 
  GPX6 MUTATED GPX6 WILD-TYPE 
         12.66          12.62 
[1] "8.1 - 23.9 (12.7)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "9100000"
D674V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPX6 MUTATED         0        0        1        1         1         1
  GPX6 WILD-TYPE       1        9       26       25        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPX6 MUTATED           0          0          0          0        0
  GPX6 WILD-TYPE         3         49         36         24       24
D674V3, multiclass
            clus
vv           GPX6 MUTATED GPX6 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              1             25
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GPX6 MUTATED     0   2   1   1
  GPX6 WILD-TYPE  11  70 121  74
D674V4, multiclass
    clus
vv   GPX6 MUTATED GPX6 WILD-TYPE
  T1            0             11
  T2            2             70
  T3            1            121
  T4            1             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  GPX6 MUTATED    3  1  0  0
  GPX6 WILD-TYPE 90 80 50 53
D674V5, multiclass
    clus
vv   GPX6 MUTATED GPX6 WILD-TYPE
  N0            3             90
  N1            1             80
  N2            0             50
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D674V6, binary
                cls
clus               0   1
  GPX6 MUTATED     4   0
  GPX6 WILD-TYPE 253  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX6 MUTATED      4    0
  GPX6 WILD-TYPE  253   18
   clus
vv  GPX6 MUTATED GPX6 WILD-TYPE
  0            4            253
  1            0             18
[1] 2 2
[1] FALSE
D674V7, binary
                cls
clus               0   1
  GPX6 MUTATED     1   3
  GPX6 WILD-TYPE 109 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX6 MUTATED      1    3
  GPX6 WILD-TYPE  109  176
        clus
vv       GPX6 MUTATED GPX6 WILD-TYPE
  FEMALE            1            109
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GPX6 MUTATED                                       0
  GPX6 WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPX6 MUTATED                                                        3
  GPX6 WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPX6 MUTATED                                                                   1
  GPX6 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GPX6 MUTATED                                                  0
  GPX6 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GPX6 MUTATED                                                          0
  GPX6 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GPX6 MUTATED                                                           0
  GPX6 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GPX6 MUTATED                                          0
  GPX6 WILD-TYPE                                        3
D674V8, multiclass
                                                                   clus
vv                                                                  GPX6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  GPX6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D674V9, binary
                cls
clus               0   1
  GPX6 MUTATED     0   4
  GPX6 WILD-TYPE   5 280
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX6 MUTATED      0    4
  GPX6 WILD-TYPE    5  280
     clus
vv    GPX6 MUTATED GPX6 WILD-TYPE
  NO             0              5
  YES            4            280
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GPX6 MUTATED     3   0   0   0
  GPX6 WILD-TYPE 224  10  10  24
D674V10, multiclass
    clus
vv   GPX6 MUTATED GPX6 WILD-TYPE
  R0            3            224
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D674V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPX6 MUTATED       2                         0     1
  GPX6 WILD-TYPE    74                         4   167
D674V12, multiclass
                           clus
vv                          GPX6 MUTATED GPX6 WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                1            167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(675) Variable = KANK4 MUTATION ANALYSIS
D675V1, survival
                 sevent
clus2               0   1
  KANK4 MUTATED     6   3
  KANK4 WILD-TYPE 175  77
  KANK4 MUTATED KANK4 WILD-TYPE 
              9             252 
  KANK4 MUTATED KANK4 WILD-TYPE 
              3              77 
$`KANK4 MUTATED`
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8687 
        6.61        34.68        23.93         1.12        13.45         8.22 
TCGA-BR-A4QL TCGA-CG-5726 TCGA-HU-A4GX 
       11.57        28.96        10.19 

$`KANK4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
       18.35        30.90         6.18         9.57        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79        15.81         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 
        0.99         6.02         0.99       105.07        12.03        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  KANK4 MUTATED KANK4 WILD-TYPE 
           1.12            0.00 
  KANK4 MUTATED KANK4 WILD-TYPE 
          34.68          105.07 
  KANK4 MUTATED KANK4 WILD-TYPE 
          11.57           12.64 
[1] "1.1 - 34.7 (11.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D675V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KANK4 MUTATED         0        1        1        0         2         0
  KANK4 WILD-TYPE       1        8       26       26        29        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KANK4 MUTATED           1          0          1          3        0
  KANK4 WILD-TYPE         2         49         35         21       24
D675V3, multiclass
            clus
vv           KANK4 MUTATED KANK4 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              2              29
  STAGE IIB              0              44
  STAGE III              1               2
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             3              21
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KANK4 MUTATED     1   2   3   3
  KANK4 WILD-TYPE  10  70 119  72
D675V4, multiclass
    clus
vv   KANK4 MUTATED KANK4 WILD-TYPE
  T1             1              10
  T2             2              70
  T3             3             119
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  KANK4 MUTATED    4  2  2  2
  KANK4 WILD-TYPE 89 79 48 51
D675V5, multiclass
    clus
vv   KANK4 MUTATED KANK4 WILD-TYPE
  N0             4              89
  N1             2              79
  N2             2              48
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D675V6, binary
                 cls
clus                0   1
  KANK4 MUTATED    10   0
  KANK4 WILD-TYPE 247  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK4 MUTATED     10    0
  KANK4 WILD-TYPE  247   18
   clus
vv  KANK4 MUTATED KANK4 WILD-TYPE
  0            10             247
  1             0              18
[1] 2 2
[1] FALSE
D675V7, binary
                 cls
clus                0   1
  KANK4 MUTATED     8   2
  KANK4 WILD-TYPE 102 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK4 MUTATED      8    2
  KANK4 WILD-TYPE  102  177
        clus
vv       KANK4 MUTATED KANK4 WILD-TYPE
  FEMALE             8             102
  MALE               2             177
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KANK4 MUTATED                                       1
  KANK4 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KANK4 MUTATED                                                        8
  KANK4 WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KANK4 MUTATED                                                                   1
  KANK4 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KANK4 MUTATED                                                  0
  KANK4 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KANK4 MUTATED                                                          0
  KANK4 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KANK4 MUTATED                                                           0
  KANK4 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KANK4 MUTATED                                          0
  KANK4 WILD-TYPE                                        3
D675V8, multiclass
                                                                   clus
vv                                                                  KANK4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  KANK4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D675V9, binary
                 cls
clus                0   1
  KANK4 MUTATED     0  10
  KANK4 WILD-TYPE   5 274
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK4 MUTATED      0   10
  KANK4 WILD-TYPE    5  274
     clus
vv    KANK4 MUTATED KANK4 WILD-TYPE
  NO              0               5
  YES            10             274
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KANK4 MUTATED     7   1   0   2
  KANK4 WILD-TYPE 220   9  10  22
D675V10, multiclass
    clus
vv   KANK4 MUTATED KANK4 WILD-TYPE
  R0             7             220
  R1             1               9
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D675V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KANK4 MUTATED       1                         0     8
  KANK4 WILD-TYPE    75                         4   160
D675V12, multiclass
                           clus
vv                          KANK4 MUTATED KANK4 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 8             160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(676) Variable = CASP1 MUTATION ANALYSIS
D676V1, survival
                 sevent
clus2               0   1
  CASP1 MUTATED     2   1
  CASP1 WILD-TYPE 179  79
  CASP1 MUTATED CASP1 WILD-TYPE 
              3             258 
  CASP1 MUTATED CASP1 WILD-TYPE 
              1              79 
$`CASP1 MUTATED`
TCGA-BR-6452 TCGA-BR-8363 TCGA-D7-6528 
       34.68         0.26        15.22 

$`CASP1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        19.50        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  CASP1 MUTATED CASP1 WILD-TYPE 
           0.26            0.00 
  CASP1 MUTATED CASP1 WILD-TYPE 
          34.68          105.07 
  CASP1 MUTATED CASP1 WILD-TYPE 
         15.220          12.605 
[1] "0.3 - 34.7 (15.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D676V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CASP1 MUTATED         0        0        2        0         1         0
  CASP1 WILD-TYPE       1        9       25       26        30        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CASP1 MUTATED           0          1          0          0        0
  CASP1 WILD-TYPE         3         48         36         24       24
D676V3, multiclass
            clus
vv           CASP1 MUTATED CASP1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CASP1 MUTATED     0   2   2   0
  CASP1 WILD-TYPE  11  70 120  75
D676V4, multiclass
    clus
vv   CASP1 MUTATED CASP1 WILD-TYPE
  T1             0              11
  T2             2              70
  T3             2             120
  T4             0              75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CASP1 MUTATED    3  1  0  0
  CASP1 WILD-TYPE 90 80 50 53
D676V5, multiclass
    clus
vv   CASP1 MUTATED CASP1 WILD-TYPE
  N0             3              90
  N1             1              80
  N2             0              50
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D676V6, binary
                 cls
clus                0   1
  CASP1 MUTATED     4   0
  CASP1 WILD-TYPE 253  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP1 MUTATED      4    0
  CASP1 WILD-TYPE  253   18
   clus
vv  CASP1 MUTATED CASP1 WILD-TYPE
  0             4             253
  1             0              18
[1] 2 2
[1] FALSE
D676V7, binary
                 cls
clus                0   1
  CASP1 MUTATED     3   1
  CASP1 WILD-TYPE 107 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP1 MUTATED      3    1
  CASP1 WILD-TYPE  107  178
        clus
vv       CASP1 MUTATED CASP1 WILD-TYPE
  FEMALE             3             107
  MALE               1             178
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CASP1 MUTATED                                       0
  CASP1 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CASP1 MUTATED                                                        3
  CASP1 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CASP1 MUTATED                                                                   0
  CASP1 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CASP1 MUTATED                                                  1
  CASP1 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CASP1 MUTATED                                                          0
  CASP1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CASP1 MUTATED                                                           0
  CASP1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CASP1 MUTATED                                          0
  CASP1 WILD-TYPE                                        3
D676V8, multiclass
                                                                   clus
vv                                                                  CASP1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  CASP1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D676V9, binary
                 cls
clus                0   1
  CASP1 MUTATED     1   3
  CASP1 WILD-TYPE   4 281
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP1 MUTATED      1    3
  CASP1 WILD-TYPE    4  281
     clus
vv    CASP1 MUTATED CASP1 WILD-TYPE
  NO              1               4
  YES             3             281
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CASP1 MUTATED     3   1   0   0
  CASP1 WILD-TYPE 224   9  10  24
D676V10, multiclass
    clus
vv   CASP1 MUTATED CASP1 WILD-TYPE
  R0             3             224
  R1             1               9
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D676V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CASP1 MUTATED       0                         0     3
  CASP1 WILD-TYPE    76                         4   165
D676V12, multiclass
                           clus
vv                          CASP1 MUTATED CASP1 WILD-TYPE
  ASIAN                                 0              76
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(677) Variable = ELL2 MUTATION ANALYSIS
D677V1, survival
                sevent
clus2              0   1
  ELL2 MUTATED     8   1
  ELL2 WILD-TYPE 173  79
  ELL2 MUTATED ELL2 WILD-TYPE 
             9            252 
  ELL2 MUTATED ELL2 WILD-TYPE 
             1             79 
$`ELL2 MUTATED`
TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-A4QL TCGA-CD-A4MI TCGA-CG-4437 TCGA-CG-5721 
        6.18        34.68        11.57         0.10         8.05         6.02 
TCGA-CG-5723 TCGA-HU-8602 TCGA-HU-A4H2 
      105.07        11.41        12.95 

$`ELL2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       18.35        30.90         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         7.99        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
       36.00         1.02         0.99         0.99        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        5.52        26.47         5.92        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  ELL2 MUTATED ELL2 WILD-TYPE 
           0.1            0.0 
  ELL2 MUTATED ELL2 WILD-TYPE 
        105.07          79.07 
  ELL2 MUTATED ELL2 WILD-TYPE 
         11.41          12.71 
[1] "0.1 - 105.1 (11.4)" "0.0 - 79.1 (12.7)" 
[1] "hr=" "3.9"
D677V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ELL2 MUTATED         0        0        1        3         1         1
  ELL2 WILD-TYPE       1        9       26       23        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ELL2 MUTATED           0          2          3          0        1
  ELL2 WILD-TYPE         3         47         33         24       23
D677V3, multiclass
            clus
vv           ELL2 MUTATED ELL2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              3             23
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            3             33
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ELL2 MUTATED     0   4   5   3
  ELL2 WILD-TYPE  11  68 117  72
D677V4, multiclass
    clus
vv   ELL2 MUTATED ELL2 WILD-TYPE
  T1            0             11
  T2            4             68
  T3            5            117
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  ELL2 MUTATED    4  6  0  2
  ELL2 WILD-TYPE 89 75 50 51
D677V5, multiclass
    clus
vv   ELL2 MUTATED ELL2 WILD-TYPE
  N0            4             89
  N1            6             75
  N2            0             50
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D677V6, binary
                cls
clus               0   1
  ELL2 MUTATED    12   0
  ELL2 WILD-TYPE 245  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELL2 MUTATED     12    0
  ELL2 WILD-TYPE  245   18
   clus
vv  ELL2 MUTATED ELL2 WILD-TYPE
  0           12            245
  1            0             18
[1] 2 2
[1] FALSE
D677V7, binary
                cls
clus               0   1
  ELL2 MUTATED     6   6
  ELL2 WILD-TYPE 104 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELL2 MUTATED      6    6
  ELL2 WILD-TYPE  104  173
        clus
vv       ELL2 MUTATED ELL2 WILD-TYPE
  FEMALE            6            104
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ELL2 MUTATED                                       1
  ELL2 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ELL2 MUTATED                                                        7
  ELL2 WILD-TYPE                                                    128
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ELL2 MUTATED                                                                   2
  ELL2 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ELL2 MUTATED                                                  1
  ELL2 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ELL2 MUTATED                                                          1
  ELL2 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ELL2 MUTATED                                                           0
  ELL2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ELL2 MUTATED                                          0
  ELL2 WILD-TYPE                                        3
D677V8, multiclass
                                                                   clus
vv                                                                  ELL2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  ELL2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D677V9, binary
                cls
clus               0   1
  ELL2 MUTATED     1  11
  ELL2 WILD-TYPE   4 273
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELL2 MUTATED      1   11
  ELL2 WILD-TYPE    4  273
     clus
vv    ELL2 MUTATED ELL2 WILD-TYPE
  NO             1              4
  YES           11            273
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ELL2 MUTATED     8   0   0   3
  ELL2 WILD-TYPE 219  10  10  21
D677V10, multiclass
    clus
vv   ELL2 MUTATED ELL2 WILD-TYPE
  R0            8            219
  R1            0             10
  R2            0             10
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D677V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ELL2 MUTATED       3                         0     5
  ELL2 WILD-TYPE    73                         4   163
D677V12, multiclass
                           clus
vv                          ELL2 MUTATED ELL2 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                5            163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(678) Variable = PIK3C2G MUTATION ANALYSIS
D678V1, survival
                   sevent
clus2                 0   1
  PIK3C2G MUTATED     6   3
  PIK3C2G WILD-TYPE 175  77
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
                9               252 
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
                3                77 
$`PIK3C2G MUTATED`
TCGA-BR-4184 TCGA-BR-7851 TCGA-BR-8078 TCGA-BR-8680 TCGA-CD-5801 TCGA-CD-A4MG 
        6.97        12.43        12.26        15.81        13.18         6.58 
TCGA-CG-4437 TCGA-CG-5721 TCGA-IN-8462 
        8.05         6.02        18.81 

$`PIK3C2G WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.15         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IP-7968 
        8.88        27.42        21.21         3.45         3.39         2.53 

  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
             6.02              0.00 
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
            18.81            105.07 
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
            12.26             12.71 
[1] "6.0 - 18.8 (12.3)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.5"
D678V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIK3C2G MUTATED         0        0        0        1         1         3
  PIK3C2G WILD-TYPE       1        9       27       25        30        41
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3C2G MUTATED           0          2          0          0        2
  PIK3C2G WILD-TYPE         3         47         36         24       22
D678V3, multiclass
            clus
vv           PIK3C2G MUTATED PIK3C2G WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 0                27
  STAGE II                 1                25
  STAGE IIA                1                30
  STAGE IIB                3                41
  STAGE III                0                 3
  STAGE IIIA               2                47
  STAGE IIIB               0                36
  STAGE IIIC               0                24
  STAGE IV                 2                22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PIK3C2G MUTATED     0   2   3   4
  PIK3C2G WILD-TYPE  11  70 119  71
D678V4, multiclass
    clus
vv   PIK3C2G MUTATED PIK3C2G WILD-TYPE
  T1               0                11
  T2               2                70
  T3               3               119
  T4               4                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  PIK3C2G MUTATED    3  6  1  0
  PIK3C2G WILD-TYPE 90 75 49 53
D678V5, multiclass
    clus
vv   PIK3C2G MUTATED PIK3C2G WILD-TYPE
  N0               3                90
  N1               6                75
  N2               1                49
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D678V6, binary
                   cls
clus                  0   1
  PIK3C2G MUTATED     8   1
  PIK3C2G WILD-TYPE 249  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2G MUTATED      8    1
  PIK3C2G WILD-TYPE  249   17
   clus
vv  PIK3C2G MUTATED PIK3C2G WILD-TYPE
  0               8               249
  1               1                17
[1] 2 2
[1] FALSE
D678V7, binary
                   cls
clus                  0   1
  PIK3C2G MUTATED     1   9
  PIK3C2G WILD-TYPE 109 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2G MUTATED      1    9
  PIK3C2G WILD-TYPE  109  170
        clus
vv       PIK3C2G MUTATED PIK3C2G WILD-TYPE
  FEMALE               1               109
  MALE                 9               170
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PIK3C2G MUTATED                                       1
  PIK3C2G WILD-TYPE                                    49
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIK3C2G MUTATED                                                        5
  PIK3C2G WILD-TYPE                                                    130
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIK3C2G MUTATED                                                                   3
  PIK3C2G WILD-TYPE                                                                37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PIK3C2G MUTATED                                                  1
  PIK3C2G WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PIK3C2G MUTATED                                                          0
  PIK3C2G WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PIK3C2G MUTATED                                                           0
  PIK3C2G WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PIK3C2G MUTATED                                          0
  PIK3C2G WILD-TYPE                                        3
D678V8, multiclass
                                                                   clus
vv                                                                  PIK3C2G MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  PIK3C2G WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D678V9, binary
                   cls
clus                  0   1
  PIK3C2G MUTATED     0  10
  PIK3C2G WILD-TYPE   5 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2G MUTATED      0   10
  PIK3C2G WILD-TYPE    5  274
     clus
vv    PIK3C2G MUTATED PIK3C2G WILD-TYPE
  NO                0                 5
  YES              10               274
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PIK3C2G MUTATED     7   0   0   2
  PIK3C2G WILD-TYPE 220  10  10  22
D678V10, multiclass
    clus
vv   PIK3C2G MUTATED PIK3C2G WILD-TYPE
  R0               7               220
  R1               0                10
  R2               0                10
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D678V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3C2G MUTATED       3                         0     5
  PIK3C2G WILD-TYPE    73                         4   163
D678V12, multiclass
                           clus
vv                          PIK3C2G MUTATED PIK3C2G WILD-TYPE
  ASIAN                                   3                73
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   5               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(679) Variable = KIAA0664 MUTATION ANALYSIS
D679V1, survival
                    sevent
clus2                  0   1
  KIAA0664 MUTATED     5   5
  KIAA0664 WILD-TYPE 176  75
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
                10                251 
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
                 5                 75 
$`KIAA0664 MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8363 TCGA-CD-A4MG TCGA-CG-5721 
       34.68        12.26         6.18         0.26         6.58         6.02 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-HU-A4GQ 
       12.03        28.96        65.10         0.10 

$`KIAA0664 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       19.50        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5727 
       36.00         1.02         0.99         0.99       105.07        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
               0.1                0.0 
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
             65.10             105.07 
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
             9.305             12.760 
[1] "0.1 - 65.1 (9.3)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.5"
D679V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0664 MUTATED         0        1        2        0         3         1
  KIAA0664 WILD-TYPE       1        8       25       26        28        43
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0664 MUTATED           0          1          0          2        3
  KIAA0664 WILD-TYPE         3         48         36         22       21
D679V3, multiclass
            clus
vv           KIAA0664 MUTATED KIAA0664 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  1                  8
  STAGE IB                  2                 25
  STAGE II                  0                 26
  STAGE IIA                 3                 28
  STAGE IIB                 1                 43
  STAGE III                 0                  3
  STAGE IIIA                1                 48
  STAGE IIIB                0                 36
  STAGE IIIC                2                 22
  STAGE IV                  3                 21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0664 MUTATED     1   2   4   6
  KIAA0664 WILD-TYPE  10  70 118  69
D679V4, multiclass
    clus
vv   KIAA0664 MUTATED KIAA0664 WILD-TYPE
  T1                1                 10
  T2                2                 70
  T3                4                118
  T4                6                 69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  KIAA0664 MUTATED    8  1  2  2
  KIAA0664 WILD-TYPE 85 80 48 51
D679V5, multiclass
    clus
vv   KIAA0664 MUTATED KIAA0664 WILD-TYPE
  N0                8                 85
  N1                1                 80
  N2                2                 48
  N3                2                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D679V6, binary
                    cls
clus                   0   1
  KIAA0664 MUTATED    12   1
  KIAA0664 WILD-TYPE 245  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0664 MUTATED     12    1
  KIAA0664 WILD-TYPE  245   17
   clus
vv  KIAA0664 MUTATED KIAA0664 WILD-TYPE
  0               12                245
  1                1                 17
[1] 2 2
[1] FALSE
D679V7, binary
                    cls
clus                   0   1
  KIAA0664 MUTATED     7   6
  KIAA0664 WILD-TYPE 103 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0664 MUTATED      7    6
  KIAA0664 WILD-TYPE  103  173
        clus
vv       KIAA0664 MUTATED KIAA0664 WILD-TYPE
  FEMALE                7                103
  MALE                  6                173
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KIAA0664 MUTATED                                       2
  KIAA0664 WILD-TYPE                                    48
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA0664 MUTATED                                                        6
  KIAA0664 WILD-TYPE                                                    129
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA0664 MUTATED                                                                   4
  KIAA0664 WILD-TYPE                                                                36
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KIAA0664 MUTATED                                                  1
  KIAA0664 WILD-TYPE                                               37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KIAA0664 MUTATED                                                          0
  KIAA0664 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KIAA0664 MUTATED                                                           0
  KIAA0664 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KIAA0664 MUTATED                                          0
  KIAA0664 WILD-TYPE                                        3
D679V8, multiclass
                                                                   clus
vv                                                                  KIAA0664 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  KIAA0664 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D679V9, binary
                    cls
clus                   0   1
  KIAA0664 MUTATED     0  13
  KIAA0664 WILD-TYPE   5 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0664 MUTATED      0   13
  KIAA0664 WILD-TYPE    5  271
     clus
vv    KIAA0664 MUTATED KIAA0664 WILD-TYPE
  NO                 0                  5
  YES               13                271
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0664 MUTATED     9   0   1   2
  KIAA0664 WILD-TYPE 218  10   9  22
D679V10, multiclass
    clus
vv   KIAA0664 MUTATED KIAA0664 WILD-TYPE
  R0                9                218
  R1                0                 10
  R2                1                  9
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D679V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA0664 MUTATED       2                         0     7
  KIAA0664 WILD-TYPE    74                         4   161
D679V12, multiclass
                           clus
vv                          KIAA0664 MUTATED KIAA0664 WILD-TYPE
  ASIAN                                    2                 74
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    7                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(680) Variable = SOS2 MUTATION ANALYSIS
D680V1, survival
                sevent
clus2              0   1
  SOS2 MUTATED    15   2
  SOS2 WILD-TYPE 166  78
  SOS2 MUTATED SOS2 WILD-TYPE 
            17            244 
  SOS2 MUTATED SOS2 WILD-TYPE 
             2             78 
$`SOS2 MUTATED`
TCGA-BR-6452 TCGA-BR-6565 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       34.68         9.17        23.93        12.26         9.60        20.55 
TCGA-BR-8372 TCGA-BR-8591 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-CD-8536 TCGA-CG-4305 
       19.17        13.45        20.42        11.57         0.10        15.95 
TCGA-CG-5728 TCGA-F1-6874 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4HD 
       65.10        14.47        11.41         0.76        27.42 

$`SOS2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        0.69         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        19.36        13.51        20.65         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
       13.78        14.76         0.62         7.99        16.24        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       26.47         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-IN-7806 
       19.36        23.84        12.30         9.67         8.88        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  SOS2 MUTATED SOS2 WILD-TYPE 
           0.1            0.0 
  SOS2 MUTATED SOS2 WILD-TYPE 
         65.10         105.07 
  SOS2 MUTATED SOS2 WILD-TYPE 
        14.470         12.575 
[1] "0.1 - 65.1 (14.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "3.5"
D680V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SOS2 MUTATED         0        1        4        2         1         4
  SOS2 WILD-TYPE       1        8       23       24        30        40
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SOS2 MUTATED           0          1          1          3        0
  SOS2 WILD-TYPE         3         48         35         21       24
D680V3, multiclass
            clus
vv           SOS2 MUTATED SOS2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              4             23
  STAGE II              2             24
  STAGE IIA             1             30
  STAGE IIB             4             40
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            3             21
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SOS2 MUTATED     2   5   4   7
  SOS2 WILD-TYPE   9  67 118  68
D680V4, multiclass
    clus
vv   SOS2 MUTATED SOS2 WILD-TYPE
  T1            2              9
  T2            5             67
  T3            4            118
  T4            7             68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  SOS2 MUTATED   11  2  1  4
  SOS2 WILD-TYPE 82 79 49 49
D680V5, multiclass
    clus
vv   SOS2 MUTATED SOS2 WILD-TYPE
  N0           11             82
  N1            2             79
  N2            1             49
  N3            4             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D680V6, binary
                cls
clus               0   1
  SOS2 MUTATED    19   0
  SOS2 WILD-TYPE 238  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS2 MUTATED     19    0
  SOS2 WILD-TYPE  238   18
   clus
vv  SOS2 MUTATED SOS2 WILD-TYPE
  0           19            238
  1            0             18
[1] 2 2
[1] FALSE
D680V7, binary
                cls
clus               0   1
  SOS2 MUTATED    10   9
  SOS2 WILD-TYPE 100 170
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS2 MUTATED     10    9
  SOS2 WILD-TYPE  100  170
        clus
vv       SOS2 MUTATED SOS2 WILD-TYPE
  FEMALE           10            100
  MALE              9            170
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SOS2 MUTATED                                       1
  SOS2 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SOS2 MUTATED                                                       13
  SOS2 WILD-TYPE                                                    122
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SOS2 MUTATED                                                                   2
  SOS2 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SOS2 MUTATED                                                  2
  SOS2 WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SOS2 MUTATED                                                          1
  SOS2 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SOS2 MUTATED                                                           0
  SOS2 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SOS2 MUTATED                                          0
  SOS2 WILD-TYPE                                        3
D680V8, multiclass
                                                                   clus
vv                                                                  SOS2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      13
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  SOS2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       122
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D680V9, binary
                cls
clus               0   1
  SOS2 MUTATED     0  19
  SOS2 WILD-TYPE   5 265
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS2 MUTATED      0   19
  SOS2 WILD-TYPE    5  265
     clus
vv    SOS2 MUTATED SOS2 WILD-TYPE
  NO             0              5
  YES           19            265
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SOS2 MUTATED    17   0   0   2
  SOS2 WILD-TYPE 210  10  10  22
D680V10, multiclass
    clus
vv   SOS2 MUTATED SOS2 WILD-TYPE
  R0           17            210
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D680V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SOS2 MUTATED       4                         0    13
  SOS2 WILD-TYPE    72                         4   155
D680V12, multiclass
                           clus
vv                          SOS2 MUTATED SOS2 WILD-TYPE
  ASIAN                                4             72
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               13            155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(681) Variable = ATL3 MUTATION ANALYSIS
D681V1, survival
                sevent
clus2              0   1
  ATL3 MUTATED     7   1
  ATL3 WILD-TYPE 174  79
  ATL3 MUTATED ATL3 WILD-TYPE 
             8            253 
  ATL3 MUTATED ATL3 WILD-TYPE 
             1             79 
$`ATL3 MUTATED`
TCGA-BR-4201 TCGA-BR-6566 TCGA-BR-8078 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CG-5721 
       30.90        32.78        12.26        11.57         0.10         6.02 
TCGA-CG-5728 TCGA-HU-A4G9 
       65.10        24.20 

$`ATL3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       11.84         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  ATL3 MUTATED ATL3 WILD-TYPE 
           0.1            0.0 
  ATL3 MUTATED ATL3 WILD-TYPE 
         65.10         105.07 
  ATL3 MUTATED ATL3 WILD-TYPE 
         18.23          12.62 
[1] "0.1 - 65.1 (18.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "4.1"
D681V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATL3 MUTATED         1        1        1        1         1         1
  ATL3 WILD-TYPE       0        8       26       25        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATL3 MUTATED           0          1          1          0        1
  ATL3 WILD-TYPE         3         48         35         24       23
D681V3, multiclass
            clus
vv           ATL3 MUTATED ATL3 WILD-TYPE
  STAGE I               1              0
  STAGE IA              1              8
  STAGE IB              1             26
  STAGE II              1             25
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ATL3 MUTATED     3   2   3   3
  ATL3 WILD-TYPE   8  70 119  72
D681V4, multiclass
    clus
vv   ATL3 MUTATED ATL3 WILD-TYPE
  T1            3              8
  T2            2             70
  T3            3            119
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  ATL3 MUTATED    6  2  0  1
  ATL3 WILD-TYPE 87 79 50 52
D681V5, multiclass
    clus
vv   ATL3 MUTATED ATL3 WILD-TYPE
  N0            6             87
  N1            2             79
  N2            0             50
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D681V6, binary
                cls
clus               0   1
  ATL3 MUTATED    11   0
  ATL3 WILD-TYPE 246  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATL3 MUTATED     11    0
  ATL3 WILD-TYPE  246   18
   clus
vv  ATL3 MUTATED ATL3 WILD-TYPE
  0           11            246
  1            0             18
[1] 2 2
[1] FALSE
D681V7, binary
                cls
clus               0   1
  ATL3 MUTATED     9   3
  ATL3 WILD-TYPE 101 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATL3 MUTATED      9    3
  ATL3 WILD-TYPE  101  176
        clus
vv       ATL3 MUTATED ATL3 WILD-TYPE
  FEMALE            9            101
  MALE              3            176
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ATL3 MUTATED                                       0
  ATL3 WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ATL3 MUTATED                                                        9
  ATL3 WILD-TYPE                                                    126
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ATL3 MUTATED                                                                   2
  ATL3 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ATL3 MUTATED                                                  1
  ATL3 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ATL3 MUTATED                                                          0
  ATL3 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ATL3 MUTATED                                                           0
  ATL3 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ATL3 MUTATED                                          0
  ATL3 WILD-TYPE                                        3
D681V8, multiclass
                                                                   clus
vv                                                                  ATL3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  ATL3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D681V9, binary
                cls
clus               0   1
  ATL3 MUTATED     0  12
  ATL3 WILD-TYPE   5 272
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATL3 MUTATED      0   12
  ATL3 WILD-TYPE    5  272
     clus
vv    ATL3 MUTATED ATL3 WILD-TYPE
  NO             0              5
  YES           12            272
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ATL3 MUTATED     8   0   0   4
  ATL3 WILD-TYPE 219  10  10  20
D681V10, multiclass
    clus
vv   ATL3 MUTATED ATL3 WILD-TYPE
  R0            8            219
  R1            0             10
  R2            0             10
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D681V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATL3 MUTATED       2                         1     7
  ATL3 WILD-TYPE    74                         3   161
D681V12, multiclass
                           clus
vv                          ATL3 MUTATED ATL3 WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                                7            161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(682) Variable = PEG3 MUTATION ANALYSIS
D682V1, survival
                sevent
clus2              0   1
  PEG3 MUTATED    22   8
  PEG3 WILD-TYPE 159  72
  PEG3 MUTATED PEG3 WILD-TYPE 
            30            231 
  PEG3 MUTATED PEG3 WILD-TYPE 
             8             72 
$`PEG3 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-8059 
        6.97        34.68        32.94        23.93        18.15        14.43 
TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8367 
        0.69        12.95         2.66        19.50         0.26        26.33 
TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-4438 TCGA-CG-4469 TCGA-CG-5721 
       19.17         1.12        15.81        54.08         7.07         6.02 
TCGA-D7-5577 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-HU-8602 
       12.36        13.35        17.19        13.78        14.76        11.41 
TCGA-HU-8604 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GT 
       12.10        11.84        24.20        11.77         8.98         6.51 

$`PEG3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 
       30.90        31.20        12.82         9.21        24.76        15.42 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       28.01        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       12.76        18.71        17.49        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        8.05        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        7.99        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.54        18.61        17.85        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-EQ-5647 TCGA-EQ-8122 
       14.27        16.44         5.92        15.16         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       14.17        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GU 
        3.25        22.75        25.81        29.98         0.10         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  PEG3 MUTATED PEG3 WILD-TYPE 
          0.26           0.00 
  PEG3 MUTATED PEG3 WILD-TYPE 
         54.08         105.07 
  PEG3 MUTATED PEG3 WILD-TYPE 
         13.15          12.59 
[1] "0.3 - 54.1 (13.1)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D682V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PEG3 MUTATED         0        2        2        1         6         3
  PEG3 WILD-TYPE       1        7       25       25        25        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PEG3 MUTATED           1          4          3          2        6
  PEG3 WILD-TYPE         2         45         33         22       18
D682V3, multiclass
            clus
vv           PEG3 MUTATED PEG3 WILD-TYPE
  STAGE I               0              1
  STAGE IA              2              7
  STAGE IB              2             25
  STAGE II              1             25
  STAGE IIA             6             25
  STAGE IIB             3             41
  STAGE III             1              2
  STAGE IIIA            4             45
  STAGE IIIB            3             33
  STAGE IIIC            2             22
  STAGE IV              6             18
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PEG3 MUTATED     3   6  12  10
  PEG3 WILD-TYPE   8  66 110  65
D682V4, multiclass
    clus
vv   PEG3 MUTATED PEG3 WILD-TYPE
  T1            3              8
  T2            6             66
  T3           12            110
  T4           10             65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  PEG3 MUTATED   11  7  6  6
  PEG3 WILD-TYPE 82 74 44 47
D682V5, multiclass
    clus
vv   PEG3 MUTATED PEG3 WILD-TYPE
  N0           11             82
  N1            7             74
  N2            6             44
  N3            6             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D682V6, binary
                cls
clus               0   1
  PEG3 MUTATED    28   2
  PEG3 WILD-TYPE 229  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  PEG3 MUTATED     28    2
  PEG3 WILD-TYPE  229   16
   clus
vv  PEG3 MUTATED PEG3 WILD-TYPE
  0           28            229
  1            2             16
[1] 2 2
[1] FALSE
D682V7, binary
                cls
clus               0   1
  PEG3 MUTATED    17  14
  PEG3 WILD-TYPE  93 165
[1] "tbl2"
                cls
clus             [,1] [,2]
  PEG3 MUTATED     17   14
  PEG3 WILD-TYPE   93  165
        clus
vv       PEG3 MUTATED PEG3 WILD-TYPE
  FEMALE           17             93
  MALE             14            165
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PEG3 MUTATED                                       4
  PEG3 WILD-TYPE                                    46
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PEG3 MUTATED                                                       13
  PEG3 WILD-TYPE                                                    122
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PEG3 MUTATED                                                                   6
  PEG3 WILD-TYPE                                                                34
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PEG3 MUTATED                                                  7
  PEG3 WILD-TYPE                                               31
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PEG3 MUTATED                                                          1
  PEG3 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PEG3 MUTATED                                                           0
  PEG3 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PEG3 MUTATED                                          0
  PEG3 WILD-TYPE                                        3
D682V8, multiclass
                                                                   clus
vv                                                                  PEG3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      13
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  PEG3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       122
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              31
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D682V9, binary
                cls
clus               0   1
  PEG3 MUTATED     0  31
  PEG3 WILD-TYPE   5 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  PEG3 MUTATED      0   31
  PEG3 WILD-TYPE    5  253
     clus
vv    PEG3 MUTATED PEG3 WILD-TYPE
  NO             0              5
  YES           31            253
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PEG3 MUTATED    27   1   0   2
  PEG3 WILD-TYPE 200   9  10  22
D682V10, multiclass
    clus
vv   PEG3 MUTATED PEG3 WILD-TYPE
  R0           27            200
  R1            1              9
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D682V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PEG3 MUTATED       8                         0    20
  PEG3 WILD-TYPE    68                         4   148
D682V12, multiclass
                           clus
vv                          PEG3 MUTATED PEG3 WILD-TYPE
  ASIAN                                8             68
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                               20            148
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(683) Variable = SMARCAL1 MUTATION ANALYSIS
D683V1, survival
                    sevent
clus2                  0   1
  SMARCAL1 MUTATED     9   2
  SMARCAL1 WILD-TYPE 172  78
  SMARCAL1 MUTATED SMARCAL1 WILD-TYPE 
                11                250 
  SMARCAL1 MUTATED SMARCAL1 WILD-TYPE 
                 2                 78 
$`SMARCAL1 MUTATED`
TCGA-BR-4191 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-7901 TCGA-BR-8360 TCGA-BR-A4QL 
       18.35        34.68        23.93         3.45         6.18        11.57 
TCGA-CD-8524 TCGA-CG-5728 TCGA-HU-8602 TCGA-HU-A4GD TCGA-HU-A4H8 
        0.07        65.10        11.41        22.75         8.88 

$`SMARCAL1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
       16.31         2.20        15.58         7.40        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       26.47         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
       19.36        23.84        12.30         9.67        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  SMARCAL1 MUTATED SMARCAL1 WILD-TYPE 
              0.07               0.00 
  SMARCAL1 MUTATED SMARCAL1 WILD-TYPE 
             65.10             105.07 
  SMARCAL1 MUTATED SMARCAL1 WILD-TYPE 
             11.57              12.64 
[1] "0.1 - 65.1 (11.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.1"
D683V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMARCAL1 MUTATED         0        0        3        1         2         3
  SMARCAL1 WILD-TYPE       1        9       24       25        29        41
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMARCAL1 MUTATED           0          0          1          0        1
  SMARCAL1 WILD-TYPE         3         49         35         24       23
D683V3, multiclass
            clus
vv           SMARCAL1 MUTATED SMARCAL1 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  3                 24
  STAGE II                  1                 25
  STAGE IIA                 2                 29
  STAGE IIB                 3                 41
  STAGE III                 0                  3
  STAGE IIIA                0                 49
  STAGE IIIB                1                 35
  STAGE IIIC                0                 24
  STAGE IV                  1                 23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SMARCAL1 MUTATED     2   2   6   2
  SMARCAL1 WILD-TYPE   9  70 116  73
D683V4, multiclass
    clus
vv   SMARCAL1 MUTATED SMARCAL1 WILD-TYPE
  T1                2                  9
  T2                2                 70
  T3                6                116
  T4                2                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  SMARCAL1 MUTATED    6  4  1  1
  SMARCAL1 WILD-TYPE 87 77 49 52
D683V5, multiclass
    clus
vv   SMARCAL1 MUTATED SMARCAL1 WILD-TYPE
  N0                6                 87
  N1                4                 77
  N2                1                 49
  N3                1                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D683V6, binary
                    cls
clus                   0   1
  SMARCAL1 MUTATED    13   0
  SMARCAL1 WILD-TYPE 244  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SMARCAL1 MUTATED     13    0
  SMARCAL1 WILD-TYPE  244   18
   clus
vv  SMARCAL1 MUTATED SMARCAL1 WILD-TYPE
  0               13                244
  1                0                 18
[1] 2 2
[1] FALSE
D683V7, binary
                    cls
clus                   0   1
  SMARCAL1 MUTATED     8   5
  SMARCAL1 WILD-TYPE 102 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SMARCAL1 MUTATED      8    5
  SMARCAL1 WILD-TYPE  102  174
        clus
vv       SMARCAL1 MUTATED SMARCAL1 WILD-TYPE
  FEMALE                8                102
  MALE                  5                174
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SMARCAL1 MUTATED                                       1
  SMARCAL1 WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SMARCAL1 MUTATED                                                        7
  SMARCAL1 WILD-TYPE                                                    128
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SMARCAL1 MUTATED                                                                   3
  SMARCAL1 WILD-TYPE                                                                37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SMARCAL1 MUTATED                                                  2
  SMARCAL1 WILD-TYPE                                               36
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SMARCAL1 MUTATED                                                          0
  SMARCAL1 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SMARCAL1 MUTATED                                                           0
  SMARCAL1 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SMARCAL1 MUTATED                                          0
  SMARCAL1 WILD-TYPE                                        3
D683V8, multiclass
                                                                   clus
vv                                                                  SMARCAL1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  SMARCAL1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D683V9, binary
                    cls
clus                   0   1
  SMARCAL1 MUTATED     0  13
  SMARCAL1 WILD-TYPE   5 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SMARCAL1 MUTATED      0   13
  SMARCAL1 WILD-TYPE    5  271
     clus
vv    SMARCAL1 MUTATED SMARCAL1 WILD-TYPE
  NO                 0                  5
  YES               13                271
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  SMARCAL1 MUTATED    10   0   0   3
  SMARCAL1 WILD-TYPE 217  10  10  21
D683V10, multiclass
    clus
vv   SMARCAL1 MUTATED SMARCAL1 WILD-TYPE
  R0               10                217
  R1                0                 10
  R2                0                 10
  RX                3                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D683V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMARCAL1 MUTATED       4                         0     8
  SMARCAL1 WILD-TYPE    72                         4   160
D683V12, multiclass
                           clus
vv                          SMARCAL1 MUTATED SMARCAL1 WILD-TYPE
  ASIAN                                    4                 72
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    8                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(684) Variable = THBS1 MUTATION ANALYSIS
D684V1, survival
                 sevent
clus2               0   1
  THBS1 MUTATED    11   1
  THBS1 WILD-TYPE 170  79
  THBS1 MUTATED THBS1 WILD-TYPE 
             12             249 
  THBS1 MUTATED THBS1 WILD-TYPE 
              1              79 
$`THBS1 MUTATED`
TCGA-BR-6707 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8591 TCGA-CD-8524 TCGA-CD-8531 
       19.89        32.94        23.93        13.45         0.07         0.10 
TCGA-CD-8536 TCGA-CG-5723 TCGA-HU-A4G8 TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GU 
        0.10       105.07        11.84        11.77        29.98         6.25 

$`THBS1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 
       26.10         9.17        32.78        25.61        18.05         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.07         0.39         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
        0.13         0.16         0.10         0.13         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         6.02         0.99        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
        3.25        22.75        25.81         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  THBS1 MUTATED THBS1 WILD-TYPE 
           0.07            0.00 
  THBS1 MUTATED THBS1 WILD-TYPE 
         105.07           79.07 
  THBS1 MUTATED THBS1 WILD-TYPE 
         12.645          12.620 
[1] "0.1 - 105.1 (12.6)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "5.6"
D684V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  THBS1 MUTATED         1        1        1        3         3         2
  THBS1 WILD-TYPE       0        8       26       23        28        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  THBS1 MUTATED           0          2          0          1        1
  THBS1 WILD-TYPE         3         47         36         23       23
D684V3, multiclass
            clus
vv           THBS1 MUTATED THBS1 WILD-TYPE
  STAGE I                1               0
  STAGE IA               1               8
  STAGE IB               1              26
  STAGE II               3              23
  STAGE IIA              3              28
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  THBS1 MUTATED     2   3   7   3
  THBS1 WILD-TYPE   9  69 115  72
D684V4, multiclass
    clus
vv   THBS1 MUTATED THBS1 WILD-TYPE
  T1             2               9
  T2             3              69
  T3             7             115
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  THBS1 MUTATED    7  6  1  1
  THBS1 WILD-TYPE 86 75 49 52
D684V5, multiclass
    clus
vv   THBS1 MUTATED THBS1 WILD-TYPE
  N0             7              86
  N1             6              75
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D684V6, binary
                 cls
clus                0   1
  THBS1 MUTATED    14   0
  THBS1 WILD-TYPE 243  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS1 MUTATED     14    0
  THBS1 WILD-TYPE  243   18
   clus
vv  THBS1 MUTATED THBS1 WILD-TYPE
  0            14             243
  1             0              18
[1] 2 2
[1] FALSE
D684V7, binary
                 cls
clus                0   1
  THBS1 MUTATED     7   8
  THBS1 WILD-TYPE 103 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS1 MUTATED      7    8
  THBS1 WILD-TYPE  103  171
        clus
vv       THBS1 MUTATED THBS1 WILD-TYPE
  FEMALE             7             103
  MALE               8             171
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  THBS1 MUTATED                                       3
  THBS1 WILD-TYPE                                    47
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  THBS1 MUTATED                                                        9
  THBS1 WILD-TYPE                                                    126
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  THBS1 MUTATED                                                                   1
  THBS1 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  THBS1 MUTATED                                                  2
  THBS1 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  THBS1 MUTATED                                                          0
  THBS1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  THBS1 MUTATED                                                           0
  THBS1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  THBS1 MUTATED                                          0
  THBS1 WILD-TYPE                                        3
D684V8, multiclass
                                                                   clus
vv                                                                  THBS1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  THBS1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D684V9, binary
                 cls
clus                0   1
  THBS1 MUTATED     0  15
  THBS1 WILD-TYPE   5 269
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS1 MUTATED      0   15
  THBS1 WILD-TYPE    5  269
     clus
vv    THBS1 MUTATED THBS1 WILD-TYPE
  NO              0               5
  YES            15             269
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  THBS1 MUTATED    12   0   0   2
  THBS1 WILD-TYPE 215  10  10  22
D684V10, multiclass
    clus
vv   THBS1 MUTATED THBS1 WILD-TYPE
  R0            12             215
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D684V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  THBS1 MUTATED       7                         1     6
  THBS1 WILD-TYPE    69                         3   162
D684V12, multiclass
                           clus
vv                          THBS1 MUTATED THBS1 WILD-TYPE
  ASIAN                                 7              69
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 6             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(685) Variable = PUS7 MUTATION ANALYSIS
D685V1, survival
                sevent
clus2              0   1
  PUS7 MUTATED     5   3
  PUS7 WILD-TYPE 176  77
  PUS7 MUTATED PUS7 WILD-TYPE 
             8            253 
  PUS7 MUTATED PUS7 WILD-TYPE 
             3             77 
$`PUS7 MUTATED`
TCGA-BR-8081 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-5720 TCGA-CG-5721 TCGA-HJ-7597 
       20.55        15.81        11.57         0.99         6.02        26.47 
TCGA-HU-A4GQ TCGA-HU-A4H8 
        0.10         8.88 

$`PUS7 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5723 
       30.97         6.97        36.00         1.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56        11.08         5.52         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        9.67        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  PUS7 MUTATED PUS7 WILD-TYPE 
           0.1            0.0 
  PUS7 MUTATED PUS7 WILD-TYPE 
         26.47         105.07 
  PUS7 MUTATED PUS7 WILD-TYPE 
        10.225         12.660 
[1] "0.1 - 26.5 (10.2)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.5"
D685V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PUS7 MUTATED         0        0        3        0         0         1
  PUS7 WILD-TYPE       1        9       24       26        31        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PUS7 MUTATED           0          1          1          1        2
  PUS7 WILD-TYPE         3         48         35         23       22
D685V3, multiclass
            clus
vv           PUS7 MUTATED PUS7 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              3             24
  STAGE II              0             26
  STAGE IIA             0             31
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            1             23
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PUS7 MUTATED     1   2   1   5
  PUS7 WILD-TYPE  10  70 121  70
D685V4, multiclass
    clus
vv   PUS7 MUTATED PUS7 WILD-TYPE
  T1            1             10
  T2            2             70
  T3            1            121
  T4            5             70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  PUS7 MUTATED    4  3  2  1
  PUS7 WILD-TYPE 89 78 48 52
D685V5, multiclass
    clus
vv   PUS7 MUTATED PUS7 WILD-TYPE
  N0            4             89
  N1            3             78
  N2            2             48
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D685V6, binary
                cls
clus               0   1
  PUS7 MUTATED     8   1
  PUS7 WILD-TYPE 249  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  PUS7 MUTATED      8    1
  PUS7 WILD-TYPE  249   17
   clus
vv  PUS7 MUTATED PUS7 WILD-TYPE
  0            8            249
  1            1             17
[1] 2 2
[1] FALSE
D685V7, binary
                cls
clus               0   1
  PUS7 MUTATED     5   5
  PUS7 WILD-TYPE 105 174
[1] "tbl2"
                cls
clus             [,1] [,2]
  PUS7 MUTATED      5    5
  PUS7 WILD-TYPE  105  174
        clus
vv       PUS7 MUTATED PUS7 WILD-TYPE
  FEMALE            5            105
  MALE              5            174
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PUS7 MUTATED                                       0
  PUS7 WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PUS7 MUTATED                                                        5
  PUS7 WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PUS7 MUTATED                                                                   1
  PUS7 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PUS7 MUTATED                                                  3
  PUS7 WILD-TYPE                                               35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PUS7 MUTATED                                                          0
  PUS7 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PUS7 MUTATED                                                           0
  PUS7 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PUS7 MUTATED                                          1
  PUS7 WILD-TYPE                                        2
D685V8, multiclass
                                                                   clus
vv                                                                  PUS7 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  PUS7 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D685V9, binary
                cls
clus               0   1
  PUS7 MUTATED     0  10
  PUS7 WILD-TYPE   5 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  PUS7 MUTATED      0   10
  PUS7 WILD-TYPE    5  274
     clus
vv    PUS7 MUTATED PUS7 WILD-TYPE
  NO             0              5
  YES           10            274
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PUS7 MUTATED     8   0   0   2
  PUS7 WILD-TYPE 219  10  10  22
D685V10, multiclass
    clus
vv   PUS7 MUTATED PUS7 WILD-TYPE
  R0            8            219
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D685V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PUS7 MUTATED       3                         0     5
  PUS7 WILD-TYPE    73                         4   163
D685V12, multiclass
                           clus
vv                          PUS7 MUTATED PUS7 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                5            163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(686) Variable = RALGDS MUTATION ANALYSIS
D686V1, survival
                  sevent
clus2                0   1
  RALGDS MUTATED     9   2
  RALGDS WILD-TYPE 172  78
  RALGDS MUTATED RALGDS WILD-TYPE 
              11              250 
  RALGDS MUTATED RALGDS WILD-TYPE 
               2               78 
$`RALGDS MUTATED`
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8368 TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-5721 
       30.90        32.94         4.31         0.10         0.10         6.02 
TCGA-CG-5726 TCGA-HJ-7597 TCGA-HU-A4G9 TCGA-HU-A4GT TCGA-HU-A4H3 
       28.96        26.47        24.20         6.51        19.36 

$`RALGDS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
        8.98        21.11        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.52         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  RALGDS MUTATED RALGDS WILD-TYPE 
             0.1              0.0 
  RALGDS MUTATED RALGDS WILD-TYPE 
           32.94           105.07 
  RALGDS MUTATED RALGDS WILD-TYPE 
          19.360           12.605 
[1] "0.1 - 32.9 (19.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.3"
D686V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RALGDS MUTATED         0        2        2        1         2         0
  RALGDS WILD-TYPE       1        7       25       25        29        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RALGDS MUTATED           0          1          1          1        2
  RALGDS WILD-TYPE         3         48         35         23       22
D686V3, multiclass
            clus
vv           RALGDS MUTATED RALGDS WILD-TYPE
  STAGE I                 0                1
  STAGE IA                2                7
  STAGE IB                2               25
  STAGE II                1               25
  STAGE IIA               2               29
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              1               23
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RALGDS MUTATED     2   2   5   3
  RALGDS WILD-TYPE   9  70 117  72
D686V4, multiclass
    clus
vv   RALGDS MUTATED RALGDS WILD-TYPE
  T1              2                9
  T2              2               70
  T3              5              117
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  RALGDS MUTATED    7  3  2  1
  RALGDS WILD-TYPE 86 78 48 52
D686V5, multiclass
    clus
vv   RALGDS MUTATED RALGDS WILD-TYPE
  N0              7               86
  N1              3               78
  N2              2               48
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D686V6, binary
                  cls
clus                 0   1
  RALGDS MUTATED    12   0
  RALGDS WILD-TYPE 245  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RALGDS MUTATED     12    0
  RALGDS WILD-TYPE  245   18
   clus
vv  RALGDS MUTATED RALGDS WILD-TYPE
  0             12              245
  1              0               18
[1] 2 2
[1] FALSE
D686V7, binary
                  cls
clus                 0   1
  RALGDS MUTATED     8   5
  RALGDS WILD-TYPE 102 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RALGDS MUTATED      8    5
  RALGDS WILD-TYPE  102  174
        clus
vv       RALGDS MUTATED RALGDS WILD-TYPE
  FEMALE              8              102
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RALGDS MUTATED                                       1
  RALGDS WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RALGDS MUTATED                                                        7
  RALGDS WILD-TYPE                                                    128
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RALGDS MUTATED                                                                   2
  RALGDS WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RALGDS MUTATED                                                  2
  RALGDS WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RALGDS MUTATED                                                          0
  RALGDS WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RALGDS MUTATED                                                           0
  RALGDS WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RALGDS MUTATED                                          1
  RALGDS WILD-TYPE                                        2
D686V8, multiclass
                                                                   clus
vv                                                                  RALGDS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       1
                                                                   clus
vv                                                                  RALGDS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D686V9, binary
                  cls
clus                 0   1
  RALGDS MUTATED     0  13
  RALGDS WILD-TYPE   5 271
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RALGDS MUTATED      0   13
  RALGDS WILD-TYPE    5  271
     clus
vv    RALGDS MUTATED RALGDS WILD-TYPE
  NO               0                5
  YES             13              271
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RALGDS MUTATED    10   0   0   2
  RALGDS WILD-TYPE 217  10  10  22
D686V10, multiclass
    clus
vv   RALGDS MUTATED RALGDS WILD-TYPE
  R0             10              217
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D686V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RALGDS MUTATED       5                         0     6
  RALGDS WILD-TYPE    71                         4   162
D686V12, multiclass
                           clus
vv                          RALGDS MUTATED RALGDS WILD-TYPE
  ASIAN                                  5               71
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(687) Variable = CNTROB MUTATION ANALYSIS
D687V1, survival
                  sevent
clus2                0   1
  CNTROB MUTATED     4   2
  CNTROB WILD-TYPE 177  78
  CNTROB MUTATED CNTROB WILD-TYPE 
               6              255 
  CNTROB MUTATED CNTROB WILD-TYPE 
               2               78 
$`CNTROB MUTATED`
TCGA-B7-5816 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8487 TCGA-CD-A48C TCGA-HU-A4GT 
       26.70         6.61        34.68         1.12        11.61         6.51 

$`CNTROB WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       30.90         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG 
        0.10         3.42         9.34        11.31        12.43         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         0.10         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  CNTROB MUTATED CNTROB WILD-TYPE 
            1.12             0.00 
  CNTROB MUTATED CNTROB WILD-TYPE 
           34.68           105.07 
  CNTROB MUTATED CNTROB WILD-TYPE 
            9.11            12.66 
[1] "1.1 - 34.7 (9.1)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1"  
D687V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CNTROB MUTATED         0        0        0        0         3         2
  CNTROB WILD-TYPE       1        9       27       26        28        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNTROB MUTATED           1          0          0          0        0
  CNTROB WILD-TYPE         2         49         36         24       24
D687V3, multiclass
            clus
vv           CNTROB MUTATED CNTROB WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               3               28
  STAGE IIB               2               42
  STAGE III               1                2
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CNTROB MUTATED     0   1   4   1
  CNTROB WILD-TYPE  11  71 118  74
D687V4, multiclass
    clus
vv   CNTROB MUTATED CNTROB WILD-TYPE
  T1              0               11
  T2              1               71
  T3              4              118
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CNTROB MUTATED    4  2  0  0
  CNTROB WILD-TYPE 89 79 50 53
D687V5, multiclass
    clus
vv   CNTROB MUTATED CNTROB WILD-TYPE
  N0              4               89
  N1              2               79
  N2              0               50
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D687V6, binary
                  cls
clus                 0   1
  CNTROB MUTATED     6   0
  CNTROB WILD-TYPE 251  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNTROB MUTATED      6    0
  CNTROB WILD-TYPE  251   18
   clus
vv  CNTROB MUTATED CNTROB WILD-TYPE
  0              6              251
  1              0               18
[1] 2 2
[1] FALSE
D687V7, binary
                  cls
clus                 0   1
  CNTROB MUTATED     6   0
  CNTROB WILD-TYPE 104 179
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNTROB MUTATED      6    0
  CNTROB WILD-TYPE  104  179
        clus
vv       CNTROB MUTATED CNTROB WILD-TYPE
  FEMALE              6              104
  MALE                0              179
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CNTROB MUTATED                                       1
  CNTROB WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CNTROB MUTATED                                                        4
  CNTROB WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CNTROB MUTATED                                                                   0
  CNTROB WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CNTROB MUTATED                                                  1
  CNTROB WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CNTROB MUTATED                                                          0
  CNTROB WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CNTROB MUTATED                                                           0
  CNTROB WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CNTROB MUTATED                                          0
  CNTROB WILD-TYPE                                        3
D687V8, multiclass
                                                                   clus
vv                                                                  CNTROB MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  CNTROB WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D687V9, binary
                  cls
clus                 0   1
  CNTROB MUTATED     0   6
  CNTROB WILD-TYPE   5 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNTROB MUTATED      0    6
  CNTROB WILD-TYPE    5  278
     clus
vv    CNTROB MUTATED CNTROB WILD-TYPE
  NO               0                5
  YES              6              278
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CNTROB MUTATED     4   0   0   1
  CNTROB WILD-TYPE 223  10  10  23
D687V10, multiclass
    clus
vv   CNTROB MUTATED CNTROB WILD-TYPE
  R0              4              223
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D687V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CNTROB MUTATED       2                         0     4
  CNTROB WILD-TYPE    74                         4   164
D687V12, multiclass
                           clus
vv                          CNTROB MUTATED CNTROB WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(688) Variable = PFAS MUTATION ANALYSIS
D688V1, survival
                sevent
clus2              0   1
  PFAS MUTATED     7   2
  PFAS WILD-TYPE 174  78
  PFAS MUTATED PFAS WILD-TYPE 
             9            252 
  PFAS MUTATED PFAS WILD-TYPE 
             2             78 
$`PFAS MUTATED`
TCGA-BR-6452 TCGA-BR-7901 TCGA-BR-8078 TCGA-BR-A4QL TCGA-CD-A4MI TCGA-CG-4305 
       34.68         3.45        12.26        11.57         0.10        15.95 
TCGA-CG-5721 TCGA-CG-5733 TCGA-HU-8602 
        6.02        21.07        11.41 

$`PFAS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73        12.43         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10         4.01        69.04         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       26.47         5.92        12.59        14.17        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  PFAS MUTATED PFAS WILD-TYPE 
           0.1            0.0 
  PFAS MUTATED PFAS WILD-TYPE 
         34.68         105.07 
  PFAS MUTATED PFAS WILD-TYPE 
         11.57          12.71 
[1] "0.1 - 34.7 (11.6)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.3"
D688V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PFAS MUTATED         0        0        0        1         1         3
  PFAS WILD-TYPE       1        9       27       25        30        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PFAS MUTATED           0          1          2          0        1
  PFAS WILD-TYPE         3         48         34         24       23
D688V3, multiclass
            clus
vv           PFAS MUTATED PFAS WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              1             25
  STAGE IIA             1             30
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            2             34
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PFAS MUTATED     0   2   4   3
  PFAS WILD-TYPE  11  70 118  72
D688V4, multiclass
    clus
vv   PFAS MUTATED PFAS WILD-TYPE
  T1            0             11
  T2            2             70
  T3            4            118
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  PFAS MUTATED    3  4  1  1
  PFAS WILD-TYPE 90 77 49 52
D688V5, multiclass
    clus
vv   PFAS MUTATED PFAS WILD-TYPE
  N0            3             90
  N1            4             77
  N2            1             49
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D688V6, binary
                cls
clus               0   1
  PFAS MUTATED     9   0
  PFAS WILD-TYPE 248  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFAS MUTATED      9    0
  PFAS WILD-TYPE  248   18
   clus
vv  PFAS MUTATED PFAS WILD-TYPE
  0            9            248
  1            0             18
[1] 2 2
[1] FALSE
D688V7, binary
                cls
clus               0   1
  PFAS MUTATED     5   4
  PFAS WILD-TYPE 105 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFAS MUTATED      5    4
  PFAS WILD-TYPE  105  175
        clus
vv       PFAS MUTATED PFAS WILD-TYPE
  FEMALE            5            105
  MALE              4            175
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PFAS MUTATED                                       1
  PFAS WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PFAS MUTATED                                                        6
  PFAS WILD-TYPE                                                    129
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PFAS MUTATED                                                                   2
  PFAS WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PFAS MUTATED                                                  0
  PFAS WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PFAS MUTATED                                                          0
  PFAS WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PFAS MUTATED                                                           0
  PFAS WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PFAS MUTATED                                          0
  PFAS WILD-TYPE                                        3
D688V8, multiclass
                                                                   clus
vv                                                                  PFAS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  PFAS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D688V9, binary
                cls
clus               0   1
  PFAS MUTATED     0   9
  PFAS WILD-TYPE   5 275
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFAS MUTATED      0    9
  PFAS WILD-TYPE    5  275
     clus
vv    PFAS MUTATED PFAS WILD-TYPE
  NO             0              5
  YES            9            275
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PFAS MUTATED     8   0   0   0
  PFAS WILD-TYPE 219  10  10  24
D688V10, multiclass
    clus
vv   PFAS MUTATED PFAS WILD-TYPE
  R0            8            219
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D688V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PFAS MUTATED       2                         0     4
  PFAS WILD-TYPE    74                         4   164
D688V12, multiclass
                           clus
vv                          PFAS MUTATED PFAS WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                4            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(689) Variable = TCF7 MUTATION ANALYSIS
D689V1, survival
                sevent
clus2              0   1
  TCF7 MUTATED     6   1
  TCF7 WILD-TYPE 175  79
  TCF7 MUTATED TCF7 WILD-TYPE 
             7            254 
  TCF7 MUTATED TCF7 WILD-TYPE 
             1             79 
$`TCF7 MUTATED`
TCGA-BR-6802 TCGA-BR-7707 TCGA-CG-5723 TCGA-CG-5727 TCGA-HU-A4GQ TCGA-HU-A4GT 
       30.90        23.93       105.07        79.07         0.10         6.51 
TCGA-HU-A4H3 
       19.36 

$`TCF7 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        6.02         0.99        12.03        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU 
       22.75        25.81        11.77        29.98         8.98         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  TCF7 MUTATED TCF7 WILD-TYPE 
           0.1            0.0 
  TCF7 MUTATED TCF7 WILD-TYPE 
        105.07          72.23 
  TCF7 MUTATED TCF7 WILD-TYPE 
        23.930         12.575 
[1] "0.1 - 105.1 (23.9)" "0.0 - 72.2 (12.6)" 
[1] "hr=" "6.9"
D689V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TCF7 MUTATED         0        0        1        3         1         0
  TCF7 WILD-TYPE       1        9       26       23        30        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TCF7 MUTATED           0          1          0          2        0
  TCF7 WILD-TYPE         3         48         36         22       24
D689V3, multiclass
            clus
vv           TCF7 MUTATED TCF7 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              3             23
  STAGE IIA             1             30
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            2             22
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TCF7 MUTATED     0   3   3   2
  TCF7 WILD-TYPE  11  69 119  73
D689V4, multiclass
    clus
vv   TCF7 MUTATED TCF7 WILD-TYPE
  T1            0             11
  T2            3             69
  T3            3            119
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  TCF7 MUTATED    3  3  2  1
  TCF7 WILD-TYPE 90 78 48 52
D689V5, multiclass
    clus
vv   TCF7 MUTATED TCF7 WILD-TYPE
  N0            3             90
  N1            3             78
  N2            2             48
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D689V6, binary
                cls
clus               0   1
  TCF7 MUTATED     9   0
  TCF7 WILD-TYPE 248  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCF7 MUTATED      9    0
  TCF7 WILD-TYPE  248   18
   clus
vv  TCF7 MUTATED TCF7 WILD-TYPE
  0            9            248
  1            0             18
[1] 2 2
[1] FALSE
D689V7, binary
                cls
clus               0   1
  TCF7 MUTATED     4   5
  TCF7 WILD-TYPE 106 174
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCF7 MUTATED      4    5
  TCF7 WILD-TYPE  106  174
        clus
vv       TCF7 MUTATED TCF7 WILD-TYPE
  FEMALE            4            106
  MALE              5            174
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TCF7 MUTATED                                       1
  TCF7 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TCF7 MUTATED                                                        4
  TCF7 WILD-TYPE                                                    131
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TCF7 MUTATED                                                                   1
  TCF7 WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TCF7 MUTATED                                                  2
  TCF7 WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TCF7 MUTATED                                                          1
  TCF7 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TCF7 MUTATED                                                           0
  TCF7 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TCF7 MUTATED                                          0
  TCF7 WILD-TYPE                                        3
D689V8, multiclass
                                                                   clus
vv                                                                  TCF7 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  TCF7 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D689V9, binary
                cls
clus               0   1
  TCF7 MUTATED     1   8
  TCF7 WILD-TYPE   4 276
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCF7 MUTATED      1    8
  TCF7 WILD-TYPE    4  276
     clus
vv    TCF7 MUTATED TCF7 WILD-TYPE
  NO             1              4
  YES            8            276
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TCF7 MUTATED     8   0   0   1
  TCF7 WILD-TYPE 219  10  10  23
D689V10, multiclass
    clus
vv   TCF7 MUTATED TCF7 WILD-TYPE
  R0            8            219
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D689V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TCF7 MUTATED       3                         0     3
  TCF7 WILD-TYPE    73                         4   165
D689V12, multiclass
                           clus
vv                          TCF7 MUTATED TCF7 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                3            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(690) Variable = GPATCH8 MUTATION ANALYSIS
D690V1, survival
                   sevent
clus2                 0   1
  GPATCH8 MUTATED    13   8
  GPATCH8 WILD-TYPE 168  72
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
               21               240 
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
                8                72 
$`GPATCH8 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8059 
       26.70         6.97         6.61        34.68        32.94        14.43 
TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8368 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 
       20.55         0.26         4.31         6.02       105.07        65.10 
TCGA-CG-5733 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8602 TCGA-HU-A4GP TCGA-HU-A4GQ 
       21.07        26.47         5.92        11.41         8.98         0.10 
TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H8 
       10.19        12.95         8.88 

$`GPATCH8 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       12.82         9.21        24.76        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       12.76        18.71        17.49         0.69        12.26         9.60 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        19.50        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       12.03        28.96        79.07         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.52        12.59        14.17        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU 
       22.75        25.81        11.77        29.98         6.51         6.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        19.36        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
              0.1               0.0 
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
           105.07             79.07 
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
            11.41             12.64 
[1] "0.1 - 105.1 (11.4)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.1"
D690V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPATCH8 MUTATED         1        0        5        1         3         3
  GPATCH8 WILD-TYPE       0        9       22       25        28        41
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPATCH8 MUTATED           2          2          1          3        1
  GPATCH8 WILD-TYPE         1         47         35         21       23
D690V3, multiclass
            clus
vv           GPATCH8 MUTATED GPATCH8 WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                 0                 9
  STAGE IB                 5                22
  STAGE II                 1                25
  STAGE IIA                3                28
  STAGE IIB                3                41
  STAGE III                2                 1
  STAGE IIIA               2                47
  STAGE IIIB               1                35
  STAGE IIIC               3                21
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GPATCH8 MUTATED     3   8   4   8
  GPATCH8 WILD-TYPE   8  64 118  67
D690V4, multiclass
    clus
vv   GPATCH8 MUTATED GPATCH8 WILD-TYPE
  T1               3                 8
  T2               8                64
  T3               4               118
  T4               8                67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  GPATCH8 MUTATED    9  8  3  2
  GPATCH8 WILD-TYPE 84 73 47 51
D690V5, multiclass
    clus
vv   GPATCH8 MUTATED GPATCH8 WILD-TYPE
  N0               9                84
  N1               8                73
  N2               3                47
  N3               2                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D690V6, binary
                   cls
clus                  0   1
  GPATCH8 MUTATED    20   0
  GPATCH8 WILD-TYPE 237  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH8 MUTATED     20    0
  GPATCH8 WILD-TYPE  237   18
   clus
vv  GPATCH8 MUTATED GPATCH8 WILD-TYPE
  0              20               237
  1               0                18
[1] 2 2
[1] FALSE
D690V7, binary
                   cls
clus                  0   1
  GPATCH8 MUTATED    15   8
  GPATCH8 WILD-TYPE  95 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH8 MUTATED     15    8
  GPATCH8 WILD-TYPE   95  171
        clus
vv       GPATCH8 MUTATED GPATCH8 WILD-TYPE
  FEMALE              15                95
  MALE                 8               171
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  GPATCH8 MUTATED                                       4
  GPATCH8 WILD-TYPE                                    46
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPATCH8 MUTATED                                                       10
  GPATCH8 WILD-TYPE                                                    125
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  GPATCH8 MUTATED                                                                   4
  GPATCH8 WILD-TYPE                                                                36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  GPATCH8 MUTATED                                                  4
  GPATCH8 WILD-TYPE                                               34
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  GPATCH8 MUTATED                                                          0
  GPATCH8 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  GPATCH8 MUTATED                                                           0
  GPATCH8 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  GPATCH8 MUTATED                                          1
  GPATCH8 WILD-TYPE                                        2
D690V8, multiclass
                                                                   clus
vv                                                                  GPATCH8 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  GPATCH8 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D690V9, binary
                   cls
clus                  0   1
  GPATCH8 MUTATED     0  23
  GPATCH8 WILD-TYPE   5 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH8 MUTATED      0   23
  GPATCH8 WILD-TYPE    5  261
     clus
vv    GPATCH8 MUTATED GPATCH8 WILD-TYPE
  NO                0                 5
  YES              23               261
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  GPATCH8 MUTATED    20   0   0   3
  GPATCH8 WILD-TYPE 207  10  10  21
D690V10, multiclass
    clus
vv   GPATCH8 MUTATED GPATCH8 WILD-TYPE
  R0              20               207
  R1               0                10
  R2               0                10
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D690V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPATCH8 MUTATED       7                         1    11
  GPATCH8 WILD-TYPE    69                         3   157
D690V12, multiclass
                           clus
vv                          GPATCH8 MUTATED GPATCH8 WILD-TYPE
  ASIAN                                   7                69
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                  11               157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(691) Variable = PSD MUTATION ANALYSIS
D691V1, survival
               sevent
clus2             0   1
  PSD MUTATED     9   4
  PSD WILD-TYPE 172  76
  PSD MUTATED PSD WILD-TYPE 
           13           248 
  PSD MUTATED PSD WILD-TYPE 
            4            76 
$`PSD MUTATED`
TCGA-BR-6706 TCGA-BR-7703 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-8589 
       18.05        24.76        12.26         0.26         1.12        15.81 
TCGA-BR-8591 TCGA-BR-8680 TCGA-CG-5726 TCGA-HJ-7597 TCGA-HU-A4G9 TCGA-HU-A4GU 
       13.45        15.81        28.96        26.47        24.20         6.25 
TCGA-HU-A4H0 
        2.10 

$`PSD WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        32.78        25.61        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       19.50        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       12.79         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 
        5.03        13.58         0.56        11.08         5.52         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        11.84         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  PSD MUTATED PSD WILD-TYPE 
         0.26          0.00 
  PSD MUTATED PSD WILD-TYPE 
        28.96        105.07 
  PSD MUTATED PSD WILD-TYPE 
       15.810        12.575 
[1] "0.3 - 29.0 (15.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.1"
D691V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PSD MUTATED         1        3        2        1         1         2
  PSD WILD-TYPE       0        6       25       25        30        42
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PSD MUTATED           0          1          1          2        1
  PSD WILD-TYPE         3         48         35         22       23
D691V3, multiclass
            clus
vv           PSD MUTATED PSD WILD-TYPE
  STAGE I              1             0
  STAGE IA             3             6
  STAGE IB             2            25
  STAGE II             1            25
  STAGE IIA            1            30
  STAGE IIB            2            42
  STAGE III            0             3
  STAGE IIIA           1            48
  STAGE IIIB           1            35
  STAGE IIIC           2            22
  STAGE IV             1            23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  PSD MUTATED     4   3   3   5
  PSD WILD-TYPE   7  69 119  70
D691V4, multiclass
    clus
vv   PSD MUTATED PSD WILD-TYPE
  T1           4             7
  T2           3            69
  T3           3           119
  T4           5            70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  PSD MUTATED    7  5  1  2
  PSD WILD-TYPE 86 76 49 51
D691V5, multiclass
    clus
vv   PSD MUTATED PSD WILD-TYPE
  N0           7            86
  N1           5            76
  N2           1            49
  N3           2            51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D691V6, binary
               cls
clus              0   1
  PSD MUTATED    13   1
  PSD WILD-TYPE 244  17
[1] "tbl2"
               cls
clus            [,1] [,2]
  PSD MUTATED     13    1
  PSD WILD-TYPE  244   17
   clus
vv  PSD MUTATED PSD WILD-TYPE
  0          13           244
  1           1            17
[1] 2 2
[1] FALSE
D691V7, binary
               cls
clus              0   1
  PSD MUTATED     6  10
  PSD WILD-TYPE 104 169
[1] "tbl2"
               cls
clus            [,1] [,2]
  PSD MUTATED      6   10
  PSD WILD-TYPE  104  169
        clus
vv       PSD MUTATED PSD WILD-TYPE
  FEMALE           6           104
  MALE            10           169
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PSD MUTATED                                       2
  PSD WILD-TYPE                                    48
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PSD MUTATED                                                        8
  PSD WILD-TYPE                                                    127
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PSD MUTATED                                                                   1
  PSD WILD-TYPE                                                                39
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PSD MUTATED                                                  2
  PSD WILD-TYPE                                               36
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PSD MUTATED                                                          1
  PSD WILD-TYPE                                                       15
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PSD MUTATED                                                           1
  PSD WILD-TYPE                                                         5
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PSD MUTATED                                          1
  PSD WILD-TYPE                                        2
D691V8, multiclass
                                                                   clus
vv                                                                  PSD MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    1
                                                                   clus
vv                                                                  PSD WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D691V9, binary
               cls
clus              0   1
  PSD MUTATED     1  15
  PSD WILD-TYPE   4 269
[1] "tbl2"
               cls
clus            [,1] [,2]
  PSD MUTATED      1   15
  PSD WILD-TYPE    4  269
     clus
vv    PSD MUTATED PSD WILD-TYPE
  NO            1             4
  YES          15           269
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  PSD MUTATED    15   0   0   1
  PSD WILD-TYPE 212  10  10  23
D691V10, multiclass
    clus
vv   PSD MUTATED PSD WILD-TYPE
  R0          15           212
  R1           0            10
  R2           0            10
  RX           1            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D691V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PSD MUTATED       4                         1     9
  PSD WILD-TYPE    72                         3   159
D691V12, multiclass
                           clus
vv                          PSD MUTATED PSD WILD-TYPE
  ASIAN                               4            72
  BLACK OR AFRICAN AMERICAN           1             3
  WHITE                               9           159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(692) Variable = MMEL1 MUTATION ANALYSIS
D692V1, survival
                 sevent
clus2               0   1
  MMEL1 MUTATED     2   3
  MMEL1 WILD-TYPE 179  77
  MMEL1 MUTATED MMEL1 WILD-TYPE 
              5             256 
  MMEL1 MUTATED MMEL1 WILD-TYPE 
              3              77 
$`MMEL1 MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-A4QL TCGA-CG-5726 TCGA-HU-A4H3 
        6.97         6.61        11.57        28.96        19.36 

$`MMEL1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  MMEL1 MUTATED MMEL1 WILD-TYPE 
           6.61            0.00 
  MMEL1 MUTATED MMEL1 WILD-TYPE 
          28.96          105.07 
  MMEL1 MUTATED MMEL1 WILD-TYPE 
          11.57           12.64 
[1] "6.6 - 29.0 (11.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.8"
D692V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MMEL1 MUTATED         0        1        1        0         0         0
  MMEL1 WILD-TYPE       1        8       26       26        31        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MMEL1 MUTATED           1          1          1          1        0
  MMEL1 WILD-TYPE         2         48         35         23       24
D692V3, multiclass
            clus
vv           MMEL1 MUTATED MMEL1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              0              31
  STAGE IIB              0              44
  STAGE III              1               2
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MMEL1 MUTATED     1   2   2   1
  MMEL1 WILD-TYPE  10  70 120  74
D692V4, multiclass
    clus
vv   MMEL1 MUTATED MMEL1 WILD-TYPE
  T1             1              10
  T2             2              70
  T3             2             120
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  MMEL1 MUTATED    2  2  0  2
  MMEL1 WILD-TYPE 91 79 50 51
D692V5, multiclass
    clus
vv   MMEL1 MUTATED MMEL1 WILD-TYPE
  N0             2              91
  N1             2              79
  N2             0              50
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D692V6, binary
                 cls
clus                0   1
  MMEL1 MUTATED     5   0
  MMEL1 WILD-TYPE 252  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMEL1 MUTATED      5    0
  MMEL1 WILD-TYPE  252   18
   clus
vv  MMEL1 MUTATED MMEL1 WILD-TYPE
  0             5             252
  1             0              18
[1] 2 2
[1] FALSE
D692V7, binary
                 cls
clus                0   1
  MMEL1 MUTATED     3   3
  MMEL1 WILD-TYPE 107 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMEL1 MUTATED      3    3
  MMEL1 WILD-TYPE  107  176
        clus
vv       MMEL1 MUTATED MMEL1 WILD-TYPE
  FEMALE             3             107
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MMEL1 MUTATED                                       1
  MMEL1 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MMEL1 MUTATED                                                        3
  MMEL1 WILD-TYPE                                                    132
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MMEL1 MUTATED                                                                   2
  MMEL1 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MMEL1 MUTATED                                                  0
  MMEL1 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MMEL1 MUTATED                                                          0
  MMEL1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MMEL1 MUTATED                                                           0
  MMEL1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MMEL1 MUTATED                                          0
  MMEL1 WILD-TYPE                                        3
D692V8, multiclass
                                                                   clus
vv                                                                  MMEL1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  MMEL1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D692V9, binary
                 cls
clus                0   1
  MMEL1 MUTATED     0   6
  MMEL1 WILD-TYPE   5 278
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMEL1 MUTATED      0    6
  MMEL1 WILD-TYPE    5  278
     clus
vv    MMEL1 MUTATED MMEL1 WILD-TYPE
  NO              0               5
  YES             6             278
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MMEL1 MUTATED     4   0   0   2
  MMEL1 WILD-TYPE 223  10  10  22
D692V10, multiclass
    clus
vv   MMEL1 MUTATED MMEL1 WILD-TYPE
  R0             4             223
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D692V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MMEL1 MUTATED       1                         0     3
  MMEL1 WILD-TYPE    75                         4   165
D692V12, multiclass
                           clus
vv                          MMEL1 MUTATED MMEL1 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(693) Variable = OSBPL2 MUTATION ANALYSIS
D693V1, survival
                  sevent
clus2                0   1
  OSBPL2 MUTATED     5   2
  OSBPL2 WILD-TYPE 176  78
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
               7              254 
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
               2               78 
$`OSBPL2 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-A4QL TCGA-CD-A487 TCGA-CG-4436 
       26.70         6.97        30.90        11.57         9.34         7.99 
TCGA-HU-A4H5 
       12.30 

$`OSBPL2 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 
       11.70         6.61         4.64         7.43        18.35         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         3.42        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
            6.97             0.00 
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
           30.90           105.07 
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
           11.57            12.71 
[1] "7.0 - 30.9 (11.6)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.2"
D693V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OSBPL2 MUTATED         0        0        2        0         0         2
  OSBPL2 WILD-TYPE       1        9       25       26        31        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OSBPL2 MUTATED           0          1          1          0        0
  OSBPL2 WILD-TYPE         3         48         35         24       24
D693V3, multiclass
            clus
vv           OSBPL2 MUTATED OSBPL2 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                2               25
  STAGE II                0               26
  STAGE IIA               0               31
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OSBPL2 MUTATED     0   3   3   1
  OSBPL2 WILD-TYPE  11  69 119  74
D693V4, multiclass
    clus
vv   OSBPL2 MUTATED OSBPL2 WILD-TYPE
  T1              0               11
  T2              3               69
  T3              3              119
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  OSBPL2 MUTATED    3  2  0  1
  OSBPL2 WILD-TYPE 90 79 50 52
D693V5, multiclass
    clus
vv   OSBPL2 MUTATED OSBPL2 WILD-TYPE
  N0              3               90
  N1              2               79
  N2              0               50
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D693V6, binary
                  cls
clus                 0   1
  OSBPL2 MUTATED     6   0
  OSBPL2 WILD-TYPE 251  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL2 MUTATED      6    0
  OSBPL2 WILD-TYPE  251   18
   clus
vv  OSBPL2 MUTATED OSBPL2 WILD-TYPE
  0              6              251
  1              0               18
[1] 2 2
[1] FALSE
D693V7, binary
                  cls
clus                 0   1
  OSBPL2 MUTATED     3   4
  OSBPL2 WILD-TYPE 107 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL2 MUTATED      3    4
  OSBPL2 WILD-TYPE  107  175
        clus
vv       OSBPL2 MUTATED OSBPL2 WILD-TYPE
  FEMALE              3              107
  MALE                4              175
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  OSBPL2 MUTATED                                       2
  OSBPL2 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OSBPL2 MUTATED                                                        3
  OSBPL2 WILD-TYPE                                                    132
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OSBPL2 MUTATED                                                                   1
  OSBPL2 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  OSBPL2 MUTATED                                                  0
  OSBPL2 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  OSBPL2 MUTATED                                                          0
  OSBPL2 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  OSBPL2 MUTATED                                                           1
  OSBPL2 WILD-TYPE                                                         5
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  OSBPL2 MUTATED                                          0
  OSBPL2 WILD-TYPE                                        3
D693V8, multiclass
                                                                   clus
vv                                                                  OSBPL2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  OSBPL2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D693V9, binary
                  cls
clus                 0   1
  OSBPL2 MUTATED     0   7
  OSBPL2 WILD-TYPE   5 277
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL2 MUTATED      0    7
  OSBPL2 WILD-TYPE    5  277
     clus
vv    OSBPL2 MUTATED OSBPL2 WILD-TYPE
  NO               0                5
  YES              7              277
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OSBPL2 MUTATED     5   0   0   2
  OSBPL2 WILD-TYPE 222  10  10  22
D693V10, multiclass
    clus
vv   OSBPL2 MUTATED OSBPL2 WILD-TYPE
  R0              5              222
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D693V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OSBPL2 MUTATED       2                         0     4
  OSBPL2 WILD-TYPE    74                         4   164
D693V12, multiclass
                           clus
vv                          OSBPL2 MUTATED OSBPL2 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(694) Variable = TOX MUTATION ANALYSIS
D694V1, survival
               sevent
clus2             0   1
  TOX MUTATED     7   0
  TOX WILD-TYPE 174  80
  TOX MUTATED TOX WILD-TYPE 
            7           254 
  TOX MUTATED TOX WILD-TYPE 
            0            80 
$`TOX MUTATED`
TCGA-BR-7851 TCGA-BR-A4J2 TCGA-BR-A4J8 TCGA-CG-5728 TCGA-F1-6874 TCGA-HU-A4GH 
       12.43        14.17        13.51        65.10        14.47        11.77 
TCGA-HU-A4H5 
       12.30 

$`TOX WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 
       13.41        13.51        12.89         8.98         0.72         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        19.36        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        0.99       105.07        12.03        28.96        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.99        16.24        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  TOX MUTATED TOX WILD-TYPE 
        11.77          0.00 
  TOX MUTATED TOX WILD-TYPE 
        65.10        105.07 
  TOX MUTATED TOX WILD-TYPE 
       13.510        12.605 
[1] "11.8 - 65.1 (13.5)" "0.0 - 105.1 (12.6)"
[1] "hr="     "2.6e+07"
D694V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TOX MUTATED         0        1        4        1         0         2
  TOX WILD-TYPE       1        8       23       25        31        42
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TOX MUTATED           0          0          1          0        0
  TOX WILD-TYPE         3         49         35         24       24
D694V3, multiclass
            clus
vv           TOX MUTATED TOX WILD-TYPE
  STAGE I              0             1
  STAGE IA             1             8
  STAGE IB             4            23
  STAGE II             1            25
  STAGE IIA            0            31
  STAGE IIB            2            42
  STAGE III            0             3
  STAGE IIIA           0            49
  STAGE IIIB           1            35
  STAGE IIIC           0            24
  STAGE IV             0            24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  TOX MUTATED     1   5   1   2
  TOX WILD-TYPE  10  67 121  73
D694V4, multiclass
    clus
vv   TOX MUTATED TOX WILD-TYPE
  T1           1            10
  T2           5            67
  T3           1           121
  T4           2            73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  TOX MUTATED    7  1  0  1
  TOX WILD-TYPE 86 80 50 52
D694V5, multiclass
    clus
vv   TOX MUTATED TOX WILD-TYPE
  N0           7            86
  N1           1            80
  N2           0            50
  N3           1            52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D694V6, binary
               cls
clus              0   1
  TOX MUTATED     9   0
  TOX WILD-TYPE 248  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  TOX MUTATED      9    0
  TOX WILD-TYPE  248   18
   clus
vv  TOX MUTATED TOX WILD-TYPE
  0           9           248
  1           0            18
[1] 2 2
[1] FALSE
D694V7, binary
               cls
clus              0   1
  TOX MUTATED     2   7
  TOX WILD-TYPE 108 172
[1] "tbl2"
               cls
clus            [,1] [,2]
  TOX MUTATED      2    7
  TOX WILD-TYPE  108  172
        clus
vv       TOX MUTATED TOX WILD-TYPE
  FEMALE           2           108
  MALE             7           172
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TOX MUTATED                                       1
  TOX WILD-TYPE                                    49
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TOX MUTATED                                                        1
  TOX WILD-TYPE                                                    134
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TOX MUTATED                                                                   4
  TOX WILD-TYPE                                                                36
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TOX MUTATED                                                  1
  TOX WILD-TYPE                                               37
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TOX MUTATED                                                          1
  TOX WILD-TYPE                                                       15
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TOX MUTATED                                                           1
  TOX WILD-TYPE                                                         5
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TOX MUTATED                                          0
  TOX WILD-TYPE                                        3
D694V8, multiclass
                                                                   clus
vv                                                                  TOX MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      1
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  TOX WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D694V9, binary
               cls
clus              0   1
  TOX MUTATED     1   8
  TOX WILD-TYPE   4 276
[1] "tbl2"
               cls
clus            [,1] [,2]
  TOX MUTATED      1    8
  TOX WILD-TYPE    4  276
     clus
vv    TOX MUTATED TOX WILD-TYPE
  NO            1             4
  YES           8           276
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  TOX MUTATED     9   0   0   0
  TOX WILD-TYPE 218  10  10  24
D694V10, multiclass
    clus
vv   TOX MUTATED TOX WILD-TYPE
  R0           9           218
  R1           0            10
  R2           0            10
  RX           0            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D694V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TOX MUTATED       3                         0     3
  TOX WILD-TYPE    73                         4   165
D694V12, multiclass
                           clus
vv                          TOX MUTATED TOX WILD-TYPE
  ASIAN                               3            73
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                               3           165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(695) Variable = ROCK1 MUTATION ANALYSIS
D695V1, survival
                 sevent
clus2               0   1
  ROCK1 MUTATED    11   2
  ROCK1 WILD-TYPE 170  78
  ROCK1 MUTATED ROCK1 WILD-TYPE 
             13             248 
  ROCK1 MUTATED ROCK1 WILD-TYPE 
              2              78 
$`ROCK1 MUTATED`
TCGA-BR-4184 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-5733 
        6.97         1.12        15.81         3.02        15.95        21.07 
TCGA-D7-6518 TCGA-D7-A4YY TCGA-F1-6874 TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-A4H0 
       19.13        13.78        14.47        11.08        11.41         2.10 
TCGA-HU-A4H3 
       19.36 

$`ROCK1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
        7.99        12.36        12.66        11.93        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 
       14.76         0.62         7.99        16.24        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
        5.03        13.58         0.56         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.25        10.19         0.26        12.95        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  ROCK1 MUTATED ROCK1 WILD-TYPE 
           1.12            0.00 
  ROCK1 MUTATED ROCK1 WILD-TYPE 
          21.07          105.07 
  ROCK1 MUTATED ROCK1 WILD-TYPE 
         13.780          12.605 
[1] "1.1 - 21.1 (13.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.7"
D695V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ROCK1 MUTATED         0        0        2        1         2         1
  ROCK1 WILD-TYPE       1        9       25       25        29        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ROCK1 MUTATED           0          4          1          2        2
  ROCK1 WILD-TYPE         3         45         35         22       22
D695V3, multiclass
            clus
vv           ROCK1 MUTATED ROCK1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               2              25
  STAGE II               1              25
  STAGE IIA              2              29
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             4              45
  STAGE IIIB             1              35
  STAGE IIIC             2              22
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ROCK1 MUTATED     0   5   4   6
  ROCK1 WILD-TYPE  11  67 118  69
D695V4, multiclass
    clus
vv   ROCK1 MUTATED ROCK1 WILD-TYPE
  T1             0              11
  T2             5              67
  T3             4             118
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ROCK1 MUTATED    6  3  2  4
  ROCK1 WILD-TYPE 87 78 48 49
D695V5, multiclass
    clus
vv   ROCK1 MUTATED ROCK1 WILD-TYPE
  N0             6              87
  N1             3              78
  N2             2              48
  N3             4              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D695V6, binary
                 cls
clus                0   1
  ROCK1 MUTATED    13   2
  ROCK1 WILD-TYPE 244  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ROCK1 MUTATED     13    2
  ROCK1 WILD-TYPE  244   16
   clus
vv  ROCK1 MUTATED ROCK1 WILD-TYPE
  0            13             244
  1             2              16
[1] 2 2
[1] FALSE
D695V7, binary
                 cls
clus                0   1
  ROCK1 MUTATED     6  10
  ROCK1 WILD-TYPE 104 169
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ROCK1 MUTATED      6   10
  ROCK1 WILD-TYPE  104  169
        clus
vv       ROCK1 MUTATED ROCK1 WILD-TYPE
  FEMALE             6             104
  MALE              10             169
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ROCK1 MUTATED                                       4
  ROCK1 WILD-TYPE                                    46
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ROCK1 MUTATED                                                        8
  ROCK1 WILD-TYPE                                                    127
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ROCK1 MUTATED                                                                   3
  ROCK1 WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ROCK1 MUTATED                                                  1
  ROCK1 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ROCK1 MUTATED                                                          0
  ROCK1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ROCK1 MUTATED                                                           0
  ROCK1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ROCK1 MUTATED                                          0
  ROCK1 WILD-TYPE                                        3
D695V8, multiclass
                                                                   clus
vv                                                                  ROCK1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ROCK1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D695V9, binary
                 cls
clus                0   1
  ROCK1 MUTATED     0  16
  ROCK1 WILD-TYPE   5 268
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ROCK1 MUTATED      0   16
  ROCK1 WILD-TYPE    5  268
     clus
vv    ROCK1 MUTATED ROCK1 WILD-TYPE
  NO              0               5
  YES            16             268
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ROCK1 MUTATED    11   1   1   3
  ROCK1 WILD-TYPE 216   9   9  21
D695V10, multiclass
    clus
vv   ROCK1 MUTATED ROCK1 WILD-TYPE
  R0            11             216
  R1             1               9
  R2             1               9
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D695V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ROCK1 MUTATED       4                         1     7
  ROCK1 WILD-TYPE    72                         3   161
D695V12, multiclass
                           clus
vv                          ROCK1 MUTATED ROCK1 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                 7             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(696) Variable = LRP12 MUTATION ANALYSIS
D696V1, survival
                 sevent
clus2               0   1
  LRP12 MUTATED    14   6
  LRP12 WILD-TYPE 167  74
  LRP12 MUTATED LRP12 WILD-TYPE 
             20             241 
  LRP12 MUTATED LRP12 WILD-TYPE 
              6              74 
$`LRP12 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-8680 
        6.97        34.68        15.95        20.55         6.18        15.81 
TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5727 
       11.57         6.58        12.62         1.02         6.02        79.07 
TCGA-D7-A4YV TCGA-F1-6874 TCGA-F1-6875 TCGA-HU-8243 TCGA-HU-8604 TCGA-HU-A4GT 
        5.92        14.47        72.23         5.92        12.10         6.51 
TCGA-HU-A4H2 TCGA-HU-A4H8 
       12.95         8.88 

$`LRP12 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6455 TCGA-BR-6456 
       30.90         6.18         9.57         6.61        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69        12.26         9.60         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
       16.31         2.20        15.58         7.40        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 
       11.31        12.43        11.61        12.20         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-A448 
       13.78        14.76         0.62         7.99        16.24        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        11.41        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         0.10         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26         2.10        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        9.67        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  LRP12 MUTATED LRP12 WILD-TYPE 
           1.02            0.00 
  LRP12 MUTATED LRP12 WILD-TYPE 
          79.07          105.07 
  LRP12 MUTATED LRP12 WILD-TYPE 
         11.835          12.760 
[1] "1.0 - 79.1 (11.8)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.3"
D696V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LRP12 MUTATED         1        1        3        1         6         2
  LRP12 WILD-TYPE       0        8       24       25        25        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRP12 MUTATED           0          2          2          1        4
  LRP12 WILD-TYPE         3         47         34         23       20
D696V3, multiclass
            clus
vv           LRP12 MUTATED LRP12 WILD-TYPE
  STAGE I                1               0
  STAGE IA               1               8
  STAGE IB               3              24
  STAGE II               1              25
  STAGE IIA              6              25
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             2              34
  STAGE IIIC             1              23
  STAGE IV               4              20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LRP12 MUTATED     2   4  11   6
  LRP12 WILD-TYPE   9  68 111  69
D696V4, multiclass
    clus
vv   LRP12 MUTATED LRP12 WILD-TYPE
  T1             2               9
  T2             4              68
  T3            11             111
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  LRP12 MUTATED   11  6  3  3
  LRP12 WILD-TYPE 82 75 47 50
D696V5, multiclass
    clus
vv   LRP12 MUTATED LRP12 WILD-TYPE
  N0            11              82
  N1             6              75
  N2             3              47
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D696V6, binary
                 cls
clus                0   1
  LRP12 MUTATED    19   2
  LRP12 WILD-TYPE 238  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP12 MUTATED     19    2
  LRP12 WILD-TYPE  238   16
   clus
vv  LRP12 MUTATED LRP12 WILD-TYPE
  0            19             238
  1             2              16
[1] 2 2
[1] FALSE
D696V7, binary
                 cls
clus                0   1
  LRP12 MUTATED     9  14
  LRP12 WILD-TYPE 101 165
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP12 MUTATED      9   14
  LRP12 WILD-TYPE  101  165
        clus
vv       LRP12 MUTATED LRP12 WILD-TYPE
  FEMALE             9             101
  MALE              14             165
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  LRP12 MUTATED                                       1
  LRP12 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LRP12 MUTATED                                                       11
  LRP12 WILD-TYPE                                                    124
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LRP12 MUTATED                                                                   4
  LRP12 WILD-TYPE                                                                36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  LRP12 MUTATED                                                  7
  LRP12 WILD-TYPE                                               31
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  LRP12 MUTATED                                                          0
  LRP12 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  LRP12 MUTATED                                                           0
  LRP12 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  LRP12 MUTATED                                          0
  LRP12 WILD-TYPE                                        3
D696V8, multiclass
                                                                   clus
vv                                                                  LRP12 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  LRP12 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               31
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D696V9, binary
                 cls
clus                0   1
  LRP12 MUTATED     0  23
  LRP12 WILD-TYPE   5 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP12 MUTATED      0   23
  LRP12 WILD-TYPE    5  261
     clus
vv    LRP12 MUTATED LRP12 WILD-TYPE
  NO              0               5
  YES            23             261
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LRP12 MUTATED    17   0   1   3
  LRP12 WILD-TYPE 210  10   9  21
D696V10, multiclass
    clus
vv   LRP12 MUTATED LRP12 WILD-TYPE
  R0            17             210
  R1             0              10
  R2             1               9
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D696V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LRP12 MUTATED       8                         2    10
  LRP12 WILD-TYPE    68                         2   158
D696V12, multiclass
                           clus
vv                          LRP12 MUTATED LRP12 WILD-TYPE
  ASIAN                                 8              68
  BLACK OR AFRICAN AMERICAN             2               2
  WHITE                                10             158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(697) Variable = C19ORF70 MUTATION ANALYSIS
D697V1, survival
                    sevent
clus2                  0   1
  C19ORF70 MUTATED     4   1
  C19ORF70 WILD-TYPE 177  79
  C19ORF70 MUTATED C19ORF70 WILD-TYPE 
                 5                256 
  C19ORF70 MUTATED C19ORF70 WILD-TYPE 
                 1                 79 
$`C19ORF70 MUTATED`
TCGA-BR-7851 TCGA-BR-8360 TCGA-BR-8361 TCGA-CD-A4MG TCGA-HU-A4G8 
       12.43         6.18        19.50         6.58        11.84 

$`C19ORF70 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        7.40         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  C19ORF70 MUTATED C19ORF70 WILD-TYPE 
              6.18               0.00 
  C19ORF70 MUTATED C19ORF70 WILD-TYPE 
             19.50             105.07 
  C19ORF70 MUTATED C19ORF70 WILD-TYPE 
             11.84              12.71 
[1] "6.2 - 19.5 (11.8)"  "0.0 - 105.1 (12.7)"
[1] "hr=" "1.2"
D697V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C19ORF70 MUTATED         0        0        0        0         2         2
  C19ORF70 WILD-TYPE       1        9       27       26        29        42
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C19ORF70 MUTATED           0          0          0          1        0
  C19ORF70 WILD-TYPE         3         49         36         23       24
D697V3, multiclass
            clus
vv           C19ORF70 MUTATED C19ORF70 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  0                 27
  STAGE II                  0                 26
  STAGE IIA                 2                 29
  STAGE IIB                 2                 42
  STAGE III                 0                  3
  STAGE IIIA                0                 49
  STAGE IIIB                0                 36
  STAGE IIIC                1                 23
  STAGE IV                  0                 24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C19ORF70 MUTATED     0   0   3   2
  C19ORF70 WILD-TYPE  11  72 119  73
D697V4, multiclass
    clus
vv   C19ORF70 MUTATED C19ORF70 WILD-TYPE
  T1                0                 11
  T2                0                 72
  T3                3                119
  T4                2                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  C19ORF70 MUTATED    3  1  1  0
  C19ORF70 WILD-TYPE 90 80 49 53
D697V5, multiclass
    clus
vv   C19ORF70 MUTATED C19ORF70 WILD-TYPE
  N0                3                 90
  N1                1                 80
  N2                1                 49
  N3                0                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D697V6, binary
                    cls
clus                   0   1
  C19ORF70 MUTATED     6   0
  C19ORF70 WILD-TYPE 251  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF70 MUTATED      6    0
  C19ORF70 WILD-TYPE  251   18
   clus
vv  C19ORF70 MUTATED C19ORF70 WILD-TYPE
  0                6                251
  1                0                 18
[1] 2 2
[1] FALSE
D697V7, binary
                    cls
clus                   0   1
  C19ORF70 MUTATED     3   3
  C19ORF70 WILD-TYPE 107 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF70 MUTATED      3    3
  C19ORF70 WILD-TYPE  107  176
        clus
vv       C19ORF70 MUTATED C19ORF70 WILD-TYPE
  FEMALE                3                107
  MALE                  3                176
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C19ORF70 MUTATED                                       2
  C19ORF70 WILD-TYPE                                    48
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C19ORF70 MUTATED                                                        2
  C19ORF70 WILD-TYPE                                                    133
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C19ORF70 MUTATED                                                                   2
  C19ORF70 WILD-TYPE                                                                38
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C19ORF70 MUTATED                                                  0
  C19ORF70 WILD-TYPE                                               38
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C19ORF70 MUTATED                                                          0
  C19ORF70 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C19ORF70 MUTATED                                                           0
  C19ORF70 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C19ORF70 MUTATED                                          0
  C19ORF70 WILD-TYPE                                        3
D697V8, multiclass
                                                                   clus
vv                                                                  C19ORF70 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  C19ORF70 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D697V9, binary
                    cls
clus                   0   1
  C19ORF70 MUTATED     0   6
  C19ORF70 WILD-TYPE   5 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF70 MUTATED      0    6
  C19ORF70 WILD-TYPE    5  278
     clus
vv    C19ORF70 MUTATED C19ORF70 WILD-TYPE
  NO                 0                  5
  YES                6                278
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C19ORF70 MUTATED     3   0   0   1
  C19ORF70 WILD-TYPE 224  10  10  23
D697V10, multiclass
    clus
vv   C19ORF70 MUTATED C19ORF70 WILD-TYPE
  R0                3                224
  R1                0                 10
  R2                0                 10
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D697V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C19ORF70 MUTATED       2                         0     4
  C19ORF70 WILD-TYPE    74                         4   164
D697V12, multiclass
                           clus
vv                          C19ORF70 MUTATED C19ORF70 WILD-TYPE
  ASIAN                                    2                 74
  BLACK OR AFRICAN AMERICAN                0                  4
  WHITE                                    4                164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(698) Variable = KIAA1217 MUTATION ANALYSIS
D698V1, survival
                    sevent
clus2                  0   1
  KIAA1217 MUTATED    14   5
  KIAA1217 WILD-TYPE 167  75
  KIAA1217 MUTATED KIAA1217 WILD-TYPE 
                19                242 
  KIAA1217 MUTATED KIAA1217 WILD-TYPE 
                 5                 75 
$`KIAA1217 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8372 TCGA-BR-8591 TCGA-BR-8676 
        6.97        34.68        23.93        19.17        13.45         7.53 
TCGA-BR-8687 TCGA-BR-A4CQ TCGA-CD-8527 TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-5723 
        8.22        22.26         0.07         0.10         1.02       105.07 
TCGA-D7-A4YY TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4GT 
       13.78        11.08         5.52        26.47        11.41         6.51 
TCGA-HU-A4GU 
        6.25 

$`KIAA1217 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8677 
        1.12        12.79        15.81         9.34         6.28         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 
       11.54        15.81        16.44         9.86        15.68        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56        13.87         7.53         6.08         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       15.16        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-HU-8243 
       17.06        59.54         5.03        13.58         0.56         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX 
       25.81        11.77        29.98         8.98         0.10        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  KIAA1217 MUTATED KIAA1217 WILD-TYPE 
              0.07               0.00 
  KIAA1217 MUTATED KIAA1217 WILD-TYPE 
            105.07              79.07 
  KIAA1217 MUTATED KIAA1217 WILD-TYPE 
             11.08              12.71 
[1] "0.1 - 105.1 (11.1)" "0.0 - 79.1 (12.7)" 
[1] "hr=" "1.3"
D698V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1217 MUTATED         0        0        2        2         3         2
  KIAA1217 WILD-TYPE       1        9       25       24        28        42
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1217 MUTATED           0          3          3          3        1
  KIAA1217 WILD-TYPE         3         46         33         21       23
D698V3, multiclass
            clus
vv           KIAA1217 MUTATED KIAA1217 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  9
  STAGE IB                  2                 25
  STAGE II                  2                 24
  STAGE IIA                 3                 28
  STAGE IIB                 2                 42
  STAGE III                 0                  3
  STAGE IIIA                3                 46
  STAGE IIIB                3                 33
  STAGE IIIC                3                 21
  STAGE IV                  1                 23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1217 MUTATED     0   4  10   5
  KIAA1217 WILD-TYPE  11  68 112  70
D698V4, multiclass
    clus
vv   KIAA1217 MUTATED KIAA1217 WILD-TYPE
  T1                0                 11
  T2                4                 68
  T3               10                112
  T4                5                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  KIAA1217 MUTATED    6  6  3  4
  KIAA1217 WILD-TYPE 87 75 47 49
D698V5, multiclass
    clus
vv   KIAA1217 MUTATED KIAA1217 WILD-TYPE
  N0                6                 87
  N1                6                 75
  N2                3                 47
  N3                4                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D698V6, binary
                    cls
clus                   0   1
  KIAA1217 MUTATED    16   1
  KIAA1217 WILD-TYPE 241  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1217 MUTATED     16    1
  KIAA1217 WILD-TYPE  241   17
   clus
vv  KIAA1217 MUTATED KIAA1217 WILD-TYPE
  0               16                241
  1                1                 17
[1] 2 2
[1] FALSE
D698V7, binary
                    cls
clus                   0   1
  KIAA1217 MUTATED     7  12
  KIAA1217 WILD-TYPE 103 167
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1217 MUTATED      7   12
  KIAA1217 WILD-TYPE  103  167
        clus
vv       KIAA1217 MUTATED KIAA1217 WILD-TYPE
  FEMALE                7                103
  MALE                 12                167
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KIAA1217 MUTATED                                       2
  KIAA1217 WILD-TYPE                                    48
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA1217 MUTATED                                                       12
  KIAA1217 WILD-TYPE                                                    123
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA1217 MUTATED                                                                   2
  KIAA1217 WILD-TYPE                                                                38
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KIAA1217 MUTATED                                                  1
  KIAA1217 WILD-TYPE                                               37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KIAA1217 MUTATED                                                          0
  KIAA1217 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KIAA1217 MUTATED                                                           0
  KIAA1217 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KIAA1217 MUTATED                                          2
  KIAA1217 WILD-TYPE                                        1
D698V8, multiclass
                                                                   clus
vv                                                                  KIAA1217 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          12
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  KIAA1217 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           123
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           1
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D698V9, binary
                    cls
clus                   0   1
  KIAA1217 MUTATED     0  19
  KIAA1217 WILD-TYPE   5 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1217 MUTATED      0   19
  KIAA1217 WILD-TYPE    5  265
     clus
vv    KIAA1217 MUTATED KIAA1217 WILD-TYPE
  NO                 0                  5
  YES               19                265
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA1217 MUTATED    14   2   1   1
  KIAA1217 WILD-TYPE 213   8   9  23
D698V10, multiclass
    clus
vv   KIAA1217 MUTATED KIAA1217 WILD-TYPE
  R0               14                213
  R1                2                  8
  R2                1                  9
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D698V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA1217 MUTATED       5                         1    11
  KIAA1217 WILD-TYPE    71                         3   157
D698V12, multiclass
                           clus
vv                          KIAA1217 MUTATED KIAA1217 WILD-TYPE
  ASIAN                                    5                 71
  BLACK OR AFRICAN AMERICAN                1                  3
  WHITE                                   11                157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(699) Variable = CENPN MUTATION ANALYSIS
D699V1, survival
                 sevent
clus2               0   1
  CENPN MUTATED     4   0
  CENPN WILD-TYPE 177  80
  CENPN MUTATED CENPN WILD-TYPE 
              4             257 
  CENPN MUTATED CENPN WILD-TYPE 
              0              80 
$`CENPN MUTATED`
TCGA-BR-8680 TCGA-CG-5721 TCGA-D7-8570 TCGA-HU-8604 
       15.81         6.02        24.72        12.10 

$`CENPN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       15.98        12.79        10.55        11.31        12.33        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        11.41        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  CENPN MUTATED CENPN WILD-TYPE 
           6.02            0.00 
  CENPN MUTATED CENPN WILD-TYPE 
          24.72          105.07 
  CENPN MUTATED CENPN WILD-TYPE 
         13.955          12.620 
[1] "6.0 - 24.7 (14.0)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "9100000"
D699V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CENPN MUTATED         0        0        0        0         1         0
  CENPN WILD-TYPE       1        9       27       26        30        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CENPN MUTATED           0          0          1          0        2
  CENPN WILD-TYPE         3         49         35         24       22
D699V3, multiclass
            clus
vv           CENPN MUTATED CENPN WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              0              44
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CENPN MUTATED     0   0   2   2
  CENPN WILD-TYPE  11  72 120  73
D699V4, multiclass
    clus
vv   CENPN MUTATED CENPN WILD-TYPE
  T1             0              11
  T2             0              72
  T3             2             120
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CENPN MUTATED    1  1  1  1
  CENPN WILD-TYPE 92 80 49 52
D699V5, multiclass
    clus
vv   CENPN MUTATED CENPN WILD-TYPE
  N0             1              92
  N1             1              80
  N2             1              49
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D699V6, binary
                 cls
clus                0   1
  CENPN MUTATED     3   1
  CENPN WILD-TYPE 254  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPN MUTATED      3    1
  CENPN WILD-TYPE  254   17
   clus
vv  CENPN MUTATED CENPN WILD-TYPE
  0             3             254
  1             1              17
[1] 2 2
[1] FALSE
D699V7, binary
                 cls
clus                0   1
  CENPN MUTATED     1   3
  CENPN WILD-TYPE 109 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPN MUTATED      1    3
  CENPN WILD-TYPE  109  176
        clus
vv       CENPN MUTATED CENPN WILD-TYPE
  FEMALE             1             109
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CENPN MUTATED                                       0
  CENPN WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CENPN MUTATED                                                        0
  CENPN WILD-TYPE                                                    135
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CENPN MUTATED                                                                   1
  CENPN WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CENPN MUTATED                                                  3
  CENPN WILD-TYPE                                               35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CENPN MUTATED                                                          0
  CENPN WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CENPN MUTATED                                                           0
  CENPN WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CENPN MUTATED                                          0
  CENPN WILD-TYPE                                        3
D699V8, multiclass
                                                                   clus
vv                                                                  CENPN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        0
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  CENPN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        135
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D699V9, binary
                 cls
clus                0   1
  CENPN MUTATED     0   4
  CENPN WILD-TYPE   5 280
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPN MUTATED      0    4
  CENPN WILD-TYPE    5  280
     clus
vv    CENPN MUTATED CENPN WILD-TYPE
  NO              0               5
  YES             4             280
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CENPN MUTATED     4   0   0   0
  CENPN WILD-TYPE 223  10  10  24
D699V10, multiclass
    clus
vv   CENPN MUTATED CENPN WILD-TYPE
  R0             4             223
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D699V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CENPN MUTATED       2                         0     1
  CENPN WILD-TYPE    74                         4   167
D699V12, multiclass
                           clus
vv                          CENPN MUTATED CENPN WILD-TYPE
  ASIAN                                 2              74
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 1             167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(700) Variable = MAN2B1 MUTATION ANALYSIS
D700V1, survival
                  sevent
clus2                0   1
  MAN2B1 MUTATED    11   4
  MAN2B1 WILD-TYPE 170  76
  MAN2B1 MUTATED MAN2B1 WILD-TYPE 
              15              246 
  MAN2B1 MUTATED MAN2B1 WILD-TYPE 
               4               76 
$`MAN2B1 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-7707 TCGA-BR-7959 TCGA-BR-8361 TCGA-BR-8487 
       26.70         6.97        23.93        18.71        19.50         1.12 
TCGA-BR-A4QL TCGA-CG-4305 TCGA-CG-4465 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5726 
       11.57        15.95         9.01         0.99         6.02        28.96 
TCGA-D7-A4YY TCGA-HU-8604 TCGA-HU-A4H3 
       13.78        12.10        19.36 

$`MAN2B1 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        3.45         9.07        12.76        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
       16.31         2.20        15.58         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       19.07        12.03         0.00        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5723 
       30.97         6.97        36.00         1.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       15.16        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  MAN2B1 MUTATED MAN2B1 WILD-TYPE 
            0.99             0.00 
  MAN2B1 MUTATED MAN2B1 WILD-TYPE 
           28.96           105.07 
  MAN2B1 MUTATED MAN2B1 WILD-TYPE 
          13.780           12.605 
[1] "1.0 - 29.0 (13.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.2"
D700V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAN2B1 MUTATED         0        1        2        1         2         1
  MAN2B1 WILD-TYPE       1        8       25       25        29        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAN2B1 MUTATED           0          2          2          2        2
  MAN2B1 WILD-TYPE         3         47         34         22       22
D700V3, multiclass
            clus
vv           MAN2B1 MUTATED MAN2B1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                2               25
  STAGE II                1               25
  STAGE IIA               2               29
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              2               34
  STAGE IIIC              2               22
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAN2B1 MUTATED     1   3   5   6
  MAN2B1 WILD-TYPE  10  69 117  69
D700V4, multiclass
    clus
vv   MAN2B1 MUTATED MAN2B1 WILD-TYPE
  T1              1               10
  T2              3               69
  T3              5              117
  T4              6               69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  MAN2B1 MUTATED    6  5  1  4
  MAN2B1 WILD-TYPE 87 76 49 49
D700V5, multiclass
    clus
vv   MAN2B1 MUTATED MAN2B1 WILD-TYPE
  N0              6               87
  N1              5               76
  N2              1               49
  N3              4               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D700V6, binary
                  cls
clus                 0   1
  MAN2B1 MUTATED    14   1
  MAN2B1 WILD-TYPE 243  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN2B1 MUTATED     14    1
  MAN2B1 WILD-TYPE  243   17
   clus
vv  MAN2B1 MUTATED MAN2B1 WILD-TYPE
  0             14              243
  1              1               17
[1] 2 2
[1] FALSE
D700V7, binary
                  cls
clus                 0   1
  MAN2B1 MUTATED     9   7
  MAN2B1 WILD-TYPE 101 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN2B1 MUTATED      9    7
  MAN2B1 WILD-TYPE  101  172
        clus
vv       MAN2B1 MUTATED MAN2B1 WILD-TYPE
  FEMALE              9              101
  MALE                7              172
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MAN2B1 MUTATED                                       3
  MAN2B1 WILD-TYPE                                    47
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MAN2B1 MUTATED                                                        9
  MAN2B1 WILD-TYPE                                                    126
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MAN2B1 MUTATED                                                                   2
  MAN2B1 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MAN2B1 MUTATED                                                  1
  MAN2B1 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MAN2B1 MUTATED                                                          1
  MAN2B1 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MAN2B1 MUTATED                                                           0
  MAN2B1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MAN2B1 MUTATED                                          0
  MAN2B1 WILD-TYPE                                        3
D700V8, multiclass
                                                                   clus
vv                                                                  MAN2B1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  MAN2B1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D700V9, binary
                  cls
clus                 0   1
  MAN2B1 MUTATED     0  16
  MAN2B1 WILD-TYPE   5 268
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN2B1 MUTATED      0   16
  MAN2B1 WILD-TYPE    5  268
     clus
vv    MAN2B1 MUTATED MAN2B1 WILD-TYPE
  NO               0                5
  YES             16              268
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MAN2B1 MUTATED    13   0   1   2
  MAN2B1 WILD-TYPE 214  10   9  22
D700V10, multiclass
    clus
vv   MAN2B1 MUTATED MAN2B1 WILD-TYPE
  R0             13              214
  R1              0               10
  R2              1                9
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D700V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAN2B1 MUTATED       2                         0     9
  MAN2B1 WILD-TYPE    74                         4   159
D700V12, multiclass
                           clus
vv                          MAN2B1 MUTATED MAN2B1 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  9              159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(701) Variable = KIAA0226 MUTATION ANALYSIS
D701V1, survival
                    sevent
clus2                  0   1
  KIAA0226 MUTATED     8   2
  KIAA0226 WILD-TYPE 173  78
  KIAA0226 MUTATED KIAA0226 WILD-TYPE 
                10                251 
  KIAA0226 MUTATED KIAA0226 WILD-TYPE 
                 2                 78 
$`KIAA0226 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8368 
       34.68        32.94         7.40        19.50         0.26         4.31 
TCGA-CG-5721 TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-A4GT 
        6.02        11.08        26.47         6.51 

$`KIAA0226 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 
       12.95         2.66        16.31         2.20        15.58         6.18 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  KIAA0226 MUTATED KIAA0226 WILD-TYPE 
              0.26               0.00 
  KIAA0226 MUTATED KIAA0226 WILD-TYPE 
             34.68             105.07 
  KIAA0226 MUTATED KIAA0226 WILD-TYPE 
              9.24              12.66 
[1] "0.3 - 34.7 (9.2)"   "0.0 - 105.1 (12.7)"
[1] "hr=" "1.8"
D701V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0226 MUTATED         1        0        3        0         4         0
  KIAA0226 WILD-TYPE       0        9       24       26        27        44
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0226 MUTATED           0          0          0          2        2
  KIAA0226 WILD-TYPE         3         49         36         22       22
D701V3, multiclass
            clus
vv           KIAA0226 MUTATED KIAA0226 WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                  0                  9
  STAGE IB                  3                 24
  STAGE II                  0                 26
  STAGE IIA                 4                 27
  STAGE IIB                 0                 44
  STAGE III                 0                  3
  STAGE IIIA                0                 49
  STAGE IIIB                0                 36
  STAGE IIIC                2                 22
  STAGE IV                  2                 22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0226 MUTATED     1   3   4   4
  KIAA0226 WILD-TYPE  10  69 118  71
D701V4, multiclass
    clus
vv   KIAA0226 MUTATED KIAA0226 WILD-TYPE
  T1                1                 10
  T2                3                 69
  T3                4                118
  T4                4                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  KIAA0226 MUTATED    7  2  2  1
  KIAA0226 WILD-TYPE 86 79 48 52
D701V5, multiclass
    clus
vv   KIAA0226 MUTATED KIAA0226 WILD-TYPE
  N0                7                 86
  N1                2                 79
  N2                2                 48
  N3                1                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D701V6, binary
                    cls
clus                   0   1
  KIAA0226 MUTATED    10   0
  KIAA0226 WILD-TYPE 247  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0226 MUTATED     10    0
  KIAA0226 WILD-TYPE  247   18
   clus
vv  KIAA0226 MUTATED KIAA0226 WILD-TYPE
  0               10                247
  1                0                 18
[1] 2 2
[1] FALSE
D701V7, binary
                    cls
clus                   0   1
  KIAA0226 MUTATED     8   4
  KIAA0226 WILD-TYPE 102 175
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0226 MUTATED      8    4
  KIAA0226 WILD-TYPE  102  175
        clus
vv       KIAA0226 MUTATED KIAA0226 WILD-TYPE
  FEMALE                8                102
  MALE                  4                175
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KIAA0226 MUTATED                                       1
  KIAA0226 WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA0226 MUTATED                                                        8
  KIAA0226 WILD-TYPE                                                    127
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KIAA0226 MUTATED                                                                   1
  KIAA0226 WILD-TYPE                                                                39
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KIAA0226 MUTATED                                                  1
  KIAA0226 WILD-TYPE                                               37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KIAA0226 MUTATED                                                          0
  KIAA0226 WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KIAA0226 MUTATED                                                           0
  KIAA0226 WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KIAA0226 MUTATED                                          1
  KIAA0226 WILD-TYPE                                        2
D701V8, multiclass
                                                                   clus
vv                                                                  KIAA0226 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  KIAA0226 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D701V9, binary
                    cls
clus                   0   1
  KIAA0226 MUTATED     0  12
  KIAA0226 WILD-TYPE   5 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0226 MUTATED      0   12
  KIAA0226 WILD-TYPE    5  272
     clus
vv    KIAA0226 MUTATED KIAA0226 WILD-TYPE
  NO                 0                  5
  YES               12                272
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  KIAA0226 MUTATED    11   0   0   1
  KIAA0226 WILD-TYPE 216  10  10  23
D701V10, multiclass
    clus
vv   KIAA0226 MUTATED KIAA0226 WILD-TYPE
  R0               11                216
  R1                0                 10
  R2                0                 10
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D701V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA0226 MUTATED       1                         2     8
  KIAA0226 WILD-TYPE    75                         2   160
D701V12, multiclass
                           clus
vv                          KIAA0226 MUTATED KIAA0226 WILD-TYPE
  ASIAN                                    1                 75
  BLACK OR AFRICAN AMERICAN                2                  2
  WHITE                                    8                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(702) Variable = SP6 MUTATION ANALYSIS
D702V1, survival
               sevent
clus2             0   1
  SP6 MUTATED     1   1
  SP6 WILD-TYPE 180  79
  SP6 MUTATED SP6 WILD-TYPE 
            2           259 
  SP6 MUTATED SP6 WILD-TYPE 
            1            79 
$`SP6 MUTATED`
TCGA-BR-8368 TCGA-CG-5733 
        4.31        21.07 

$`SP6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10         4.01        69.04         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  SP6 MUTATED SP6 WILD-TYPE 
         4.31          0.00 
  SP6 MUTATED SP6 WILD-TYPE 
        21.07        105.07 
  SP6 MUTATED SP6 WILD-TYPE 
        12.69         12.62 
[1] "4.3 - 21.1 (12.7)"  "0.0 - 105.1 (12.6)"
[1] "Remove cluster labels:" "SP6 MUTATED"           
D702V2, continuous
[1] "Remove cluster labels:" "SP6 MUTATED"           
clus
  SP6 MUTATED SP6 WILD-TYPE 
            2           282 
   TCGA-B7-5816    TCGA-B7-5818    TCGA-BR-4183    TCGA-BR-4184    TCGA-BR-4187 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-4188    TCGA-BR-4191    TCGA-BR-4201    TCGA-BR-4253    TCGA-BR-4255 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-4256    TCGA-BR-4257    TCGA-BR-4267    TCGA-BR-4279    TCGA-BR-4280 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-4292    TCGA-BR-4294    TCGA-BR-4357    TCGA-BR-4361    TCGA-BR-4362 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-4363    TCGA-BR-4366    TCGA-BR-4368    TCGA-BR-4369    TCGA-BR-4370 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-4371    TCGA-BR-6452    TCGA-BR-6453    TCGA-BR-6454    TCGA-BR-6455 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-6456    TCGA-BR-6457    TCGA-BR-6458    TCGA-BR-6563    TCGA-BR-6564 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-6565    TCGA-BR-6566    TCGA-BR-6705    TCGA-BR-6706    TCGA-BR-6707 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-6710    TCGA-BR-6801    TCGA-BR-6802    TCGA-BR-6803    TCGA-BR-6852 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-7196    TCGA-BR-7197    TCGA-BR-7703    TCGA-BR-7707    TCGA-BR-7715 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-7716    TCGA-BR-7717    TCGA-BR-7722    TCGA-BR-7723    TCGA-BR-7851 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-7901    TCGA-BR-7957    TCGA-BR-7958    TCGA-BR-7959    TCGA-BR-8058 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-8059    TCGA-BR-8077    TCGA-BR-8078    TCGA-BR-8080    TCGA-BR-8081 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-8284    TCGA-BR-8286    TCGA-BR-8289    TCGA-BR-8291    TCGA-BR-8295 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-8296    TCGA-BR-8297    TCGA-BR-8360    TCGA-BR-8361    TCGA-BR-8363 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-8364    TCGA-BR-8365    TCGA-BR-8366    TCGA-BR-8367    TCGA-BR-8369 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-8370    TCGA-BR-8371    TCGA-BR-8372    TCGA-BR-8373    TCGA-BR-8380 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-8381    TCGA-BR-8382    TCGA-BR-8384    TCGA-BR-8483    TCGA-BR-8484 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-8485    TCGA-BR-8486    TCGA-BR-8487    TCGA-BR-8588    TCGA-BR-8589 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-8590    TCGA-BR-8591    TCGA-BR-8592    TCGA-BR-8676    TCGA-BR-8677 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-8678    TCGA-BR-8679    TCGA-BR-8680    TCGA-BR-8682    TCGA-BR-8683 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-8686    TCGA-BR-8687    TCGA-BR-8690    TCGA-BR-A44T    TCGA-BR-A44U 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-A452    TCGA-BR-A453    TCGA-BR-A4CQ    TCGA-BR-A4CR    TCGA-BR-A4CS 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-A4IU    TCGA-BR-A4IV    TCGA-BR-A4IY    TCGA-BR-A4IZ    TCGA-BR-A4J1 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-A4J2    TCGA-BR-A4J4    TCGA-BR-A4J6    TCGA-BR-A4J7    TCGA-BR-A4J8 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-A4PD    TCGA-BR-A4PE    TCGA-BR-A4PF    TCGA-BR-A4QI    TCGA-BR-A4QL 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-A4QM    TCGA-CD-5798    TCGA-CD-5799    TCGA-CD-5802    TCGA-CD-5803 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-CD-5804    TCGA-CD-5813    TCGA-CD-8524    TCGA-CD-8525    TCGA-CD-8526 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-CD-8527    TCGA-CD-8528    TCGA-CD-8529    TCGA-CD-8530    TCGA-CD-8531 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-CD-8532    TCGA-CD-8534    TCGA-CD-8535    TCGA-CD-8536    TCGA-CD-A486 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-CD-A487    TCGA-CD-A489    TCGA-CD-A48A    TCGA-CD-A48C    TCGA-CD-A4MG 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-CD-A4MH    TCGA-CD-A4MI    TCGA-CD-A4MJ    TCGA-CG-4300    TCGA-CG-4301 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-CG-4304    TCGA-CG-4305    TCGA-CG-4306    TCGA-CG-4436    TCGA-CG-4437 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-CG-4438    TCGA-CG-4440    TCGA-CG-4441    TCGA-CG-4442    TCGA-CG-4443 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-CG-4444    TCGA-CG-4449    TCGA-CG-4455    TCGA-CG-4462    TCGA-CG-4465 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-CG-4466    TCGA-CG-4469    TCGA-CG-4474    TCGA-CG-4475    TCGA-CG-4476 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-CG-4477    TCGA-CG-5717    TCGA-CG-5718    TCGA-CG-5719    TCGA-CG-5720 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-CG-5721    TCGA-CG-5722    TCGA-CG-5723    TCGA-CG-5724    TCGA-CG-5726 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-CG-5727    TCGA-CG-5728    TCGA-CG-5730    TCGA-CG-5732    TCGA-CG-5734 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-D7-5577    TCGA-D7-5578    TCGA-D7-5579    TCGA-D7-6518    TCGA-D7-6519 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-D7-6520    TCGA-D7-6521    TCGA-D7-6522    TCGA-D7-6524    TCGA-D7-6525 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-D7-6526    TCGA-D7-6527    TCGA-D7-6528    TCGA-D7-6815    TCGA-D7-6817 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-D7-6818    TCGA-D7-6820    TCGA-D7-6822    TCGA-D7-8570    TCGA-D7-8572 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-D7-8573    TCGA-D7-8574    TCGA-D7-8575    TCGA-D7-8576    TCGA-D7-8578 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-D7-8579    TCGA-D7-A4YT    TCGA-D7-A4YU    TCGA-D7-A4YV    TCGA-D7-A4YX 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-D7-A4YY    TCGA-D7-A4Z0    TCGA-EQ-5647    TCGA-EQ-8122    TCGA-EQ-A4SO 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-F1-6177    TCGA-F1-6874    TCGA-F1-6875    TCGA-F1-A448    TCGA-FP-7735 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-FP-7829    TCGA-FP-7916    TCGA-FP-7998    TCGA-FP-8099    TCGA-FP-8209 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-FP-8210    TCGA-FP-8211    TCGA-FP-8631    TCGA-FP-A4BE    TCGA-FP-A4BF 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-HJ-7597    TCGA-HU-8243    TCGA-HU-8245    TCGA-HU-8249    TCGA-HU-8602 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-HU-8604    TCGA-HU-8608    TCGA-HU-8610    TCGA-HU-A4G2    TCGA-HU-A4G3 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-HU-A4G6    TCGA-HU-A4G8    TCGA-HU-A4G9    TCGA-HU-A4GC    TCGA-HU-A4GD 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-HU-A4GF    TCGA-HU-A4GH    TCGA-HU-A4GN    TCGA-HU-A4GP    TCGA-HU-A4GQ 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-HU-A4GT    TCGA-HU-A4GU    TCGA-HU-A4GX    TCGA-HU-A4GY    TCGA-HU-A4H0 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-HU-A4H2    TCGA-HU-A4H3    TCGA-HU-A4H4    TCGA-HU-A4H5    TCGA-HU-A4H6 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-HU-A4H8    TCGA-HU-A4HD    TCGA-IN-7806    TCGA-IN-7808    TCGA-IN-8462 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-IN-8663    TCGA-IP-7968 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" 
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SP6 MUTATED         0        0        1        1         0         0
  SP6 WILD-TYPE       1        9       26       25        31        44
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SP6 MUTATED           0          1          0          0        0
  SP6 WILD-TYPE         3         48         36         24       24
D702V3, multiclass
            clus
vv           SP6 MUTATED SP6 WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             9
  STAGE IB             1            26
  STAGE II             1            25
  STAGE IIA            0            31
  STAGE IIB            0            44
  STAGE III            0             3
  STAGE IIIA           1            48
  STAGE IIIB           0            36
  STAGE IIIC           0            24
  STAGE IV             0            24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  SP6 MUTATED     0   3   0   0
  SP6 WILD-TYPE  11  69 122  75
D702V4, multiclass
    clus
vv   SP6 MUTATED SP6 WILD-TYPE
  T1           0            11
  T2           3            69
  T3           0           122
  T4           0            75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  SP6 MUTATED    1  1  1  0
  SP6 WILD-TYPE 92 80 49 53
D702V5, multiclass
    clus
vv   SP6 MUTATED SP6 WILD-TYPE
  N0           1            92
  N1           1            80
  N2           1            49
  N3           0            53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D702V6, binary
               cls
clus              0   1
  SP6 MUTATED     3   0
  SP6 WILD-TYPE 254  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP6 MUTATED      3    0
  SP6 WILD-TYPE  254   18
   clus
vv  SP6 MUTATED SP6 WILD-TYPE
  0           3           254
  1           0            18
[1] 2 2
[1] FALSE
D702V7, binary
               cls
clus              0   1
  SP6 MUTATED     2   1
  SP6 WILD-TYPE 108 178
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP6 MUTATED      2    1
  SP6 WILD-TYPE  108  178
        clus
vv       SP6 MUTATED SP6 WILD-TYPE
  FEMALE           2           108
  MALE             1           178
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SP6 MUTATED                                       0
  SP6 WILD-TYPE                                    50
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SP6 MUTATED                                                        1
  SP6 WILD-TYPE                                                    134
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SP6 MUTATED                                                                   1
  SP6 WILD-TYPE                                                                39
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SP6 MUTATED                                                  0
  SP6 WILD-TYPE                                               38
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SP6 MUTATED                                                          1
  SP6 WILD-TYPE                                                       15
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SP6 MUTATED                                                           0
  SP6 WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SP6 MUTATED                                          0
  SP6 WILD-TYPE                                        3
D702V8, multiclass
                                                                   clus
vv                                                                  SP6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      1
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  SP6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D702V9, binary
               cls
clus              0   1
  SP6 MUTATED     1   2
  SP6 WILD-TYPE   4 282
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP6 MUTATED      1    2
  SP6 WILD-TYPE    4  282
     clus
vv    SP6 MUTATED SP6 WILD-TYPE
  NO            1             4
  YES           2           282
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  SP6 MUTATED     3   0   0   0
  SP6 WILD-TYPE 224  10  10  24
D702V10, multiclass
    clus
vv   SP6 MUTATED SP6 WILD-TYPE
  R0           3           224
  R1           0            10
  R2           0            10
  RX           0            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D702V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SP6 MUTATED       0                         0     1
  SP6 WILD-TYPE    76                         4   167
D702V12, multiclass
[1] "Remove cluster labels:" "SP6 MUTATED"           
clus
  SP6 MUTATED SP6 WILD-TYPE 
            1           247 
   TCGA-B7-5816    TCGA-B7-5818    TCGA-BR-4183    TCGA-BR-4184    TCGA-BR-4187 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-4188    TCGA-BR-4191    TCGA-BR-4201    TCGA-BR-4253    TCGA-BR-4255 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-4256    TCGA-BR-4257    TCGA-BR-4267    TCGA-BR-4279    TCGA-BR-4280 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-4292    TCGA-BR-4294    TCGA-BR-4357    TCGA-BR-4361    TCGA-BR-4362 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-4363    TCGA-BR-4366    TCGA-BR-4368    TCGA-BR-4369    TCGA-BR-4370 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-4371    TCGA-BR-6452    TCGA-BR-6453    TCGA-BR-6454    TCGA-BR-6455 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-6456    TCGA-BR-6457    TCGA-BR-6458    TCGA-BR-6563    TCGA-BR-6564 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-6565    TCGA-BR-6566    TCGA-BR-6705    TCGA-BR-6706    TCGA-BR-6707 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-6710    TCGA-BR-6801    TCGA-BR-6802    TCGA-BR-6803    TCGA-BR-6852 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-7196    TCGA-BR-7197    TCGA-BR-7703    TCGA-BR-7707    TCGA-BR-7715 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-7716    TCGA-BR-7717    TCGA-BR-7722    TCGA-BR-7723    TCGA-BR-7851 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-7901    TCGA-BR-7957    TCGA-BR-7958    TCGA-BR-7959    TCGA-BR-8058 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-8059    TCGA-BR-8077    TCGA-BR-8078    TCGA-BR-8080    TCGA-BR-8081 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-8284    TCGA-BR-8286    TCGA-BR-8289    TCGA-BR-8291    TCGA-BR-8295 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-8296    TCGA-BR-8297    TCGA-BR-8360    TCGA-BR-8361    TCGA-BR-8363 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-8364    TCGA-BR-8365    TCGA-BR-8366    TCGA-BR-8367    TCGA-BR-8369 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-8370    TCGA-BR-8371    TCGA-BR-8372    TCGA-BR-8373    TCGA-BR-8380 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-8381    TCGA-BR-8382    TCGA-BR-8384    TCGA-BR-8483    TCGA-BR-8484 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-8485    TCGA-BR-8486    TCGA-BR-8487    TCGA-BR-8588    TCGA-BR-8589 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-8590    TCGA-BR-8591    TCGA-BR-8592    TCGA-BR-8676    TCGA-BR-8677 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-8678    TCGA-BR-8679    TCGA-BR-8680    TCGA-BR-8682    TCGA-BR-8683 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-8686    TCGA-BR-8687    TCGA-BR-8690    TCGA-BR-A44T    TCGA-BR-A44U 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-A452    TCGA-BR-A453    TCGA-BR-A4CQ    TCGA-BR-A4CR    TCGA-BR-A4CS 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-A4IU    TCGA-BR-A4IV    TCGA-BR-A4IY    TCGA-BR-A4IZ    TCGA-BR-A4J1 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-A4J2    TCGA-BR-A4J4    TCGA-BR-A4J6    TCGA-BR-A4J7    TCGA-BR-A4J8 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-A4PD    TCGA-BR-A4PE    TCGA-BR-A4PF    TCGA-BR-A4QI    TCGA-BR-A4QL 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-BR-A4QM    TCGA-CD-5798    TCGA-CD-5799    TCGA-CD-5800    TCGA-CD-5801 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-CD-5802    TCGA-CD-5803    TCGA-CD-5804    TCGA-CD-5813    TCGA-CD-8524 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-CD-8525    TCGA-CD-8526    TCGA-CD-8527    TCGA-CD-8528    TCGA-CD-8529 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-CD-8530    TCGA-CD-8531    TCGA-CD-8532    TCGA-CD-8534    TCGA-CD-8535 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-CD-8536    TCGA-CD-A486    TCGA-CD-A487    TCGA-CD-A489    TCGA-CD-A48A 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-CD-A48C    TCGA-CD-A4MG    TCGA-CD-A4MH    TCGA-CD-A4MI    TCGA-CD-A4MJ 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-D7-5577    TCGA-D7-5578    TCGA-D7-5579    TCGA-D7-6518    TCGA-D7-6519 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-D7-6520    TCGA-D7-6521    TCGA-D7-6522    TCGA-D7-6524    TCGA-D7-6525 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-D7-6526    TCGA-D7-6527    TCGA-D7-6528    TCGA-D7-6815    TCGA-D7-6817 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-D7-6818    TCGA-D7-6820    TCGA-D7-6822    TCGA-D7-8570    TCGA-D7-8572 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-D7-8573    TCGA-D7-8574    TCGA-D7-8575    TCGA-D7-8576    TCGA-D7-8578 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-D7-8579    TCGA-D7-A4YT    TCGA-D7-A4YU    TCGA-D7-A4YV    TCGA-D7-A4YX 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-D7-A4YY    TCGA-D7-A4Z0    TCGA-EQ-5647    TCGA-EQ-8122    TCGA-EQ-A4SO 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-F1-6177    TCGA-F1-6874    TCGA-F1-6875    TCGA-F1-A448    TCGA-FP-7735 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-FP-7829    TCGA-FP-7916    TCGA-FP-7998    TCGA-FP-8099    TCGA-FP-8209 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-FP-8210    TCGA-FP-8211    TCGA-FP-8631    TCGA-FP-A4BE    TCGA-FP-A4BF 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-HJ-7597    TCGA-HU-8243    TCGA-HU-8245    TCGA-HU-8249    TCGA-HU-8602 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-HU-8604    TCGA-HU-8608    TCGA-HU-8610    TCGA-HU-A4G2    TCGA-HU-A4G3 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-HU-A4G6    TCGA-HU-A4G8    TCGA-HU-A4G9    TCGA-HU-A4GC    TCGA-HU-A4GD 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-HU-A4GF    TCGA-HU-A4GH    TCGA-HU-A4GN    TCGA-HU-A4GP    TCGA-HU-A4GQ 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-HU-A4GT    TCGA-HU-A4GU    TCGA-HU-A4GX    TCGA-HU-A4GY    TCGA-HU-A4H0 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-HU-A4H2    TCGA-HU-A4H3    TCGA-HU-A4H4    TCGA-HU-A4H5    TCGA-HU-A4H6 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-HU-A4H8    TCGA-HU-A4HD    TCGA-IN-7806    TCGA-IN-7808    TCGA-IN-8462 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" "SP6 WILD-TYPE" 
   TCGA-IN-8663    TCGA-IP-7968 
"SP6 WILD-TYPE" "SP6 WILD-TYPE" 

Clustering(703) Variable = CHST9 MUTATION ANALYSIS
D703V1, survival
                 sevent
clus2               0   1
  CHST9 MUTATED     2   2
  CHST9 WILD-TYPE 179  78
  CHST9 MUTATED CHST9 WILD-TYPE 
              4             257 
  CHST9 MUTATED CHST9 WILD-TYPE 
              2              78 
$`CHST9 MUTATED`
TCGA-BR-4184 TCGA-BR-7958 TCGA-BR-8680 TCGA-D7-A4YV 
        6.97        12.76        15.81         5.92 

$`CHST9 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 
       28.73        12.43         3.45         9.07        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       14.27        16.44        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  CHST9 MUTATED CHST9 WILD-TYPE 
           5.92            0.00 
  CHST9 MUTATED CHST9 WILD-TYPE 
          15.81          105.07 
  CHST9 MUTATED CHST9 WILD-TYPE 
          9.865          12.620 
[1] "5.9 - 15.8 (9.9)"   "0.0 - 105.1 (12.6)"
[1] "hr=" "2.5"
D703V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CHST9 MUTATED         0        0        0        0         0         1
  CHST9 WILD-TYPE       1        9       27       26        31        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHST9 MUTATED           0          1          1          0        2
  CHST9 WILD-TYPE         3         48         35         24       22
D703V3, multiclass
            clus
vv           CHST9 MUTATED CHST9 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              0              31
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CHST9 MUTATED     1   0   2   3
  CHST9 WILD-TYPE  10  72 120  72
D703V4, multiclass
    clus
vv   CHST9 MUTATED CHST9 WILD-TYPE
  T1             1              10
  T2             0              72
  T3             2             120
  T4             3              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CHST9 MUTATED    1  2  2  0
  CHST9 WILD-TYPE 92 79 48 53
D703V5, multiclass
    clus
vv   CHST9 MUTATED CHST9 WILD-TYPE
  N0             1              92
  N1             2              79
  N2             2              48
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D703V6, binary
                 cls
clus                0   1
  CHST9 MUTATED     4   1
  CHST9 WILD-TYPE 253  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHST9 MUTATED      4    1
  CHST9 WILD-TYPE  253   17
   clus
vv  CHST9 MUTATED CHST9 WILD-TYPE
  0             4             253
  1             1              17
[1] 2 2
[1] FALSE
D703V7, binary
                 cls
clus                0   1
  CHST9 MUTATED     3   3
  CHST9 WILD-TYPE 107 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHST9 MUTATED      3    3
  CHST9 WILD-TYPE  107  176
        clus
vv       CHST9 MUTATED CHST9 WILD-TYPE
  FEMALE             3             107
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CHST9 MUTATED                                       0
  CHST9 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CHST9 MUTATED                                                        4
  CHST9 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CHST9 MUTATED                                                                   0
  CHST9 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CHST9 MUTATED                                                  2
  CHST9 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CHST9 MUTATED                                                          0
  CHST9 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CHST9 MUTATED                                                           0
  CHST9 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CHST9 MUTATED                                          0
  CHST9 WILD-TYPE                                        3
D703V8, multiclass
                                                                   clus
vv                                                                  CHST9 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  CHST9 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D703V9, binary
                 cls
clus                0   1
  CHST9 MUTATED     0   6
  CHST9 WILD-TYPE   5 278
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHST9 MUTATED      0    6
  CHST9 WILD-TYPE    5  278
     clus
vv    CHST9 MUTATED CHST9 WILD-TYPE
  NO              0               5
  YES             6             278
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CHST9 MUTATED     3   0   0   3
  CHST9 WILD-TYPE 224  10  10  21
D703V10, multiclass
    clus
vv   CHST9 MUTATED CHST9 WILD-TYPE
  R0             3             224
  R1             0              10
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D703V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CHST9 MUTATED       1                         0     5
  CHST9 WILD-TYPE    75                         4   163
D703V12, multiclass
                           clus
vv                          CHST9 MUTATED CHST9 WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(704) Variable = ETV1 MUTATION ANALYSIS
D704V1, survival
                sevent
clus2              0   1
  ETV1 MUTATED     7   2
  ETV1 WILD-TYPE 174  78
  ETV1 MUTATED ETV1 WILD-TYPE 
             9            252 
  ETV1 MUTATED ETV1 WILD-TYPE 
             2             78 
$`ETV1 MUTATED`
TCGA-BR-8360 TCGA-BR-8372 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-5721 TCGA-CG-5733 
        6.18        19.17        15.81        11.57         6.02        21.07 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6822 
       10.26        15.98        12.33 

$`ETV1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       15.22        12.79        10.55        11.31        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  ETV1 MUTATED ETV1 WILD-TYPE 
          6.02           0.00 
  ETV1 MUTATED ETV1 WILD-TYPE 
         21.07         105.07 
  ETV1 MUTATED ETV1 WILD-TYPE 
         12.33          12.64 
[1] "6.0 - 21.1 (12.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D704V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ETV1 MUTATED         0        0        1        1         1         1
  ETV1 WILD-TYPE       1        9       26       25        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ETV1 MUTATED           0          1          1          1        2
  ETV1 WILD-TYPE         3         48         35         23       22
D704V3, multiclass
            clus
vv           ETV1 MUTATED ETV1 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              1             25
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            1             23
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ETV1 MUTATED     0   4   2   3
  ETV1 WILD-TYPE  11  68 120  72
D704V4, multiclass
    clus
vv   ETV1 MUTATED ETV1 WILD-TYPE
  T1            0             11
  T2            4             68
  T3            2            120
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  ETV1 MUTATED    2  3  3  2
  ETV1 WILD-TYPE 91 78 47 51
D704V5, multiclass
    clus
vv   ETV1 MUTATED ETV1 WILD-TYPE
  N0            2             91
  N1            3             78
  N2            3             47
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D704V6, binary
                cls
clus               0   1
  ETV1 MUTATED     9   1
  ETV1 WILD-TYPE 248  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETV1 MUTATED      9    1
  ETV1 WILD-TYPE  248   17
   clus
vv  ETV1 MUTATED ETV1 WILD-TYPE
  0            9            248
  1            1             17
[1] 2 2
[1] FALSE
D704V7, binary
                cls
clus               0   1
  ETV1 MUTATED     4   6
  ETV1 WILD-TYPE 106 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETV1 MUTATED      4    6
  ETV1 WILD-TYPE  106  173
        clus
vv       ETV1 MUTATED ETV1 WILD-TYPE
  FEMALE            4            106
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ETV1 MUTATED                                       0
  ETV1 WILD-TYPE                                    50
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ETV1 MUTATED                                                        3
  ETV1 WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ETV1 MUTATED                                                                   3
  ETV1 WILD-TYPE                                                                37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ETV1 MUTATED                                                  3
  ETV1 WILD-TYPE                                               35
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ETV1 MUTATED                                                          0
  ETV1 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ETV1 MUTATED                                                           1
  ETV1 WILD-TYPE                                                         5
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ETV1 MUTATED                                          0
  ETV1 WILD-TYPE                                        3
D704V8, multiclass
                                                                   clus
vv                                                                  ETV1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  ETV1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D704V9, binary
                cls
clus               0   1
  ETV1 MUTATED     0  10
  ETV1 WILD-TYPE   5 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETV1 MUTATED      0   10
  ETV1 WILD-TYPE    5  274
     clus
vv    ETV1 MUTATED ETV1 WILD-TYPE
  NO             0              5
  YES           10            274
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ETV1 MUTATED     9   0   0   1
  ETV1 WILD-TYPE 218  10  10  23
D704V10, multiclass
    clus
vv   ETV1 MUTATED ETV1 WILD-TYPE
  R0            9            218
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D704V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ETV1 MUTATED       1                         0     7
  ETV1 WILD-TYPE    75                         4   161
D704V12, multiclass
                           clus
vv                          ETV1 MUTATED ETV1 WILD-TYPE
  ASIAN                                1             75
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                7            161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(705) Variable = NOL6 MUTATION ANALYSIS
D705V1, survival
                sevent
clus2              0   1
  NOL6 MUTATED     9   7
  NOL6 WILD-TYPE 172  73
  NOL6 MUTATED NOL6 WILD-TYPE 
            16            245 
  NOL6 MUTATED NOL6 WILD-TYPE 
             7             73 
$`NOL6 MUTATED`
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-7959 TCGA-BR-8363 TCGA-BR-8680 
       34.68        32.78        23.93        18.71         0.26        15.81 
TCGA-CD-A489 TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-5733 TCGA-D7-A4YV 
       11.31         6.58         1.02         9.01        21.07         5.92 
TCGA-F1-6874 TCGA-FP-A4BE TCGA-HU-A4G9 TCGA-HU-A4GT 
       14.47        11.08        24.20         6.51 

$`NOL6 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        9.17        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        3.45         9.07        12.76        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
        9.34        12.43        11.61        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
       12.03         0.00        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  NOL6 MUTATED NOL6 WILD-TYPE 
          0.26           0.00 
  NOL6 MUTATED NOL6 WILD-TYPE 
         34.68         105.07 
  NOL6 MUTATED NOL6 WILD-TYPE 
         12.89          12.62 
[1] "0.3 - 34.7 (12.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D705V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NOL6 MUTATED         0        1        3        0         6         1
  NOL6 WILD-TYPE       1        8       24       26        25        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NOL6 MUTATED           0          2          0          0        3
  NOL6 WILD-TYPE         3         47         36         24       21
D705V3, multiclass
            clus
vv           NOL6 MUTATED NOL6 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              3             24
  STAGE II              0             26
  STAGE IIA             6             25
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              3             21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NOL6 MUTATED     1   4   8   3
  NOL6 WILD-TYPE  10  68 114  72
D705V4, multiclass
    clus
vv   NOL6 MUTATED NOL6 WILD-TYPE
  T1            1             10
  T2            4             68
  T3            8            114
  T4            3             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  NOL6 MUTATED   10  3  3  1
  NOL6 WILD-TYPE 83 78 47 52
D705V5, multiclass
    clus
vv   NOL6 MUTATED NOL6 WILD-TYPE
  N0           10             83
  N1            3             78
  N2            3             47
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D705V6, binary
                cls
clus               0   1
  NOL6 MUTATED    14   3
  NOL6 WILD-TYPE 243  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOL6 MUTATED     14    3
  NOL6 WILD-TYPE  243   15
   clus
vv  NOL6 MUTATED NOL6 WILD-TYPE
  0           14            243
  1            3             15
[1] 2 2
[1] FALSE
D705V7, binary
                cls
clus               0   1
  NOL6 MUTATED    10   7
  NOL6 WILD-TYPE 100 172
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOL6 MUTATED     10    7
  NOL6 WILD-TYPE  100  172
        clus
vv       NOL6 MUTATED NOL6 WILD-TYPE
  FEMALE           10            100
  MALE              7            172
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NOL6 MUTATED                                       3
  NOL6 WILD-TYPE                                    47
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NOL6 MUTATED                                                        7
  NOL6 WILD-TYPE                                                    128
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NOL6 MUTATED                                                                   2
  NOL6 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NOL6 MUTATED                                                  4
  NOL6 WILD-TYPE                                               34
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NOL6 MUTATED                                                          1
  NOL6 WILD-TYPE                                                       15
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NOL6 MUTATED                                                           0
  NOL6 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NOL6 MUTATED                                          0
  NOL6 WILD-TYPE                                        3
D705V8, multiclass
                                                                   clus
vv                                                                  NOL6 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  NOL6 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D705V9, binary
                cls
clus               0   1
  NOL6 MUTATED     0  17
  NOL6 WILD-TYPE   5 267
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOL6 MUTATED      0   17
  NOL6 WILD-TYPE    5  267
     clus
vv    NOL6 MUTATED NOL6 WILD-TYPE
  NO             0              5
  YES           17            267
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NOL6 MUTATED    12   0   2   1
  NOL6 WILD-TYPE 215  10   8  23
D705V10, multiclass
    clus
vv   NOL6 MUTATED NOL6 WILD-TYPE
  R0           12            215
  R1            0             10
  R2            2              8
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D705V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NOL6 MUTATED       5                         1     8
  NOL6 WILD-TYPE    71                         3   160
D705V12, multiclass
                           clus
vv                          NOL6 MUTATED NOL6 WILD-TYPE
  ASIAN                                5             71
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                                8            160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(706) Variable = TAC4 MUTATION ANALYSIS
D706V1, survival
                sevent
clus2              0   1
  TAC4 MUTATED     3   0
  TAC4 WILD-TYPE 178  80
  TAC4 MUTATED TAC4 WILD-TYPE 
             3            258 
  TAC4 MUTATED TAC4 WILD-TYPE 
             0             80 
$`TAC4 MUTATED`
TCGA-BR-7707 TCGA-CG-5723 TCGA-HU-A4GU 
       23.93       105.07         6.25 

$`TAC4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         6.02         0.99        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  TAC4 MUTATED TAC4 WILD-TYPE 
          6.25           0.00 
  TAC4 MUTATED TAC4 WILD-TYPE 
        105.07          79.07 
  TAC4 MUTATED TAC4 WILD-TYPE 
        23.930         12.605 
[1] "6.2 - 105.1 (23.9)" "0.0 - 79.1 (12.6)" 
[1] "hr="   "3e+07"
D706V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TAC4 MUTATED         0        0        1        1         0         1
  TAC4 WILD-TYPE       1        9       26       25        31        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TAC4 MUTATED           0          0          0          0        0
  TAC4 WILD-TYPE         3         49         36         24       24
D706V3, multiclass
            clus
vv           TAC4 MUTATED TAC4 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              1             25
  STAGE IIA             0             31
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              0             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TAC4 MUTATED     0   2   1   0
  TAC4 WILD-TYPE  11  70 121  75
D706V4, multiclass
    clus
vv   TAC4 MUTATED TAC4 WILD-TYPE
  T1            0             11
  T2            2             70
  T3            1            121
  T4            0             75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  TAC4 MUTATED    1  2  0  0
  TAC4 WILD-TYPE 92 79 50 53
D706V5, multiclass
    clus
vv   TAC4 MUTATED TAC4 WILD-TYPE
  N0            1             92
  N1            2             79
  N2            0             50
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D706V6, binary
                cls
clus               0   1
  TAC4 MUTATED     3   0
  TAC4 WILD-TYPE 254  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAC4 MUTATED      3    0
  TAC4 WILD-TYPE  254   18
   clus
vv  TAC4 MUTATED TAC4 WILD-TYPE
  0            3            254
  1            0             18
[1] 2 2
[1] FALSE
D706V7, binary
                cls
clus               0   1
  TAC4 MUTATED     1   2
  TAC4 WILD-TYPE 109 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAC4 MUTATED      1    2
  TAC4 WILD-TYPE  109  177
        clus
vv       TAC4 MUTATED TAC4 WILD-TYPE
  FEMALE            1            109
  MALE              2            177
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TAC4 MUTATED                                       1
  TAC4 WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TAC4 MUTATED                                                        2
  TAC4 WILD-TYPE                                                    133
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TAC4 MUTATED                                                                   0
  TAC4 WILD-TYPE                                                                40
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TAC4 MUTATED                                                  0
  TAC4 WILD-TYPE                                               38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TAC4 MUTATED                                                          0
  TAC4 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TAC4 MUTATED                                                           0
  TAC4 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TAC4 MUTATED                                          0
  TAC4 WILD-TYPE                                        3
D706V8, multiclass
                                                                   clus
vv                                                                  TAC4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  TAC4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D706V9, binary
                cls
clus               0   1
  TAC4 MUTATED     0   3
  TAC4 WILD-TYPE   5 281
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAC4 MUTATED      0    3
  TAC4 WILD-TYPE    5  281
     clus
vv    TAC4 MUTATED TAC4 WILD-TYPE
  NO             0              5
  YES            3            281
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TAC4 MUTATED     3   0   0   0
  TAC4 WILD-TYPE 224  10  10  24
D706V10, multiclass
    clus
vv   TAC4 MUTATED TAC4 WILD-TYPE
  R0            3            224
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D706V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TAC4 MUTATED       1                         0     1
  TAC4 WILD-TYPE    75                         4   167
D706V12, multiclass
[1] "Remove cluster labels:" "TAC4 MUTATED"          
clus
  TAC4 MUTATED TAC4 WILD-TYPE 
             2            246 
    TCGA-B7-5816     TCGA-B7-5818     TCGA-BR-4183     TCGA-BR-4184 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-4187     TCGA-BR-4188     TCGA-BR-4191     TCGA-BR-4201 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-4253     TCGA-BR-4255     TCGA-BR-4256     TCGA-BR-4257 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-4267     TCGA-BR-4279     TCGA-BR-4280     TCGA-BR-4292 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-4294     TCGA-BR-4357     TCGA-BR-4361     TCGA-BR-4362 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-4363     TCGA-BR-4366     TCGA-BR-4368     TCGA-BR-4369 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-4370     TCGA-BR-4371     TCGA-BR-6452     TCGA-BR-6453 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-6454     TCGA-BR-6455     TCGA-BR-6456     TCGA-BR-6457 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-6458     TCGA-BR-6563     TCGA-BR-6564     TCGA-BR-6565 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-6566     TCGA-BR-6705     TCGA-BR-6706     TCGA-BR-6707 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-6710     TCGA-BR-6801     TCGA-BR-6802     TCGA-BR-6803 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-6852     TCGA-BR-7196     TCGA-BR-7197     TCGA-BR-7703 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-7715     TCGA-BR-7716     TCGA-BR-7717     TCGA-BR-7722 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-7723     TCGA-BR-7851     TCGA-BR-7901     TCGA-BR-7957 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-7958     TCGA-BR-7959     TCGA-BR-8058     TCGA-BR-8059 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-8077     TCGA-BR-8078     TCGA-BR-8080     TCGA-BR-8081 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-8284     TCGA-BR-8286     TCGA-BR-8289     TCGA-BR-8291 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-8295     TCGA-BR-8296     TCGA-BR-8297     TCGA-BR-8360 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-8361     TCGA-BR-8363     TCGA-BR-8364     TCGA-BR-8365 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-8366     TCGA-BR-8367     TCGA-BR-8368     TCGA-BR-8369 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-8370     TCGA-BR-8371     TCGA-BR-8372     TCGA-BR-8373 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-8380     TCGA-BR-8381     TCGA-BR-8382     TCGA-BR-8384 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-8483     TCGA-BR-8484     TCGA-BR-8485     TCGA-BR-8486 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-8487     TCGA-BR-8588     TCGA-BR-8589     TCGA-BR-8590 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-8591     TCGA-BR-8592     TCGA-BR-8676     TCGA-BR-8677 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-8678     TCGA-BR-8679     TCGA-BR-8680     TCGA-BR-8682 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-8683     TCGA-BR-8686     TCGA-BR-8687     TCGA-BR-8690 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-A44T     TCGA-BR-A44U     TCGA-BR-A452     TCGA-BR-A453 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-A4CQ     TCGA-BR-A4CR     TCGA-BR-A4CS     TCGA-BR-A4IU 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-A4IV     TCGA-BR-A4IY     TCGA-BR-A4IZ     TCGA-BR-A4J1 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-A4J2     TCGA-BR-A4J4     TCGA-BR-A4J6     TCGA-BR-A4J7 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-A4J8     TCGA-BR-A4PD     TCGA-BR-A4PE     TCGA-BR-A4PF 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-BR-A4QI     TCGA-BR-A4QL     TCGA-BR-A4QM     TCGA-CD-5798 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-CD-5799     TCGA-CD-5800     TCGA-CD-5801     TCGA-CD-5802 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-CD-5803     TCGA-CD-5804     TCGA-CD-5813     TCGA-CD-8524 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-CD-8525     TCGA-CD-8526     TCGA-CD-8527     TCGA-CD-8528 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-CD-8529     TCGA-CD-8530     TCGA-CD-8531     TCGA-CD-8532 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-CD-8534     TCGA-CD-8535     TCGA-CD-8536     TCGA-CD-A486 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-CD-A487     TCGA-CD-A489     TCGA-CD-A48A     TCGA-CD-A48C 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-CD-A4MG     TCGA-CD-A4MH     TCGA-CD-A4MI     TCGA-CD-A4MJ 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-D7-5577     TCGA-D7-5578     TCGA-D7-5579     TCGA-D7-6518 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-D7-6519     TCGA-D7-6520     TCGA-D7-6521     TCGA-D7-6522 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-D7-6524     TCGA-D7-6525     TCGA-D7-6526     TCGA-D7-6527 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-D7-6528     TCGA-D7-6815     TCGA-D7-6817     TCGA-D7-6818 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-D7-6820     TCGA-D7-6822     TCGA-D7-8570     TCGA-D7-8572 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-D7-8573     TCGA-D7-8574     TCGA-D7-8575     TCGA-D7-8576 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-D7-8578     TCGA-D7-8579     TCGA-D7-A4YT     TCGA-D7-A4YU 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-D7-A4YV     TCGA-D7-A4YX     TCGA-D7-A4YY     TCGA-D7-A4Z0 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-EQ-5647     TCGA-EQ-8122     TCGA-EQ-A4SO     TCGA-F1-6177 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-F1-6874     TCGA-F1-6875     TCGA-F1-A448     TCGA-FP-7735 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-FP-7829     TCGA-FP-7916     TCGA-FP-7998     TCGA-FP-8099 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-FP-8209     TCGA-FP-8210     TCGA-FP-8211     TCGA-FP-8631 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-FP-A4BE     TCGA-FP-A4BF     TCGA-HJ-7597     TCGA-HU-8243 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-HU-8245     TCGA-HU-8249     TCGA-HU-8602     TCGA-HU-8604 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-HU-8608     TCGA-HU-8610     TCGA-HU-A4G2     TCGA-HU-A4G3 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-HU-A4G6     TCGA-HU-A4G8     TCGA-HU-A4G9     TCGA-HU-A4GC 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-HU-A4GD     TCGA-HU-A4GF     TCGA-HU-A4GH     TCGA-HU-A4GN 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-HU-A4GP     TCGA-HU-A4GQ     TCGA-HU-A4GT     TCGA-HU-A4GX 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-HU-A4GY     TCGA-HU-A4H0     TCGA-HU-A4H2     TCGA-HU-A4H3 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-HU-A4H4     TCGA-HU-A4H5     TCGA-HU-A4H6     TCGA-HU-A4H8 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-HU-A4HD     TCGA-IN-7806     TCGA-IN-7808     TCGA-IN-8462 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-IN-8663     TCGA-IP-7968 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 

Clustering(707) Variable = RNMT MUTATION ANALYSIS
D707V1, survival
                sevent
clus2              0   1
  RNMT MUTATED     6   1
  RNMT WILD-TYPE 175  79
  RNMT MUTATED RNMT WILD-TYPE 
             7            254 
  RNMT MUTATED RNMT WILD-TYPE 
             1             79 
$`RNMT MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-5721 
       26.70        34.68        12.26        15.81         6.58         6.02 
TCGA-CG-5723 
      105.07 

$`RNMT WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
       36.00         1.02         0.99         0.99        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  RNMT MUTATED RNMT WILD-TYPE 
          6.02           0.00 
  RNMT MUTATED RNMT WILD-TYPE 
        105.07          79.07 
  RNMT MUTATED RNMT WILD-TYPE 
        15.810         12.605 
[1] "6.0 - 105.1 (15.8)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "4.3"
D707V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RNMT MUTATED         0        0        0        1         2         2
  RNMT WILD-TYPE       1        9       27       25        29        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNMT MUTATED           0          0          0          0        2
  RNMT WILD-TYPE         3         49         36         24       22
D707V3, multiclass
            clus
vv           RNMT MUTATED RNMT WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              0             27
  STAGE II              1             25
  STAGE IIA             2             29
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            0             49
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RNMT MUTATED     0   1   2   4
  RNMT WILD-TYPE  11  71 120  71
D707V4, multiclass
    clus
vv   RNMT MUTATED RNMT WILD-TYPE
  T1            0             11
  T2            1             71
  T3            2            120
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  RNMT MUTATED    4  2  1  0
  RNMT WILD-TYPE 89 79 49 53
D707V5, multiclass
    clus
vv   RNMT MUTATED RNMT WILD-TYPE
  N0            4             89
  N1            2             79
  N2            1             49
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D707V6, binary
                cls
clus               0   1
  RNMT MUTATED     7   1
  RNMT WILD-TYPE 250  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  RNMT MUTATED      7    1
  RNMT WILD-TYPE  250   17
   clus
vv  RNMT MUTATED RNMT WILD-TYPE
  0            7            250
  1            1             17
[1] 2 2
[1] FALSE
D707V7, binary
                cls
clus               0   1
  RNMT MUTATED     4   4
  RNMT WILD-TYPE 106 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  RNMT MUTATED      4    4
  RNMT WILD-TYPE  106  175
        clus
vv       RNMT MUTATED RNMT WILD-TYPE
  FEMALE            4            106
  MALE              4            175
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RNMT MUTATED                                       2
  RNMT WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RNMT MUTATED                                                        4
  RNMT WILD-TYPE                                                    131
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RNMT MUTATED                                                                   1
  RNMT WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RNMT MUTATED                                                  1
  RNMT WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RNMT MUTATED                                                          0
  RNMT WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RNMT MUTATED                                                           0
  RNMT WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RNMT MUTATED                                          0
  RNMT WILD-TYPE                                        3
D707V8, multiclass
                                                                   clus
vv                                                                  RNMT MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  RNMT WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D707V9, binary
                cls
clus               0   1
  RNMT MUTATED     0   8
  RNMT WILD-TYPE   5 276
[1] "tbl2"
                cls
clus             [,1] [,2]
  RNMT MUTATED      0    8
  RNMT WILD-TYPE    5  276
     clus
vv    RNMT MUTATED RNMT WILD-TYPE
  NO             0              5
  YES            8            276
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RNMT MUTATED     6   0   0   1
  RNMT WILD-TYPE 221  10  10  23
D707V10, multiclass
    clus
vv   RNMT MUTATED RNMT WILD-TYPE
  R0            6            221
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D707V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RNMT MUTATED       2                         0     4
  RNMT WILD-TYPE    74                         4   164
D707V12, multiclass
                           clus
vv                          RNMT MUTATED RNMT WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                4            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(708) Variable = HOOK1 MUTATION ANALYSIS
D708V1, survival
                 sevent
clus2               0   1
  HOOK1 MUTATED     4   1
  HOOK1 WILD-TYPE 177  79
  HOOK1 MUTATED HOOK1 WILD-TYPE 
              5             256 
  HOOK1 MUTATED HOOK1 WILD-TYPE 
              1              79 
$`HOOK1 MUTATED`
TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8487 TCGA-BR-A4QL TCGA-CG-5717 
       34.68        20.55         1.12        11.57         6.97 

$`HOOK1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       17.49        14.43         0.69        12.26         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  HOOK1 MUTATED HOOK1 WILD-TYPE 
           1.12            0.00 
  HOOK1 MUTATED HOOK1 WILD-TYPE 
          34.68          105.07 
  HOOK1 MUTATED HOOK1 WILD-TYPE 
          11.57           12.64 
[1] "1.1 - 34.7 (11.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.7"
D708V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HOOK1 MUTATED         0        0        0        1         2         1
  HOOK1 WILD-TYPE       1        9       27       25        29        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HOOK1 MUTATED           0          1          1          0        0
  HOOK1 WILD-TYPE         3         48         35         24       24
D708V3, multiclass
            clus
vv           HOOK1 MUTATED HOOK1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              2              29
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HOOK1 MUTATED     0   1   3   2
  HOOK1 WILD-TYPE  11  71 119  73
D708V4, multiclass
    clus
vv   HOOK1 MUTATED HOOK1 WILD-TYPE
  T1             0              11
  T2             1              71
  T3             3             119
  T4             2              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  HOOK1 MUTATED    4  1  0  1
  HOOK1 WILD-TYPE 89 80 50 52
D708V5, multiclass
    clus
vv   HOOK1 MUTATED HOOK1 WILD-TYPE
  N0             4              89
  N1             1              80
  N2             0              50
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D708V6, binary
                 cls
clus                0   1
  HOOK1 MUTATED     6   0
  HOOK1 WILD-TYPE 251  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOOK1 MUTATED      6    0
  HOOK1 WILD-TYPE  251   18
   clus
vv  HOOK1 MUTATED HOOK1 WILD-TYPE
  0             6             251
  1             0              18
[1] 2 2
[1] FALSE
D708V7, binary
                 cls
clus                0   1
  HOOK1 MUTATED     5   1
  HOOK1 WILD-TYPE 105 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOOK1 MUTATED      5    1
  HOOK1 WILD-TYPE  105  178
        clus
vv       HOOK1 MUTATED HOOK1 WILD-TYPE
  FEMALE             5             105
  MALE               1             178
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  HOOK1 MUTATED                                       0
  HOOK1 WILD-TYPE                                    50
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HOOK1 MUTATED                                                        6
  HOOK1 WILD-TYPE                                                    129
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HOOK1 MUTATED                                                                   0
  HOOK1 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  HOOK1 MUTATED                                                  0
  HOOK1 WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  HOOK1 MUTATED                                                          0
  HOOK1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  HOOK1 MUTATED                                                           0
  HOOK1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  HOOK1 MUTATED                                          0
  HOOK1 WILD-TYPE                                        3
D708V8, multiclass
                                                                   clus
vv                                                                  HOOK1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  HOOK1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D708V9, binary
                 cls
clus                0   1
  HOOK1 MUTATED     0   6
  HOOK1 WILD-TYPE   5 278
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOOK1 MUTATED      0    6
  HOOK1 WILD-TYPE    5  278
     clus
vv    HOOK1 MUTATED HOOK1 WILD-TYPE
  NO              0               5
  YES             6             278
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HOOK1 MUTATED     5   0   0   1
  HOOK1 WILD-TYPE 222  10  10  23
D708V10, multiclass
    clus
vv   HOOK1 MUTATED HOOK1 WILD-TYPE
  R0             5             222
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D708V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HOOK1 MUTATED       0                         0     5
  HOOK1 WILD-TYPE    76                         4   163
D708V12, multiclass
                           clus
vv                          HOOK1 MUTATED HOOK1 WILD-TYPE
  ASIAN                                 0              76
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(709) Variable = CCDC25 MUTATION ANALYSIS
D709V1, survival
                  sevent
clus2                0   1
  CCDC25 MUTATED     1   1
  CCDC25 WILD-TYPE 180  79
  CCDC25 MUTATED CCDC25 WILD-TYPE 
               2              259 
  CCDC25 MUTATED CCDC25 WILD-TYPE 
               1               79 
$`CCDC25 MUTATED`
TCGA-BR-6452 TCGA-CD-A4MG 
       34.68         6.58 

$`CCDC25 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  CCDC25 MUTATED CCDC25 WILD-TYPE 
            6.58             0.00 
  CCDC25 MUTATED CCDC25 WILD-TYPE 
           34.68           105.07 
  CCDC25 MUTATED CCDC25 WILD-TYPE 
           20.63            12.62 
[1] "6.6 - 34.7 (20.6)"  "0.0 - 105.1 (12.6)"
[1] "Remove cluster labels:" "CCDC25 MUTATED"        
D709V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC25 MUTATED         0        0        0        0         2         0
  CCDC25 WILD-TYPE       1        9       27       26        29        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC25 MUTATED           0          0          0          0        0
  CCDC25 WILD-TYPE         3         49         36         24       24
D709V3, multiclass
[1] "Remove cluster labels:" "CCDC25 MUTATED"        
clus
  CCDC25 MUTATED CCDC25 WILD-TYPE 
               2              272 
      TCGA-B7-5816       TCGA-B7-5818       TCGA-BR-4183       TCGA-BR-4184 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-4253       TCGA-BR-4255       TCGA-BR-4267       TCGA-BR-4279 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-4280       TCGA-BR-4361       TCGA-BR-4368       TCGA-BR-6453 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-6454       TCGA-BR-6455       TCGA-BR-6456       TCGA-BR-6457 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-6458       TCGA-BR-6563       TCGA-BR-6564       TCGA-BR-6565 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-6566       TCGA-BR-6705       TCGA-BR-6706       TCGA-BR-6707 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-6710       TCGA-BR-6801       TCGA-BR-6802       TCGA-BR-6803 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-6852       TCGA-BR-7196       TCGA-BR-7197       TCGA-BR-7703 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-7707       TCGA-BR-7715       TCGA-BR-7716       TCGA-BR-7717 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-7722       TCGA-BR-7723       TCGA-BR-7851       TCGA-BR-7901 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-7957       TCGA-BR-7958       TCGA-BR-7959       TCGA-BR-8058 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8059       TCGA-BR-8077       TCGA-BR-8078       TCGA-BR-8080 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8081       TCGA-BR-8284       TCGA-BR-8286       TCGA-BR-8289 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8291       TCGA-BR-8295       TCGA-BR-8296       TCGA-BR-8297 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8360       TCGA-BR-8361       TCGA-BR-8363       TCGA-BR-8364 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8365       TCGA-BR-8366       TCGA-BR-8367       TCGA-BR-8368 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8369       TCGA-BR-8370       TCGA-BR-8371       TCGA-BR-8372 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8373       TCGA-BR-8380       TCGA-BR-8381       TCGA-BR-8382 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8384       TCGA-BR-8483       TCGA-BR-8484       TCGA-BR-8485 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8486       TCGA-BR-8487       TCGA-BR-8588       TCGA-BR-8589 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8590       TCGA-BR-8591       TCGA-BR-8592       TCGA-BR-8676 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8677       TCGA-BR-8678       TCGA-BR-8679       TCGA-BR-8680 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8682       TCGA-BR-8683       TCGA-BR-8686       TCGA-BR-8687 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8690       TCGA-BR-A44T       TCGA-BR-A44U       TCGA-BR-A452 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A453       TCGA-BR-A4CQ       TCGA-BR-A4CR       TCGA-BR-A4CS 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A4IU       TCGA-BR-A4IV       TCGA-BR-A4IY       TCGA-BR-A4IZ 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A4J1       TCGA-BR-A4J2       TCGA-BR-A4J4       TCGA-BR-A4J6 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A4J7       TCGA-BR-A4J8       TCGA-BR-A4PD       TCGA-BR-A4PE 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A4PF       TCGA-BR-A4QI       TCGA-BR-A4QL       TCGA-BR-A4QM 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CD-5798       TCGA-CD-5799       TCGA-CD-5800       TCGA-CD-5801 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CD-5802       TCGA-CD-5803       TCGA-CD-5804       TCGA-CD-5813 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CD-8524       TCGA-CD-8525       TCGA-CD-8526       TCGA-CD-8527 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CD-8528       TCGA-CD-8529       TCGA-CD-8530       TCGA-CD-8531 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CD-8532       TCGA-CD-8534       TCGA-CD-8535       TCGA-CD-8536 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CD-A486       TCGA-CD-A487       TCGA-CD-A489       TCGA-CD-A48A 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CD-A48C       TCGA-CD-A4MH       TCGA-CD-A4MI       TCGA-CD-A4MJ 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4300       TCGA-CG-4301       TCGA-CG-4304       TCGA-CG-4305 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4306       TCGA-CG-4436       TCGA-CG-4437       TCGA-CG-4438 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4440       TCGA-CG-4441       TCGA-CG-4442       TCGA-CG-4443 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4444       TCGA-CG-4449       TCGA-CG-4455       TCGA-CG-4462 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4465       TCGA-CG-4466       TCGA-CG-4469       TCGA-CG-4474 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4475       TCGA-CG-4476       TCGA-CG-4477       TCGA-CG-5717 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-5718       TCGA-CG-5719       TCGA-CG-5720       TCGA-CG-5721 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-5722       TCGA-CG-5723       TCGA-CG-5724       TCGA-CG-5726 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-5727       TCGA-CG-5728       TCGA-CG-5730       TCGA-CG-5732 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-5733       TCGA-CG-5734       TCGA-D7-5577       TCGA-D7-5578 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-5579       TCGA-D7-6518       TCGA-D7-6519       TCGA-D7-6520 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-6521       TCGA-D7-6522       TCGA-D7-6524       TCGA-D7-6525 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-6526       TCGA-D7-6527       TCGA-D7-6528       TCGA-D7-6815 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-6817       TCGA-D7-6818       TCGA-D7-6820       TCGA-D7-6822 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-8570       TCGA-D7-8572       TCGA-D7-8573       TCGA-D7-8574 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-8575       TCGA-D7-8576       TCGA-D7-8578       TCGA-D7-8579 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-A4YT       TCGA-D7-A4YU       TCGA-D7-A4YV       TCGA-D7-A4YX 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-A4YY       TCGA-D7-A4Z0       TCGA-EQ-5647       TCGA-EQ-8122 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-EQ-A4SO       TCGA-F1-6177       TCGA-F1-6874       TCGA-F1-6875 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-F1-A448       TCGA-FP-7735       TCGA-FP-7829       TCGA-FP-7916 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-FP-7998       TCGA-FP-8099       TCGA-FP-8209       TCGA-FP-8210 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-FP-8211       TCGA-FP-8631       TCGA-FP-A4BE       TCGA-FP-A4BF 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HF-7132       TCGA-HF-7133       TCGA-HF-7136       TCGA-HJ-7597 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-8243       TCGA-HU-8245       TCGA-HU-8249       TCGA-HU-8602 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-8604       TCGA-HU-8608       TCGA-HU-8610       TCGA-HU-A4G2 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4G3       TCGA-HU-A4G6       TCGA-HU-A4G8       TCGA-HU-A4G9 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4GC       TCGA-HU-A4GD       TCGA-HU-A4GF       TCGA-HU-A4GH 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4GN       TCGA-HU-A4GP       TCGA-HU-A4GQ       TCGA-HU-A4GT 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4GU       TCGA-HU-A4GX       TCGA-HU-A4GY       TCGA-HU-A4H0 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4H2       TCGA-HU-A4H3       TCGA-HU-A4H4       TCGA-HU-A4H5 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4H6       TCGA-HU-A4H8       TCGA-HU-A4HD       TCGA-IN-7806 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-IN-7808       TCGA-IN-8462       TCGA-IN-8663       TCGA-IP-7968 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
                  vv
clus                T1  T2  T3  T4
  CCDC25 MUTATED     1   0   2   0
  CCDC25 WILD-TYPE  10  72 120  75
D709V4, multiclass
    clus
vv   CCDC25 MUTATED CCDC25 WILD-TYPE
  T1              1               10
  T2              0               72
  T3              2              120
  T4              0               75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CCDC25 MUTATED    2  0  0  0
  CCDC25 WILD-TYPE 91 81 50 53
D709V5, multiclass
[1] "Remove cluster labels:" "CCDC25 MUTATED"        
clus
  CCDC25 MUTATED CCDC25 WILD-TYPE 
               2              275 
      TCGA-B7-5816       TCGA-B7-5818       TCGA-BR-4183       TCGA-BR-4184 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-4188       TCGA-BR-4191       TCGA-BR-4253       TCGA-BR-4255 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-4256       TCGA-BR-4267       TCGA-BR-4279       TCGA-BR-4280 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-4361       TCGA-BR-4362       TCGA-BR-4368       TCGA-BR-6453 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-6454       TCGA-BR-6455       TCGA-BR-6456       TCGA-BR-6457 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-6458       TCGA-BR-6563       TCGA-BR-6564       TCGA-BR-6565 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-6566       TCGA-BR-6705       TCGA-BR-6706       TCGA-BR-6707 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-6710       TCGA-BR-6801       TCGA-BR-6802       TCGA-BR-6803 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-6852       TCGA-BR-7196       TCGA-BR-7197       TCGA-BR-7703 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-7707       TCGA-BR-7715       TCGA-BR-7716       TCGA-BR-7717 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-7722       TCGA-BR-7723       TCGA-BR-7851       TCGA-BR-7901 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-7957       TCGA-BR-7958       TCGA-BR-7959       TCGA-BR-8058 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8059       TCGA-BR-8077       TCGA-BR-8078       TCGA-BR-8080 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8081       TCGA-BR-8284       TCGA-BR-8286       TCGA-BR-8289 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8291       TCGA-BR-8295       TCGA-BR-8296       TCGA-BR-8297 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8360       TCGA-BR-8361       TCGA-BR-8363       TCGA-BR-8364 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8365       TCGA-BR-8366       TCGA-BR-8367       TCGA-BR-8368 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8369       TCGA-BR-8370       TCGA-BR-8371       TCGA-BR-8372 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8373       TCGA-BR-8380       TCGA-BR-8381       TCGA-BR-8382 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8384       TCGA-BR-8483       TCGA-BR-8484       TCGA-BR-8485 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8486       TCGA-BR-8487       TCGA-BR-8588       TCGA-BR-8589 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8590       TCGA-BR-8591       TCGA-BR-8592       TCGA-BR-8676 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8677       TCGA-BR-8678       TCGA-BR-8679       TCGA-BR-8680 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8682       TCGA-BR-8683       TCGA-BR-8686       TCGA-BR-8687 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8690       TCGA-BR-A44T       TCGA-BR-A44U       TCGA-BR-A452 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A453       TCGA-BR-A4CQ       TCGA-BR-A4CR       TCGA-BR-A4CS 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A4IU       TCGA-BR-A4IV       TCGA-BR-A4IY       TCGA-BR-A4IZ 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A4J1       TCGA-BR-A4J2       TCGA-BR-A4J4       TCGA-BR-A4J6 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A4J8       TCGA-BR-A4PD       TCGA-BR-A4PE       TCGA-BR-A4PF 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A4QI       TCGA-BR-A4QL       TCGA-BR-A4QM       TCGA-CD-5798 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CD-5799       TCGA-CD-5800       TCGA-CD-5801       TCGA-CD-5802 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CD-5803       TCGA-CD-5804       TCGA-CD-5813       TCGA-CD-8524 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CD-8525       TCGA-CD-8526       TCGA-CD-8527       TCGA-CD-8528 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CD-8529       TCGA-CD-8530       TCGA-CD-8531       TCGA-CD-8532 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CD-8534       TCGA-CD-8535       TCGA-CD-8536       TCGA-CD-A486 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CD-A487       TCGA-CD-A489       TCGA-CD-A48A       TCGA-CD-A48C 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CD-A4MH       TCGA-CD-A4MI       TCGA-CD-A4MJ       TCGA-CG-4300 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4301       TCGA-CG-4304       TCGA-CG-4305       TCGA-CG-4306 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4436       TCGA-CG-4437       TCGA-CG-4438       TCGA-CG-4440 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4441       TCGA-CG-4442       TCGA-CG-4443       TCGA-CG-4444 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4449       TCGA-CG-4455       TCGA-CG-4462       TCGA-CG-4465 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4466       TCGA-CG-4469       TCGA-CG-4474       TCGA-CG-4475 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4476       TCGA-CG-4477       TCGA-CG-5717       TCGA-CG-5718 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-5719       TCGA-CG-5720       TCGA-CG-5721       TCGA-CG-5722 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-5723       TCGA-CG-5724       TCGA-CG-5726       TCGA-CG-5727 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-5728       TCGA-CG-5730       TCGA-CG-5732       TCGA-CG-5733 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-5734       TCGA-D7-5577       TCGA-D7-5578       TCGA-D7-5579 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-6518       TCGA-D7-6519       TCGA-D7-6520       TCGA-D7-6521 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-6522       TCGA-D7-6524       TCGA-D7-6525       TCGA-D7-6526 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-6527       TCGA-D7-6528       TCGA-D7-6815       TCGA-D7-6817 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-6818       TCGA-D7-6820       TCGA-D7-6822       TCGA-D7-8570 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-8572       TCGA-D7-8573       TCGA-D7-8574       TCGA-D7-8575 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-8576       TCGA-D7-8578       TCGA-D7-8579       TCGA-D7-A4YT 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-A4YU       TCGA-D7-A4YV       TCGA-D7-A4YX       TCGA-D7-A4YY 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-A4Z0       TCGA-EQ-5647       TCGA-EQ-8122       TCGA-EQ-A4SO 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-F1-6177       TCGA-F1-6874       TCGA-F1-6875       TCGA-F1-A448 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-FP-7735       TCGA-FP-7829       TCGA-FP-7916       TCGA-FP-7998 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-FP-8099       TCGA-FP-8209       TCGA-FP-8210       TCGA-FP-8211 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-FP-8631       TCGA-FP-A4BE       TCGA-FP-A4BF       TCGA-HF-7132 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HF-7133       TCGA-HF-7136       TCGA-HJ-7597       TCGA-HU-8243 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-8245       TCGA-HU-8249       TCGA-HU-8602       TCGA-HU-8604 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-8608       TCGA-HU-8610       TCGA-HU-A4G2       TCGA-HU-A4G3 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4G6       TCGA-HU-A4G8       TCGA-HU-A4G9       TCGA-HU-A4GC 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4GD       TCGA-HU-A4GF       TCGA-HU-A4GH       TCGA-HU-A4GN 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4GP       TCGA-HU-A4GQ       TCGA-HU-A4GT       TCGA-HU-A4GU 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4GX       TCGA-HU-A4GY       TCGA-HU-A4H0       TCGA-HU-A4H2 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4H3       TCGA-HU-A4H4       TCGA-HU-A4H5       TCGA-HU-A4H6 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4H8       TCGA-HU-A4HD       TCGA-IN-7806       TCGA-IN-7808 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-IN-8462       TCGA-IN-8663       TCGA-IP-7968 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
D709V6, binary
                  cls
clus                 0   1
  CCDC25 MUTATED     3   0
  CCDC25 WILD-TYPE 254  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC25 MUTATED      3    0
  CCDC25 WILD-TYPE  254   18
   clus
vv  CCDC25 MUTATED CCDC25 WILD-TYPE
  0              3              254
  1              0               18
[1] 2 2
[1] FALSE
D709V7, binary
                  cls
clus                 0   1
  CCDC25 MUTATED     2   1
  CCDC25 WILD-TYPE 108 178
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC25 MUTATED      2    1
  CCDC25 WILD-TYPE  108  178
        clus
vv       CCDC25 MUTATED CCDC25 WILD-TYPE
  FEMALE              2              108
  MALE                1              178
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CCDC25 MUTATED                                       1
  CCDC25 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CCDC25 MUTATED                                                        2
  CCDC25 WILD-TYPE                                                    133
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CCDC25 MUTATED                                                                   0
  CCDC25 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CCDC25 MUTATED                                                  0
  CCDC25 WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CCDC25 MUTATED                                                          0
  CCDC25 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CCDC25 MUTATED                                                           0
  CCDC25 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CCDC25 MUTATED                                          0
  CCDC25 WILD-TYPE                                        3
D709V8, multiclass
                                                                   clus
vv                                                                  CCDC25 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  CCDC25 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D709V9, binary
                  cls
clus                 0   1
  CCDC25 MUTATED     0   3
  CCDC25 WILD-TYPE   5 281
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC25 MUTATED      0    3
  CCDC25 WILD-TYPE    5  281
     clus
vv    CCDC25 MUTATED CCDC25 WILD-TYPE
  NO               0                5
  YES              3              281
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CCDC25 MUTATED     1   0   0   1
  CCDC25 WILD-TYPE 226  10  10  23
D709V10, multiclass
[1] "Remove cluster labels:" "CCDC25 MUTATED"        
clus
  CCDC25 MUTATED CCDC25 WILD-TYPE 
               2              269 
      TCGA-B7-5816       TCGA-B7-5818       TCGA-BR-4183       TCGA-BR-4184 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-4187       TCGA-BR-4188       TCGA-BR-4191       TCGA-BR-4201 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-4253       TCGA-BR-4255       TCGA-BR-4256       TCGA-BR-4257 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-4267       TCGA-BR-4279       TCGA-BR-4280       TCGA-BR-4294 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-4357       TCGA-BR-4361       TCGA-BR-4362       TCGA-BR-4363 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-4366       TCGA-BR-4368       TCGA-BR-4369       TCGA-BR-4370 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-4371       TCGA-BR-6453       TCGA-BR-6454       TCGA-BR-6455 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-6456       TCGA-BR-6457       TCGA-BR-6458       TCGA-BR-6563 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-6564       TCGA-BR-6565       TCGA-BR-6566       TCGA-BR-6705 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-6706       TCGA-BR-6707       TCGA-BR-6710       TCGA-BR-6801 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-6802       TCGA-BR-6803       TCGA-BR-6852       TCGA-BR-7196 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-7197       TCGA-BR-7703       TCGA-BR-7707       TCGA-BR-7715 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-7716       TCGA-BR-7717       TCGA-BR-7722       TCGA-BR-7723 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-7851       TCGA-BR-7901       TCGA-BR-7957       TCGA-BR-7958 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-7959       TCGA-BR-8058       TCGA-BR-8059       TCGA-BR-8077 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8078       TCGA-BR-8080       TCGA-BR-8081       TCGA-BR-8284 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8286       TCGA-BR-8289       TCGA-BR-8291       TCGA-BR-8295 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8296       TCGA-BR-8297       TCGA-BR-8360       TCGA-BR-8361 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8363       TCGA-BR-8364       TCGA-BR-8365       TCGA-BR-8366 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8367       TCGA-BR-8368       TCGA-BR-8369       TCGA-BR-8370 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8371       TCGA-BR-8372       TCGA-BR-8373       TCGA-BR-8380 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8381       TCGA-BR-8382       TCGA-BR-8384       TCGA-BR-8483 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8484       TCGA-BR-8485       TCGA-BR-8486       TCGA-BR-8487 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8588       TCGA-BR-8589       TCGA-BR-8590       TCGA-BR-8591 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8592       TCGA-BR-8676       TCGA-BR-8677       TCGA-BR-8678 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8679       TCGA-BR-8680       TCGA-BR-8682       TCGA-BR-8683 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8686       TCGA-BR-8687       TCGA-BR-8690       TCGA-BR-A44T 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A44U       TCGA-BR-A452       TCGA-BR-A453       TCGA-BR-A4CQ 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A4CR       TCGA-BR-A4CS       TCGA-BR-A4IU       TCGA-BR-A4IV 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A4IY       TCGA-BR-A4IZ       TCGA-BR-A4J1       TCGA-BR-A4J2 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A4J4       TCGA-BR-A4J6       TCGA-BR-A4J7       TCGA-BR-A4J8 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A4PD       TCGA-BR-A4PE       TCGA-BR-A4PF       TCGA-BR-A4QI 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A4QL       TCGA-BR-A4QM       TCGA-CD-5800       TCGA-CD-5801 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CD-5804       TCGA-CD-8524       TCGA-CD-8525       TCGA-CD-8526 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CD-8527       TCGA-CD-8528       TCGA-CD-8529       TCGA-CD-8530 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CD-8531       TCGA-CD-8532       TCGA-CD-8534       TCGA-CD-8535 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CD-8536       TCGA-CD-A487       TCGA-CG-4300       TCGA-CG-4301 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4304       TCGA-CG-4305       TCGA-CG-4306       TCGA-CG-4436 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4437       TCGA-CG-4438       TCGA-CG-4440       TCGA-CG-4441 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4442       TCGA-CG-4443       TCGA-CG-4444       TCGA-CG-4449 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4455       TCGA-CG-4462       TCGA-CG-4465       TCGA-CG-4466 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4469       TCGA-CG-4474       TCGA-CG-4475       TCGA-CG-4476 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4477       TCGA-CG-5717       TCGA-CG-5718       TCGA-CG-5719 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-5720       TCGA-CG-5721       TCGA-CG-5722       TCGA-CG-5723 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-5724       TCGA-CG-5726       TCGA-CG-5727       TCGA-CG-5728 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-5730       TCGA-CG-5732       TCGA-CG-5733       TCGA-CG-5734 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-5577       TCGA-D7-5578       TCGA-D7-5579       TCGA-D7-6518 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-6519       TCGA-D7-6520       TCGA-D7-6521       TCGA-D7-6522 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-6524       TCGA-D7-6525       TCGA-D7-6526       TCGA-D7-6527 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-6528       TCGA-D7-6815       TCGA-D7-6817       TCGA-D7-6818 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-6820       TCGA-D7-6822       TCGA-D7-8570       TCGA-D7-8572 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-8573       TCGA-D7-8574       TCGA-D7-8575       TCGA-D7-8576 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-8578       TCGA-D7-8579       TCGA-D7-A4YT       TCGA-D7-A4YU 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-A4YV       TCGA-D7-A4YX       TCGA-D7-A4YY       TCGA-D7-A4Z0 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-EQ-5647       TCGA-EQ-A4SO       TCGA-F1-6177       TCGA-F1-6874 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-F1-6875       TCGA-F1-A448       TCGA-FP-7735       TCGA-FP-7829 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-FP-7998       TCGA-FP-8099       TCGA-FP-8209       TCGA-FP-8211 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-FP-8631       TCGA-FP-A4BE       TCGA-FP-A4BF       TCGA-HF-7132 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HF-7133       TCGA-HF-7136       TCGA-HJ-7597       TCGA-HU-8243 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-8245       TCGA-HU-8249       TCGA-HU-8602       TCGA-HU-8604 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-8608       TCGA-HU-8610       TCGA-HU-A4G2       TCGA-HU-A4G3 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4G6       TCGA-HU-A4G9       TCGA-HU-A4GC       TCGA-HU-A4GD 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4GF       TCGA-HU-A4GH       TCGA-HU-A4GN       TCGA-HU-A4GP 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4GQ       TCGA-HU-A4GT       TCGA-HU-A4GU       TCGA-HU-A4GX 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4GY       TCGA-HU-A4H0       TCGA-HU-A4H2       TCGA-HU-A4H3 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4H4       TCGA-HU-A4H5       TCGA-HU-A4H6       TCGA-HU-A4H8 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4HD       TCGA-IN-7806       TCGA-IN-8462       TCGA-IN-8663 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-IP-7968 
"CCDC25 WILD-TYPE" 
D709V11, continuous
[1] "Remove cluster labels:" "CCDC25 MUTATED"        
clus
  CCDC25 MUTATED CCDC25 WILD-TYPE 
               1              250 
      TCGA-B7-5816       TCGA-BR-4183       TCGA-BR-4184       TCGA-BR-4188 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-4191       TCGA-BR-4253       TCGA-BR-4255       TCGA-BR-4256 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-4267       TCGA-BR-4279       TCGA-BR-4280       TCGA-BR-4361 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-4362       TCGA-BR-4368       TCGA-BR-6453       TCGA-BR-6454 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-6455       TCGA-BR-6456       TCGA-BR-6457       TCGA-BR-6458 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-6563       TCGA-BR-6564       TCGA-BR-6565       TCGA-BR-6566 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-6705       TCGA-BR-6706       TCGA-BR-6707       TCGA-BR-6710 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-6801       TCGA-BR-6802       TCGA-BR-6803       TCGA-BR-6852 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-7196       TCGA-BR-7197       TCGA-BR-7703       TCGA-BR-7707 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-7715       TCGA-BR-7716       TCGA-BR-7717       TCGA-BR-7722 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-7723       TCGA-BR-7851       TCGA-BR-7901       TCGA-BR-7957 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-7958       TCGA-BR-7959       TCGA-BR-8058       TCGA-BR-8059 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8077       TCGA-BR-8078       TCGA-BR-8080       TCGA-BR-8081 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8284       TCGA-BR-8286       TCGA-BR-8289       TCGA-BR-8291 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8295       TCGA-BR-8296       TCGA-BR-8297       TCGA-BR-8360 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8361       TCGA-BR-8363       TCGA-BR-8364       TCGA-BR-8365 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8366       TCGA-BR-8367       TCGA-BR-8368       TCGA-BR-8369 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8370       TCGA-BR-8371       TCGA-BR-8372       TCGA-BR-8373 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8380       TCGA-BR-8381       TCGA-BR-8382       TCGA-BR-8384 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8483       TCGA-BR-8484       TCGA-BR-8485       TCGA-BR-8486 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8487       TCGA-BR-8588       TCGA-BR-8589       TCGA-BR-8590 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8591       TCGA-BR-8592       TCGA-BR-8676       TCGA-BR-8677 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8678       TCGA-BR-8679       TCGA-BR-8680       TCGA-BR-8682 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-8683       TCGA-BR-8686       TCGA-BR-8687       TCGA-BR-8690 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A44T       TCGA-BR-A44U       TCGA-BR-A452       TCGA-BR-A453 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A4CQ       TCGA-BR-A4CR       TCGA-BR-A4CS       TCGA-BR-A4IU 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A4IV       TCGA-BR-A4IY       TCGA-BR-A4IZ       TCGA-BR-A4J1 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A4J2       TCGA-BR-A4J4       TCGA-BR-A4J6       TCGA-BR-A4J8 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A4PD       TCGA-BR-A4PE       TCGA-BR-A4PF       TCGA-BR-A4QI 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-BR-A4QL       TCGA-BR-A4QM       TCGA-CD-5804       TCGA-CD-8525 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CD-8526       TCGA-CD-8531       TCGA-CD-8535       TCGA-CD-A487 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4301       TCGA-CG-4304       TCGA-CG-4305       TCGA-CG-4436 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4437       TCGA-CG-4438       TCGA-CG-4440       TCGA-CG-4441 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4442       TCGA-CG-4443       TCGA-CG-4444       TCGA-CG-4449 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4455       TCGA-CG-4462       TCGA-CG-4465       TCGA-CG-4466 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4469       TCGA-CG-4474       TCGA-CG-4475       TCGA-CG-4476 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-4477       TCGA-CG-5717       TCGA-CG-5718       TCGA-CG-5719 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-5720       TCGA-CG-5721       TCGA-CG-5722       TCGA-CG-5723 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-5724       TCGA-CG-5726       TCGA-CG-5727       TCGA-CG-5728 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-CG-5730       TCGA-CG-5732       TCGA-CG-5733       TCGA-CG-5734 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-5577       TCGA-D7-5578       TCGA-D7-5579       TCGA-D7-6518 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-6519       TCGA-D7-6520       TCGA-D7-6521       TCGA-D7-6522 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-6524       TCGA-D7-6525       TCGA-D7-6526       TCGA-D7-6527 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-6528       TCGA-D7-6815       TCGA-D7-6817       TCGA-D7-6818 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-6820       TCGA-D7-6822       TCGA-D7-8570       TCGA-D7-8572 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-8573       TCGA-D7-8574       TCGA-D7-8575       TCGA-D7-8576 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-8578       TCGA-D7-8579       TCGA-D7-A4YT       TCGA-D7-A4YU 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-D7-A4YV       TCGA-D7-A4YX       TCGA-D7-A4YY       TCGA-D7-A4Z0 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-EQ-5647       TCGA-EQ-8122       TCGA-EQ-A4SO       TCGA-F1-6177 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-F1-6874       TCGA-F1-6875       TCGA-F1-A448       TCGA-FP-7735 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-FP-7829       TCGA-FP-7916       TCGA-FP-7998       TCGA-FP-8099 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-FP-8209       TCGA-FP-8210       TCGA-FP-8211       TCGA-FP-8631 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-FP-A4BE       TCGA-FP-A4BF       TCGA-HF-7132       TCGA-HF-7133 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HF-7136       TCGA-HJ-7597       TCGA-HU-8243       TCGA-HU-8245 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-8249       TCGA-HU-8602       TCGA-HU-8604       TCGA-HU-8608 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-8610       TCGA-HU-A4G2       TCGA-HU-A4G3       TCGA-HU-A4G6 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4G8       TCGA-HU-A4G9       TCGA-HU-A4GC       TCGA-HU-A4GD 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4GF       TCGA-HU-A4GH       TCGA-HU-A4GN       TCGA-HU-A4GP 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4GQ       TCGA-HU-A4GT       TCGA-HU-A4GU       TCGA-HU-A4GX 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4GY       TCGA-HU-A4H0       TCGA-HU-A4H2       TCGA-HU-A4H3 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4H4       TCGA-HU-A4H5       TCGA-HU-A4H6       TCGA-HU-A4H8 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-HU-A4HD       TCGA-IN-7806       TCGA-IN-7808       TCGA-IN-8462 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
      TCGA-IN-8663       TCGA-IP-7968 
"CCDC25 WILD-TYPE" "CCDC25 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC25 MUTATED       1                         0     2
  CCDC25 WILD-TYPE    75                         4   166
D709V12, multiclass
                           clus
vv                          CCDC25 MUTATED CCDC25 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  2              166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(710) Variable = IQSEC2 MUTATION ANALYSIS
D710V1, survival
                  sevent
clus2                0   1
  IQSEC2 MUTATED     7   5
  IQSEC2 WILD-TYPE 174  75
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
              12              249 
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
               5               75 
$`IQSEC2 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7957 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8372 
        6.97        34.68         9.07         0.26         4.31        19.17 
TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-5721 TCGA-D7-6528 TCGA-D7-A4YV TCGA-HU-A4G9 
       11.57         6.58         6.02        15.22         5.92        24.20 

$`IQSEC2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         3.45        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
       19.50        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        10.26        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       16.44        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        11.84         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
            0.26             0.00 
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
           34.68           105.07 
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
            8.02            12.76 
[1] "0.3 - 34.7 (8.0)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "1.7"
D710V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IQSEC2 MUTATED         0        1        3        0         2         1
  IQSEC2 WILD-TYPE       1        8       24       26        29        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IQSEC2 MUTATED           0          1          1          1        2
  IQSEC2 WILD-TYPE         3         48         35         23       22
D710V3, multiclass
            clus
vv           IQSEC2 MUTATED IQSEC2 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                3               24
  STAGE II                0               26
  STAGE IIA               2               29
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              1               35
  STAGE IIIC              1               23
  STAGE IV                2               22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IQSEC2 MUTATED     1   3   6   2
  IQSEC2 WILD-TYPE  10  69 116  73
D710V4, multiclass
    clus
vv   IQSEC2 MUTATED IQSEC2 WILD-TYPE
  T1              1               10
  T2              3               69
  T3              6              116
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  IQSEC2 MUTATED    6  3  0  3
  IQSEC2 WILD-TYPE 87 78 50 50
D710V5, multiclass
    clus
vv   IQSEC2 MUTATED IQSEC2 WILD-TYPE
  N0              6               87
  N1              3               78
  N2              0               50
  N3              3               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D710V6, binary
                  cls
clus                 0   1
  IQSEC2 MUTATED    10   1
  IQSEC2 WILD-TYPE 247  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQSEC2 MUTATED     10    1
  IQSEC2 WILD-TYPE  247   17
   clus
vv  IQSEC2 MUTATED IQSEC2 WILD-TYPE
  0             10              247
  1              1               17
[1] 2 2
[1] FALSE
D710V7, binary
                  cls
clus                 0   1
  IQSEC2 MUTATED     8   4
  IQSEC2 WILD-TYPE 102 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQSEC2 MUTATED      8    4
  IQSEC2 WILD-TYPE  102  175
        clus
vv       IQSEC2 MUTATED IQSEC2 WILD-TYPE
  FEMALE              8              102
  MALE                4              175
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  IQSEC2 MUTATED                                       1
  IQSEC2 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IQSEC2 MUTATED                                                        6
  IQSEC2 WILD-TYPE                                                    129
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IQSEC2 MUTATED                                                                   2
  IQSEC2 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  IQSEC2 MUTATED                                                  3
  IQSEC2 WILD-TYPE                                               35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  IQSEC2 MUTATED                                                          0
  IQSEC2 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  IQSEC2 MUTATED                                                           0
  IQSEC2 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  IQSEC2 MUTATED                                          0
  IQSEC2 WILD-TYPE                                        3
D710V8, multiclass
                                                                   clus
vv                                                                  IQSEC2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  IQSEC2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D710V9, binary
                  cls
clus                 0   1
  IQSEC2 MUTATED     0  12
  IQSEC2 WILD-TYPE   5 272
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQSEC2 MUTATED      0   12
  IQSEC2 WILD-TYPE    5  272
     clus
vv    IQSEC2 MUTATED IQSEC2 WILD-TYPE
  NO               0                5
  YES             12              272
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  IQSEC2 MUTATED    10   0   0   1
  IQSEC2 WILD-TYPE 217  10  10  23
D710V10, multiclass
    clus
vv   IQSEC2 MUTATED IQSEC2 WILD-TYPE
  R0             10              217
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D710V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IQSEC2 MUTATED       2                         0     9
  IQSEC2 WILD-TYPE    74                         4   159
D710V12, multiclass
                           clus
vv                          IQSEC2 MUTATED IQSEC2 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  9              159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(711) Variable = IBTK MUTATION ANALYSIS
D711V1, survival
                sevent
clus2              0   1
  IBTK MUTATED    10   4
  IBTK WILD-TYPE 171  76
  IBTK MUTATED IBTK WILD-TYPE 
            14            247 
  IBTK MUTATED IBTK WILD-TYPE 
             4             76 
$`IBTK MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8360 TCGA-BR-8680 
       26.70         6.97        30.90        32.94         6.18        15.81 
TCGA-CD-A4MI TCGA-CG-4465 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 TCGA-FP-A4BE 
        0.10         9.01       105.07        65.10        21.07        11.08 
TCGA-HU-8602 TCGA-HU-A4GQ 
       11.41         0.10 

$`IBTK WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       31.20        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
       16.31         2.20        15.58         7.40        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       47.05        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        6.02         0.99        12.03        28.96        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  IBTK MUTATED IBTK WILD-TYPE 
           0.1            0.0 
  IBTK MUTATED IBTK WILD-TYPE 
        105.07          79.07 
  IBTK MUTATED IBTK WILD-TYPE 
         13.61          12.62 
[1] "0.1 - 105.1 (13.6)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "1.8"
D711V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IBTK MUTATED         0        0        2        1         3         2
  IBTK WILD-TYPE       1        9       25       25        28        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IBTK MUTATED           0          3          1          2        3
  IBTK WILD-TYPE         3         46         35         22       21
D711V3, multiclass
            clus
vv           IBTK MUTATED IBTK WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              1             25
  STAGE IIA             3             28
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            3             46
  STAGE IIIB            1             35
  STAGE IIIC            2             22
  STAGE IV              3             21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IBTK MUTATED     0   4   6   7
  IBTK WILD-TYPE  11  68 116  68
D711V4, multiclass
    clus
vv   IBTK MUTATED IBTK WILD-TYPE
  T1            0             11
  T2            4             68
  T3            6            116
  T4            7             68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  IBTK MUTATED    7  3  5  2
  IBTK WILD-TYPE 86 78 45 51
D711V5, multiclass
    clus
vv   IBTK MUTATED IBTK WILD-TYPE
  N0            7             86
  N1            3             78
  N2            5             45
  N3            2             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D711V6, binary
                cls
clus               0   1
  IBTK MUTATED    15   2
  IBTK WILD-TYPE 242  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED     15    2
  IBTK WILD-TYPE  242   16
   clus
vv  IBTK MUTATED IBTK WILD-TYPE
  0           15            242
  1            2             16
[1] 2 2
[1] FALSE
D711V7, binary
                cls
clus               0   1
  IBTK MUTATED     8  10
  IBTK WILD-TYPE 102 169
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED      8   10
  IBTK WILD-TYPE  102  169
        clus
vv       IBTK MUTATED IBTK WILD-TYPE
  FEMALE            8            102
  MALE             10            169
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  IBTK MUTATED                                       4
  IBTK WILD-TYPE                                    46
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IBTK MUTATED                                                        8
  IBTK WILD-TYPE                                                    127
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IBTK MUTATED                                                                   4
  IBTK WILD-TYPE                                                                36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  IBTK MUTATED                                                  2
  IBTK WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  IBTK MUTATED                                                          0
  IBTK WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  IBTK MUTATED                                                           0
  IBTK WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  IBTK MUTATED                                          0
  IBTK WILD-TYPE                                        3
D711V8, multiclass
                                                                   clus
vv                                                                  IBTK MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  IBTK WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D711V9, binary
                cls
clus               0   1
  IBTK MUTATED     0  18
  IBTK WILD-TYPE   5 266
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED      0   18
  IBTK WILD-TYPE    5  266
     clus
vv    IBTK MUTATED IBTK WILD-TYPE
  NO             0              5
  YES           18            266
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IBTK MUTATED    13   0   1   3
  IBTK WILD-TYPE 214  10   9  21
D711V10, multiclass
    clus
vv   IBTK MUTATED IBTK WILD-TYPE
  R0           13            214
  R1            0             10
  R2            1              9
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D711V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IBTK MUTATED       4                         1     7
  IBTK WILD-TYPE    72                         3   161
D711V12, multiclass
                           clus
vv                          IBTK MUTATED IBTK WILD-TYPE
  ASIAN                                4             72
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                                7            161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(712) Variable = TDRD3 MUTATION ANALYSIS
D712V1, survival
                 sevent
clus2               0   1
  TDRD3 MUTATED     5   4
  TDRD3 WILD-TYPE 176  76
  TDRD3 MUTATED TDRD3 WILD-TYPE 
              9             252 
  TDRD3 MUTATED TDRD3 WILD-TYPE 
              4              76 
$`TDRD3 MUTATED`
TCGA-BR-7901 TCGA-BR-8680 TCGA-BR-A4J1 TCGA-CD-8530 TCGA-D7-A4YV TCGA-HU-A4G8 
        3.45        15.81         0.72         0.16         5.92        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GQ TCGA-HU-A4GT 
       24.20         0.10         6.51 

$`TDRD3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73        12.43         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       13.51        12.89         8.98        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.07         0.10         0.13         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
       16.44        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
        5.59        12.30         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  TDRD3 MUTATED TDRD3 WILD-TYPE 
            0.1             0.0 
  TDRD3 MUTATED TDRD3 WILD-TYPE 
          24.20          105.07 
  TDRD3 MUTATED TDRD3 WILD-TYPE 
          5.920          12.775 
[1] "0.1 - 24.2 (5.9)"   "0.0 - 105.1 (12.8)"
[1] "hr=" "3"  
D712V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TDRD3 MUTATED         0        1        0        1         1         3
  TDRD3 WILD-TYPE       1        8       27       25        30        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TDRD3 MUTATED           0          2          0          1        1
  TDRD3 WILD-TYPE         3         47         36         23       23
D712V3, multiclass
            clus
vv           TDRD3 MUTATED TDRD3 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              1              30
  STAGE IIB              3              41
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             0              36
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TDRD3 MUTATED     2   0   5   4
  TDRD3 WILD-TYPE   9  72 117  71
D712V4, multiclass
    clus
vv   TDRD3 MUTATED TDRD3 WILD-TYPE
  T1             2               9
  T2             0              72
  T3             5             117
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  TDRD3 MUTATED    4  4  2  0
  TDRD3 WILD-TYPE 89 77 48 53
D712V5, multiclass
    clus
vv   TDRD3 MUTATED TDRD3 WILD-TYPE
  N0             4              89
  N1             4              77
  N2             2              48
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D712V6, binary
                 cls
clus                0   1
  TDRD3 MUTATED    10   1
  TDRD3 WILD-TYPE 247  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD3 MUTATED     10    1
  TDRD3 WILD-TYPE  247   17
   clus
vv  TDRD3 MUTATED TDRD3 WILD-TYPE
  0            10             247
  1             1              17
[1] 2 2
[1] FALSE
D712V7, binary
                 cls
clus                0   1
  TDRD3 MUTATED     6   5
  TDRD3 WILD-TYPE 104 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD3 MUTATED      6    5
  TDRD3 WILD-TYPE  104  174
        clus
vv       TDRD3 MUTATED TDRD3 WILD-TYPE
  FEMALE             6             104
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TDRD3 MUTATED                                       2
  TDRD3 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TDRD3 MUTATED                                                        4
  TDRD3 WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TDRD3 MUTATED                                                                   0
  TDRD3 WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TDRD3 MUTATED                                                  5
  TDRD3 WILD-TYPE                                               33
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TDRD3 MUTATED                                                          0
  TDRD3 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TDRD3 MUTATED                                                           0
  TDRD3 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TDRD3 MUTATED                                          0
  TDRD3 WILD-TYPE                                        3
D712V8, multiclass
                                                                   clus
vv                                                                  TDRD3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  TDRD3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D712V9, binary
                 cls
clus                0   1
  TDRD3 MUTATED     0  11
  TDRD3 WILD-TYPE   5 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD3 MUTATED      0   11
  TDRD3 WILD-TYPE    5  273
     clus
vv    TDRD3 MUTATED TDRD3 WILD-TYPE
  NO              0               5
  YES            11             273
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TDRD3 MUTATED     8   0   0   2
  TDRD3 WILD-TYPE 219  10  10  22
D712V10, multiclass
    clus
vv   TDRD3 MUTATED TDRD3 WILD-TYPE
  R0             8             219
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D712V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TDRD3 MUTATED       7                         0     4
  TDRD3 WILD-TYPE    69                         4   164
D712V12, multiclass
                           clus
vv                          TDRD3 MUTATED TDRD3 WILD-TYPE
  ASIAN                                 7              69
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 4             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(713) Variable = HS6ST2 MUTATION ANALYSIS
D713V1, survival
                  sevent
clus2                0   1
  HS6ST2 MUTATED     3   1
  HS6ST2 WILD-TYPE 178  79
  HS6ST2 MUTATED HS6ST2 WILD-TYPE 
               4              257 
  HS6ST2 MUTATED HS6ST2 WILD-TYPE 
               1               79 
$`HS6ST2 MUTATED`
TCGA-BR-8487 TCGA-BR-8591 TCGA-CG-4465 TCGA-HU-A4H4 
        1.12        13.45         9.01        23.84 

$`HS6ST2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       19.07        12.03         0.00        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       12.95        19.36        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  HS6ST2 MUTATED HS6ST2 WILD-TYPE 
            1.12             0.00 
  HS6ST2 MUTATED HS6ST2 WILD-TYPE 
           23.84           105.07 
  HS6ST2 MUTATED HS6ST2 WILD-TYPE 
           11.23            12.62 
[1] "1.1 - 23.8 (11.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1"  
D713V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HS6ST2 MUTATED         0        0        0        1         1         1
  HS6ST2 WILD-TYPE       1        9       27       25        30        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HS6ST2 MUTATED           0          1          0          1        1
  HS6ST2 WILD-TYPE         3         48         36         23       23
D713V3, multiclass
            clus
vv           HS6ST2 MUTATED HS6ST2 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                1               25
  STAGE IIA               1               30
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HS6ST2 MUTATED     1   2   1   3
  HS6ST2 WILD-TYPE  10  70 121  72
D713V4, multiclass
    clus
vv   HS6ST2 MUTATED HS6ST2 WILD-TYPE
  T1              1               10
  T2              2               70
  T3              1              121
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  HS6ST2 MUTATED    2  1  1  2
  HS6ST2 WILD-TYPE 91 80 49 51
D713V5, multiclass
    clus
vv   HS6ST2 MUTATED HS6ST2 WILD-TYPE
  N0              2               91
  N1              1               80
  N2              1               49
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D713V6, binary
                  cls
clus                 0   1
  HS6ST2 MUTATED     6   1
  HS6ST2 WILD-TYPE 251  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HS6ST2 MUTATED      6    1
  HS6ST2 WILD-TYPE  251   17
   clus
vv  HS6ST2 MUTATED HS6ST2 WILD-TYPE
  0              6              251
  1              1               17
[1] 2 2
[1] FALSE
D713V7, binary
                  cls
clus                 0   1
  HS6ST2 MUTATED     5   2
  HS6ST2 WILD-TYPE 105 177
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HS6ST2 MUTATED      5    2
  HS6ST2 WILD-TYPE  105  177
        clus
vv       HS6ST2 MUTATED HS6ST2 WILD-TYPE
  FEMALE              5              105
  MALE                2              177
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  HS6ST2 MUTATED                                       1
  HS6ST2 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HS6ST2 MUTATED                                                        4
  HS6ST2 WILD-TYPE                                                    131
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HS6ST2 MUTATED                                                                   0
  HS6ST2 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  HS6ST2 MUTATED                                                  1
  HS6ST2 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  HS6ST2 MUTATED                                                          1
  HS6ST2 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  HS6ST2 MUTATED                                                           0
  HS6ST2 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  HS6ST2 MUTATED                                          0
  HS6ST2 WILD-TYPE                                        3
D713V8, multiclass
                                                                   clus
vv                                                                  HS6ST2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  HS6ST2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D713V9, binary
                  cls
clus                 0   1
  HS6ST2 MUTATED     1   6
  HS6ST2 WILD-TYPE   4 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HS6ST2 MUTATED      1    6
  HS6ST2 WILD-TYPE    4  278
     clus
vv    HS6ST2 MUTATED HS6ST2 WILD-TYPE
  NO               1                4
  YES              6              278
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  HS6ST2 MUTATED     4   0   1   2
  HS6ST2 WILD-TYPE 223  10   9  22
D713V10, multiclass
    clus
vv   HS6ST2 MUTATED HS6ST2 WILD-TYPE
  R0              4              223
  R1              0               10
  R2              1                9
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D713V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HS6ST2 MUTATED       1                         0     4
  HS6ST2 WILD-TYPE    75                         4   164
D713V12, multiclass
                           clus
vv                          HS6ST2 MUTATED HS6ST2 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(714) Variable = EPB41L5 MUTATION ANALYSIS
D714V1, survival
                   sevent
clus2                 0   1
  EPB41L5 MUTATED     6   2
  EPB41L5 WILD-TYPE 175  78
  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
                8               253 
  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
                2                78 
$`EPB41L5 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A4MG 
        6.97        34.68        32.94        13.45        15.81         6.58 
TCGA-HU-A4G8 TCGA-HU-A4GX 
       11.84        10.19 

$`EPB41L5 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51         6.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
             6.58              0.00 
  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
            34.68            105.07 
  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
           12.645            12.620 
[1] "6.6 - 34.7 (12.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.5"
D714V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPB41L5 MUTATED         0        0        0        0         3         1
  EPB41L5 WILD-TYPE       1        9       27       26        28        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EPB41L5 MUTATED           0          1          0          2        1
  EPB41L5 WILD-TYPE         3         48         36         22       23
D714V3, multiclass
            clus
vv           EPB41L5 MUTATED EPB41L5 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 0                27
  STAGE II                 0                26
  STAGE IIA                3                28
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               1                48
  STAGE IIIB               0                36
  STAGE IIIC               2                22
  STAGE IV                 1                23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  EPB41L5 MUTATED     0   0   5   3
  EPB41L5 WILD-TYPE  11  72 117  72
D714V4, multiclass
    clus
vv   EPB41L5 MUTATED EPB41L5 WILD-TYPE
  T1               0                11
  T2               0                72
  T3               5               117
  T4               3                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  EPB41L5 MUTATED    3  2  2  1
  EPB41L5 WILD-TYPE 90 79 48 52
D714V5, multiclass
    clus
vv   EPB41L5 MUTATED EPB41L5 WILD-TYPE
  N0               3                90
  N1               2                79
  N2               2                48
  N3               1                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D714V6, binary
                   cls
clus                  0   1
  EPB41L5 MUTATED     6   1
  EPB41L5 WILD-TYPE 251  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EPB41L5 MUTATED      6    1
  EPB41L5 WILD-TYPE  251   17
   clus
vv  EPB41L5 MUTATED EPB41L5 WILD-TYPE
  0               6               251
  1               1                17
[1] 2 2
[1] FALSE
D714V7, binary
                   cls
clus                  0   1
  EPB41L5 MUTATED     4   4
  EPB41L5 WILD-TYPE 106 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EPB41L5 MUTATED      4    4
  EPB41L5 WILD-TYPE  106  175
        clus
vv       EPB41L5 MUTATED EPB41L5 WILD-TYPE
  FEMALE               4               106
  MALE                 4               175
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  EPB41L5 MUTATED                                       3
  EPB41L5 WILD-TYPE                                    47
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EPB41L5 MUTATED                                                        4
  EPB41L5 WILD-TYPE                                                    131
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EPB41L5 MUTATED                                                                   0
  EPB41L5 WILD-TYPE                                                                40
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  EPB41L5 MUTATED                                                  1
  EPB41L5 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  EPB41L5 MUTATED                                                          0
  EPB41L5 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  EPB41L5 MUTATED                                                           0
  EPB41L5 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  EPB41L5 MUTATED                                          0
  EPB41L5 WILD-TYPE                                        3
D714V8, multiclass
                                                                   clus
vv                                                                  EPB41L5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  EPB41L5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D714V9, binary
                   cls
clus                  0   1
  EPB41L5 MUTATED     0   8
  EPB41L5 WILD-TYPE   5 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EPB41L5 MUTATED      0    8
  EPB41L5 WILD-TYPE    5  276
     clus
vv    EPB41L5 MUTATED EPB41L5 WILD-TYPE
  NO                0                 5
  YES               8               276
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  EPB41L5 MUTATED     5   0   0   1
  EPB41L5 WILD-TYPE 222  10  10  23
D714V10, multiclass
    clus
vv   EPB41L5 MUTATED EPB41L5 WILD-TYPE
  R0               5               222
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D714V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EPB41L5 MUTATED       4                         0     4
  EPB41L5 WILD-TYPE    72                         4   164
D714V12, multiclass
                           clus
vv                          EPB41L5 MUTATED EPB41L5 WILD-TYPE
  ASIAN                                   4                72
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   4               164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(715) Variable = ARID5B MUTATION ANALYSIS
D715V1, survival
                  sevent
clus2                0   1
  ARID5B MUTATED     7   1
  ARID5B WILD-TYPE 174  79
  ARID5B MUTATED ARID5B WILD-TYPE 
               8              253 
  ARID5B MUTATED ARID5B WILD-TYPE 
               1               79 
$`ARID5B MUTATED`
TCGA-BR-7851 TCGA-BR-8284 TCGA-BR-8361 TCGA-BR-8372 TCGA-CG-4305 TCGA-CG-4466 
       12.43         8.05        19.50        19.17        15.95        18.97 
TCGA-CG-5721 TCGA-HU-8602 
        6.02        11.41 

$`ARID5B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        5.52        26.47         5.92        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  ARID5B MUTATED ARID5B WILD-TYPE 
            6.02             0.00 
  ARID5B MUTATED ARID5B WILD-TYPE 
           19.50           105.07 
  ARID5B MUTATED ARID5B WILD-TYPE 
           14.19            12.62 
[1] "6.0 - 19.5 (14.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.4"
D715V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARID5B MUTATED         1        0        1        1         0         2
  ARID5B WILD-TYPE       0        9       26       25        31        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID5B MUTATED           0          0          0          3        1
  ARID5B WILD-TYPE         3         49         36         21       23
D715V3, multiclass
            clus
vv           ARID5B MUTATED ARID5B WILD-TYPE
  STAGE I                 1                0
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                1               25
  STAGE IIA               0               31
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              3               21
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARID5B MUTATED     1   2   0   6
  ARID5B WILD-TYPE  10  70 122  69
D715V4, multiclass
    clus
vv   ARID5B MUTATED ARID5B WILD-TYPE
  T1              1               10
  T2              2               70
  T3              0              122
  T4              6               69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ARID5B MUTATED    3  4  1  2
  ARID5B WILD-TYPE 90 77 49 51
D715V5, multiclass
    clus
vv   ARID5B MUTATED ARID5B WILD-TYPE
  N0              3               90
  N1              4               77
  N2              1               49
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D715V6, binary
                  cls
clus                 0   1
  ARID5B MUTATED    10   0
  ARID5B WILD-TYPE 247  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5B MUTATED     10    0
  ARID5B WILD-TYPE  247   18
   clus
vv  ARID5B MUTATED ARID5B WILD-TYPE
  0             10              247
  1              0               18
[1] 2 2
[1] FALSE
D715V7, binary
                  cls
clus                 0   1
  ARID5B MUTATED     6   5
  ARID5B WILD-TYPE 104 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5B MUTATED      6    5
  ARID5B WILD-TYPE  104  174
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  FEMALE              6              104
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ARID5B MUTATED                                       1
  ARID5B WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ARID5B MUTATED                                                        6
  ARID5B WILD-TYPE                                                    129
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ARID5B MUTATED                                                                   4
  ARID5B WILD-TYPE                                                                36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ARID5B MUTATED                                                  0
  ARID5B WILD-TYPE                                               38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ARID5B MUTATED                                                          0
  ARID5B WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ARID5B MUTATED                                                           0
  ARID5B WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ARID5B MUTATED                                          0
  ARID5B WILD-TYPE                                        3
D715V8, multiclass
                                                                   clus
vv                                                                  ARID5B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ARID5B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D715V9, binary
                  cls
clus                 0   1
  ARID5B MUTATED     0  11
  ARID5B WILD-TYPE   5 273
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5B MUTATED      0   11
  ARID5B WILD-TYPE    5  273
     clus
vv    ARID5B MUTATED ARID5B WILD-TYPE
  NO               0                5
  YES             11              273
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ARID5B MUTATED     9   0   0   2
  ARID5B WILD-TYPE 218  10  10  22
D715V10, multiclass
    clus
vv   ARID5B MUTATED ARID5B WILD-TYPE
  R0              9              218
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D715V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID5B MUTATED       1                         1     6
  ARID5B WILD-TYPE    75                         3   162
D715V12, multiclass
                           clus
vv                          ARID5B MUTATED ARID5B WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(716) Variable = HECA MUTATION ANALYSIS
D716V1, survival
                sevent
clus2              0   1
  HECA MUTATED     9   2
  HECA WILD-TYPE 172  78
  HECA MUTATED HECA WILD-TYPE 
            11            250 
  HECA MUTATED HECA WILD-TYPE 
             2             78 
$`HECA MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-8078 TCGA-BR-8368 TCGA-CD-8531 
       30.90        34.68        30.90        12.26         4.31         0.10 
TCGA-CD-A4MJ TCGA-CG-5721 TCGA-HJ-7597 TCGA-HU-A4G3 TCGA-HU-A4G9 
       12.62         6.02        26.47         5.59        24.20 

$`HECA WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       18.35         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.13         0.16         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
       14.76         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
        0.76        24.30        12.30        11.84         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         9.67         8.88        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  HECA MUTATED HECA WILD-TYPE 
           0.1            0.0 
  HECA MUTATED HECA WILD-TYPE 
         34.68         105.07 
  HECA MUTATED HECA WILD-TYPE 
        12.620         12.625 
[1] "0.1 - 34.7 (12.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.3"
D716V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HECA MUTATED         0        1        3        0         1         2
  HECA WILD-TYPE       1        8       24       26        30        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HECA MUTATED           0          2          0          0        1
  HECA WILD-TYPE         3         47         36         24       23
D716V3, multiclass
            clus
vv           HECA MUTATED HECA WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              3             24
  STAGE II              0             26
  STAGE IIA             1             30
  STAGE IIB             2             42
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            0             36
  STAGE IIIC            0             24
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HECA MUTATED     1   5   3   2
  HECA WILD-TYPE  10  67 119  73
D716V4, multiclass
    clus
vv   HECA MUTATED HECA WILD-TYPE
  T1            1             10
  T2            5             67
  T3            3            119
  T4            2             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  HECA MUTATED    6  3  2  0
  HECA WILD-TYPE 87 78 48 53
D716V5, multiclass
    clus
vv   HECA MUTATED HECA WILD-TYPE
  N0            6             87
  N1            3             78
  N2            2             48
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D716V6, binary
                cls
clus               0   1
  HECA MUTATED    11   0
  HECA WILD-TYPE 246  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  HECA MUTATED     11    0
  HECA WILD-TYPE  246   18
   clus
vv  HECA MUTATED HECA WILD-TYPE
  0           11            246
  1            0             18
[1] 2 2
[1] FALSE
D716V7, binary
                cls
clus               0   1
  HECA MUTATED     8   4
  HECA WILD-TYPE 102 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  HECA MUTATED      8    4
  HECA WILD-TYPE  102  175
        clus
vv       HECA MUTATED HECA WILD-TYPE
  FEMALE            8            102
  MALE              4            175
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  HECA MUTATED                                       1
  HECA WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HECA MUTATED                                                        7
  HECA WILD-TYPE                                                    128
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HECA MUTATED                                                                   1
  HECA WILD-TYPE                                                                39
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  HECA MUTATED                                                  2
  HECA WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  HECA MUTATED                                                          0
  HECA WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  HECA MUTATED                                                           0
  HECA WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  HECA MUTATED                                          1
  HECA WILD-TYPE                                        2
D716V8, multiclass
                                                                   clus
vv                                                                  HECA MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  HECA WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D716V9, binary
                cls
clus               0   1
  HECA MUTATED     0  12
  HECA WILD-TYPE   5 272
[1] "tbl2"
                cls
clus             [,1] [,2]
  HECA MUTATED      0   12
  HECA WILD-TYPE    5  272
     clus
vv    HECA MUTATED HECA WILD-TYPE
  NO             0              5
  YES           12            272
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  HECA MUTATED     9   0   0   2
  HECA WILD-TYPE 218  10  10  22
D716V10, multiclass
    clus
vv   HECA MUTATED HECA WILD-TYPE
  R0            9            218
  R1            0             10
  R2            0             10
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D716V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HECA MUTATED       4                         0     7
  HECA WILD-TYPE    72                         4   161
D716V12, multiclass
                           clus
vv                          HECA MUTATED HECA WILD-TYPE
  ASIAN                                4             72
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                7            161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(717) Variable = RHOBTB2 MUTATION ANALYSIS
D717V1, survival
                   sevent
clus2                 0   1
  RHOBTB2 MUTATED     7   7
  RHOBTB2 WILD-TYPE 174  73
  RHOBTB2 MUTATED RHOBTB2 WILD-TYPE 
               14               247 
  RHOBTB2 MUTATED RHOBTB2 WILD-TYPE 
                7                73 
$`RHOBTB2 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8363 TCGA-BR-8484 
        6.97        30.90        34.68        32.78         0.26        25.18 
TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-5718 TCGA-CG-5721 TCGA-CG-5733 
       13.45        11.57         6.58        36.00         6.02        21.07 
TCGA-HU-8602 TCGA-HU-A4GT 
       11.41         6.51 

$`RHOBTB2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       13.68        19.33        39.12        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       15.81         9.34         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
       30.97         6.97         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  RHOBTB2 MUTATED RHOBTB2 WILD-TYPE 
             0.26              0.00 
  RHOBTB2 MUTATED RHOBTB2 WILD-TYPE 
            36.00            105.07 
  RHOBTB2 MUTATED RHOBTB2 WILD-TYPE 
            12.51             12.62 
[1] "0.3 - 36.0 (12.5)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.3"
D717V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RHOBTB2 MUTATED         0        0        1        1         4         1
  RHOBTB2 WILD-TYPE       1        9       26       25        27        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RHOBTB2 MUTATED           0          3          1          1        2
  RHOBTB2 WILD-TYPE         3         46         35         23       22
D717V3, multiclass
            clus
vv           RHOBTB2 MUTATED RHOBTB2 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 1                26
  STAGE II                 1                25
  STAGE IIA                4                27
  STAGE IIB                1                43
  STAGE III                0                 3
  STAGE IIIA               3                46
  STAGE IIIB               1                35
  STAGE IIIC               1                23
  STAGE IV                 2                22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RHOBTB2 MUTATED     0   4   6   5
  RHOBTB2 WILD-TYPE  11  68 116  70
D717V4, multiclass
    clus
vv   RHOBTB2 MUTATED RHOBTB2 WILD-TYPE
  T1               0                11
  T2               4                68
  T3               6               116
  T4               5                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  RHOBTB2 MUTATED    6  4  2  2
  RHOBTB2 WILD-TYPE 87 77 48 51
D717V5, multiclass
    clus
vv   RHOBTB2 MUTATED RHOBTB2 WILD-TYPE
  N0               6                87
  N1               4                77
  N2               2                48
  N3               2                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D717V6, binary
                   cls
clus                  0   1
  RHOBTB2 MUTATED    15   0
  RHOBTB2 WILD-TYPE 242  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RHOBTB2 MUTATED     15    0
  RHOBTB2 WILD-TYPE  242   18
   clus
vv  RHOBTB2 MUTATED RHOBTB2 WILD-TYPE
  0              15               242
  1               0                18
[1] 2 2
[1] FALSE
D717V7, binary
                   cls
clus                  0   1
  RHOBTB2 MUTATED    11   5
  RHOBTB2 WILD-TYPE  99 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RHOBTB2 MUTATED     11    5
  RHOBTB2 WILD-TYPE   99  174
        clus
vv       RHOBTB2 MUTATED RHOBTB2 WILD-TYPE
  FEMALE              11                99
  MALE                 5               174
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RHOBTB2 MUTATED                                       2
  RHOBTB2 WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RHOBTB2 MUTATED                                                       10
  RHOBTB2 WILD-TYPE                                                    125
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RHOBTB2 MUTATED                                                                   3
  RHOBTB2 WILD-TYPE                                                                37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RHOBTB2 MUTATED                                                  1
  RHOBTB2 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RHOBTB2 MUTATED                                                          0
  RHOBTB2 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RHOBTB2 MUTATED                                                           0
  RHOBTB2 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RHOBTB2 MUTATED                                          0
  RHOBTB2 WILD-TYPE                                        3
D717V8, multiclass
                                                                   clus
vv                                                                  RHOBTB2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  RHOBTB2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D717V9, binary
                   cls
clus                  0   1
  RHOBTB2 MUTATED     0  16
  RHOBTB2 WILD-TYPE   5 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RHOBTB2 MUTATED      0   16
  RHOBTB2 WILD-TYPE    5  268
     clus
vv    RHOBTB2 MUTATED RHOBTB2 WILD-TYPE
  NO                0                 5
  YES              16               268
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  RHOBTB2 MUTATED    11   0   0   4
  RHOBTB2 WILD-TYPE 216  10  10  20
D717V10, multiclass
    clus
vv   RHOBTB2 MUTATED RHOBTB2 WILD-TYPE
  R0              11               216
  R1               0                10
  R2               0                10
  RX               4                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D717V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RHOBTB2 MUTATED       3                         0    10
  RHOBTB2 WILD-TYPE    73                         4   158
D717V12, multiclass
                           clus
vv                          RHOBTB2 MUTATED RHOBTB2 WILD-TYPE
  ASIAN                                   3                73
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                  10               158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(718) Variable = EML3 MUTATION ANALYSIS
D718V1, survival
                sevent
clus2              0   1
  EML3 MUTATED     8   2
  EML3 WILD-TYPE 173  78
  EML3 MUTATED EML3 WILD-TYPE 
            10            251 
  EML3 MUTATED EML3 WILD-TYPE 
             2             78 
$`EML3 MUTATED`
TCGA-BR-7851 TCGA-BR-8078 TCGA-BR-8363 TCGA-CD-5801 TCGA-CG-5721 TCGA-FP-8099 
       12.43        12.26         0.26        13.18         6.02        17.06 
TCGA-HU-A4G9 TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       24.20         6.51         6.25        10.19 

$`EML3 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        19.50        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
       11.57         5.13         2.83         3.25        13.15         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       14.07        22.29        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        11.84         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
       29.98         8.98         0.10         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  EML3 MUTATED EML3 WILD-TYPE 
          0.26           0.00 
  EML3 MUTATED EML3 WILD-TYPE 
         24.20         105.07 
  EML3 MUTATED EML3 WILD-TYPE 
        11.225         12.760 
[1] "0.3 - 24.2 (11.2)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.1"
D718V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EML3 MUTATED         0        1        1        0         2         3
  EML3 WILD-TYPE       1        8       26       26        29        41
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EML3 MUTATED           0          1          0          1        1
  EML3 WILD-TYPE         3         48         36         23       23
D718V3, multiclass
            clus
vv           EML3 MUTATED EML3 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             2             29
  STAGE IIB             3             41
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            1             23
  STAGE IV              1             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EML3 MUTATED     1   1   4   4
  EML3 WILD-TYPE  10  71 118  71
D718V4, multiclass
    clus
vv   EML3 MUTATED EML3 WILD-TYPE
  T1            1             10
  T2            1             71
  T3            4            118
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  EML3 MUTATED    6  3  1  0
  EML3 WILD-TYPE 87 78 49 53
D718V5, multiclass
    clus
vv   EML3 MUTATED EML3 WILD-TYPE
  N0            6             87
  N1            3             78
  N2            1             49
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D718V6, binary
                cls
clus               0   1
  EML3 MUTATED     9   0
  EML3 WILD-TYPE 248  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  EML3 MUTATED      9    0
  EML3 WILD-TYPE  248   18
   clus
vv  EML3 MUTATED EML3 WILD-TYPE
  0            9            248
  1            0             18
[1] 2 2
[1] FALSE
D718V7, binary
                cls
clus               0   1
  EML3 MUTATED     5   5
  EML3 WILD-TYPE 105 174
[1] "tbl2"
                cls
clus             [,1] [,2]
  EML3 MUTATED      5    5
  EML3 WILD-TYPE  105  174
        clus
vv       EML3 MUTATED EML3 WILD-TYPE
  FEMALE            5            105
  MALE              5            174
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  EML3 MUTATED                                       2
  EML3 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EML3 MUTATED                                                        4
  EML3 WILD-TYPE                                                    131
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EML3 MUTATED                                                                   2
  EML3 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  EML3 MUTATED                                                  2
  EML3 WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  EML3 MUTATED                                                          0
  EML3 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  EML3 MUTATED                                                           0
  EML3 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  EML3 MUTATED                                          0
  EML3 WILD-TYPE                                        3
D718V8, multiclass
                                                                   clus
vv                                                                  EML3 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  EML3 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D718V9, binary
                cls
clus               0   1
  EML3 MUTATED     0  10
  EML3 WILD-TYPE   5 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  EML3 MUTATED      0   10
  EML3 WILD-TYPE    5  274
     clus
vv    EML3 MUTATED EML3 WILD-TYPE
  NO             0              5
  YES           10            274
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EML3 MUTATED    10   0   0   0
  EML3 WILD-TYPE 217  10  10  24
D718V10, multiclass
    clus
vv   EML3 MUTATED EML3 WILD-TYPE
  R0           10            217
  R1            0             10
  R2            0             10
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D718V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EML3 MUTATED       5                         0     4
  EML3 WILD-TYPE    71                         4   164
D718V12, multiclass
                           clus
vv                          EML3 MUTATED EML3 WILD-TYPE
  ASIAN                                5             71
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                4            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(719) Variable = EIF2C4 MUTATION ANALYSIS
D719V1, survival
                  sevent
clus2                0   1
  EIF2C4 MUTATED     6   3
  EIF2C4 WILD-TYPE 175  77
  EIF2C4 MUTATED EIF2C4 WILD-TYPE 
               9              252 
  EIF2C4 MUTATED EIF2C4 WILD-TYPE 
               3               77 
$`EIF2C4 MUTATED`
TCGA-BR-6566 TCGA-BR-8059 TCGA-BR-8373 TCGA-BR-8591 TCGA-BR-8680 TCGA-CG-4306 
       32.78        14.43        14.79        13.45        15.81         1.02 
TCGA-EQ-5647 TCGA-HU-A4H3 TCGA-HU-A4H4 
        0.62        19.36        23.84 

$`EIF2C4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       15.16        13.78        14.76         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        0.26         2.10        12.95        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  EIF2C4 MUTATED EIF2C4 WILD-TYPE 
            0.62             0.00 
  EIF2C4 MUTATED EIF2C4 WILD-TYPE 
           32.78           105.07 
  EIF2C4 MUTATED EIF2C4 WILD-TYPE 
          14.790           12.495 
[1] "0.6 - 32.8 (14.8)"  "0.0 - 105.1 (12.5)"
[1] "hr=" "1"  
D719V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EIF2C4 MUTATED         0        0        0        0         1         1
  EIF2C4 WILD-TYPE       1        9       27       26        30        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF2C4 MUTATED           1          1          0          2        3
  EIF2C4 WILD-TYPE         2         48         36         22       21
D719V3, multiclass
            clus
vv           EIF2C4 MUTATED EIF2C4 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               1               43
  STAGE III               1                2
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              2               22
  STAGE IV                3               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EIF2C4 MUTATED     0   1   3   6
  EIF2C4 WILD-TYPE  11  71 119  69
D719V4, multiclass
    clus
vv   EIF2C4 MUTATED EIF2C4 WILD-TYPE
  T1              0               11
  T2              1               71
  T3              3              119
  T4              6               69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  EIF2C4 MUTATED    1  2  3  3
  EIF2C4 WILD-TYPE 92 79 47 50
D719V5, multiclass
    clus
vv   EIF2C4 MUTATED EIF2C4 WILD-TYPE
  N0              1               92
  N1              2               79
  N2              3               47
  N3              3               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D719V6, binary
                  cls
clus                 0   1
  EIF2C4 MUTATED     6   3
  EIF2C4 WILD-TYPE 251  15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF2C4 MUTATED      6    3
  EIF2C4 WILD-TYPE  251   15
   clus
vv  EIF2C4 MUTATED EIF2C4 WILD-TYPE
  0              6              251
  1              3               15
[1] 2 2
[1] FALSE
D719V7, binary
                  cls
clus                 0   1
  EIF2C4 MUTATED     5   5
  EIF2C4 WILD-TYPE 105 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF2C4 MUTATED      5    5
  EIF2C4 WILD-TYPE  105  174
        clus
vv       EIF2C4 MUTATED EIF2C4 WILD-TYPE
  FEMALE              5              105
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  EIF2C4 MUTATED                                       1
  EIF2C4 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EIF2C4 MUTATED                                                        5
  EIF2C4 WILD-TYPE                                                    130
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  EIF2C4 MUTATED                                                                   2
  EIF2C4 WILD-TYPE                                                                38
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  EIF2C4 MUTATED                                                  2
  EIF2C4 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  EIF2C4 MUTATED                                                          0
  EIF2C4 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  EIF2C4 MUTATED                                                           0
  EIF2C4 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  EIF2C4 MUTATED                                          0
  EIF2C4 WILD-TYPE                                        3
D719V8, multiclass
                                                                   clus
vv                                                                  EIF2C4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  EIF2C4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D719V9, binary
                  cls
clus                 0   1
  EIF2C4 MUTATED     0  10
  EIF2C4 WILD-TYPE   5 274
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF2C4 MUTATED      0   10
  EIF2C4 WILD-TYPE    5  274
     clus
vv    EIF2C4 MUTATED EIF2C4 WILD-TYPE
  NO               0                5
  YES             10              274
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  EIF2C4 MUTATED     7   0   2   1
  EIF2C4 WILD-TYPE 220  10   8  23
D719V10, multiclass
    clus
vv   EIF2C4 MUTATED EIF2C4 WILD-TYPE
  R0              7              220
  R1              0               10
  R2              2                8
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D719V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EIF2C4 MUTATED       3                         0     6
  EIF2C4 WILD-TYPE    73                         4   162
D719V12, multiclass
                           clus
vv                          EIF2C4 MUTATED EIF2C4 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(720) Variable = LSS MUTATION ANALYSIS
D720V1, survival
               sevent
clus2             0   1
  LSS MUTATED     5   2
  LSS WILD-TYPE 176  78
  LSS MUTATED LSS WILD-TYPE 
            7           254 
  LSS MUTATED LSS WILD-TYPE 
            2            78 
$`LSS MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8591 TCGA-CD-A4MG TCGA-HU-A4G8 
       26.70        34.68        32.78        13.45         6.58        11.84 
TCGA-HU-A4GQ 
        0.10 

$`LSS WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  LSS MUTATED LSS WILD-TYPE 
          0.1           0.0 
  LSS MUTATED LSS WILD-TYPE 
        34.68        105.07 
  LSS MUTATED LSS WILD-TYPE 
       13.450        12.605 
[1] "0.1 - 34.7 (13.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.5"
D720V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LSS MUTATED         0        0        0        1         3         2
  LSS WILD-TYPE       1        9       27       25        28        42
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LSS MUTATED           0          0          0          2        0
  LSS WILD-TYPE         3         49         36         22       24
D720V3, multiclass
            clus
vv           LSS MUTATED LSS WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             9
  STAGE IB             0            27
  STAGE II             1            25
  STAGE IIA            3            28
  STAGE IIB            2            42
  STAGE III            0             3
  STAGE IIIA           0            49
  STAGE IIIB           0            36
  STAGE IIIC           2            22
  STAGE IV             0            24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  LSS MUTATED     0   1   4   3
  LSS WILD-TYPE  11  71 118  72
D720V4, multiclass
    clus
vv   LSS MUTATED LSS WILD-TYPE
  T1           0            11
  T2           1            71
  T3           4           118
  T4           3            72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  LSS MUTATED    4  3  1  1
  LSS WILD-TYPE 89 78 49 52
D720V5, multiclass
    clus
vv   LSS MUTATED LSS WILD-TYPE
  N0           4            89
  N1           3            78
  N2           1            49
  N3           1            52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D720V6, binary
               cls
clus              0   1
  LSS MUTATED     9   0
  LSS WILD-TYPE 248  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  LSS MUTATED      9    0
  LSS WILD-TYPE  248   18
   clus
vv  LSS MUTATED LSS WILD-TYPE
  0           9           248
  1           0            18
[1] 2 2
[1] FALSE
D720V7, binary
               cls
clus              0   1
  LSS MUTATED     5   4
  LSS WILD-TYPE 105 175
[1] "tbl2"
               cls
clus            [,1] [,2]
  LSS MUTATED      5    4
  LSS WILD-TYPE  105  175
        clus
vv       LSS MUTATED LSS WILD-TYPE
  FEMALE           5           105
  MALE             4           175
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  LSS MUTATED                                       3
  LSS WILD-TYPE                                    47
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LSS MUTATED                                                        4
  LSS WILD-TYPE                                                    131
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LSS MUTATED                                                                   0
  LSS WILD-TYPE                                                                40
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  LSS MUTATED                                                  1
  LSS WILD-TYPE                                               37
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  LSS MUTATED                                                          1
  LSS WILD-TYPE                                                       15
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  LSS MUTATED                                                           0
  LSS WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  LSS MUTATED                                          0
  LSS WILD-TYPE                                        3
D720V8, multiclass
                                                                   clus
vv                                                                  LSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  LSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D720V9, binary
               cls
clus              0   1
  LSS MUTATED     1   8
  LSS WILD-TYPE   4 276
[1] "tbl2"
               cls
clus            [,1] [,2]
  LSS MUTATED      1    8
  LSS WILD-TYPE    4  276
     clus
vv    LSS MUTATED LSS WILD-TYPE
  NO            1             4
  YES           8           276
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  LSS MUTATED     6   0   0   1
  LSS WILD-TYPE 221  10  10  23
D720V10, multiclass
    clus
vv   LSS MUTATED LSS WILD-TYPE
  R0           6           221
  R1           0            10
  R2           0            10
  RX           1            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D720V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LSS MUTATED       3                         0     5
  LSS WILD-TYPE    73                         4   163
D720V12, multiclass
                           clus
vv                          LSS MUTATED LSS WILD-TYPE
  ASIAN                               3            73
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                               5           163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(721) Variable = MMP10 MUTATION ANALYSIS
D721V1, survival
                 sevent
clus2               0   1
  MMP10 MUTATED     7   1
  MMP10 WILD-TYPE 174  79
  MMP10 MUTATED MMP10 WILD-TYPE 
              8             253 
  MMP10 MUTATED MMP10 WILD-TYPE 
              1              79 
$`MMP10 MUTATED`
TCGA-BR-7851 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-5721 TCGA-CG-5733 
       12.43        13.45        15.81        11.57         6.02        21.07 
TCGA-HU-8245 TCGA-HU-A4H3 
       12.59        19.36 

$`MMP10 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        9.34         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8602 
       11.08         5.52        26.47         5.92        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  MMP10 MUTATED MMP10 WILD-TYPE 
           6.02            0.00 
  MMP10 MUTATED MMP10 WILD-TYPE 
          21.07          105.07 
  MMP10 MUTATED MMP10 WILD-TYPE 
          13.02           12.62 
[1] "6.0 - 21.1 (13.0)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.4"
D721V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MMP10 MUTATED         0        0        0        0         1         1
  MMP10 WILD-TYPE       1        9       27       26        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MMP10 MUTATED           0          1          1          2        2
  MMP10 WILD-TYPE         3         48         35         22       22
D721V3, multiclass
            clus
vv           MMP10 MUTATED MMP10 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             1              35
  STAGE IIIC             2              22
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MMP10 MUTATED     0   1   2   5
  MMP10 WILD-TYPE  11  71 120  70
D721V4, multiclass
    clus
vv   MMP10 MUTATED MMP10 WILD-TYPE
  T1             0              11
  T2             1              71
  T3             2             120
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  MMP10 MUTATED    2  1  2  3
  MMP10 WILD-TYPE 91 80 48 50
D721V5, multiclass
    clus
vv   MMP10 MUTATED MMP10 WILD-TYPE
  N0             2              91
  N1             1              80
  N2             2              48
  N3             3              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D721V6, binary
                 cls
clus                0   1
  MMP10 MUTATED     7   1
  MMP10 WILD-TYPE 250  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP10 MUTATED      7    1
  MMP10 WILD-TYPE  250   17
   clus
vv  MMP10 MUTATED MMP10 WILD-TYPE
  0             7             250
  1             1              17
[1] 2 2
[1] FALSE
D721V7, binary
                 cls
clus                0   1
  MMP10 MUTATED     3   5
  MMP10 WILD-TYPE 107 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP10 MUTATED      3    5
  MMP10 WILD-TYPE  107  174
        clus
vv       MMP10 MUTATED MMP10 WILD-TYPE
  FEMALE             3             107
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MMP10 MUTATED                                       1
  MMP10 WILD-TYPE                                    49
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MMP10 MUTATED                                                        2
  MMP10 WILD-TYPE                                                    133
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MMP10 MUTATED                                                                   3
  MMP10 WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MMP10 MUTATED                                                  1
  MMP10 WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MMP10 MUTATED                                                          0
  MMP10 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MMP10 MUTATED                                                           1
  MMP10 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MMP10 MUTATED                                          0
  MMP10 WILD-TYPE                                        3
D721V8, multiclass
                                                                   clus
vv                                                                  MMP10 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  MMP10 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D721V9, binary
                 cls
clus                0   1
  MMP10 MUTATED     0   8
  MMP10 WILD-TYPE   5 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP10 MUTATED      0    8
  MMP10 WILD-TYPE    5  276
     clus
vv    MMP10 MUTATED MMP10 WILD-TYPE
  NO              0               5
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MMP10 MUTATED     8   0   0   0
  MMP10 WILD-TYPE 219  10  10  24
D721V10, multiclass
    clus
vv   MMP10 MUTATED MMP10 WILD-TYPE
  R0             8             219
  R1             0              10
  R2             0              10
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D721V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MMP10 MUTATED       3                         0     3
  MMP10 WILD-TYPE    73                         4   165
D721V12, multiclass
                           clus
vv                          MMP10 MUTATED MMP10 WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 3             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(722) Variable = SLC7A13 MUTATION ANALYSIS
D722V1, survival
                   sevent
clus2                 0   1
  SLC7A13 MUTATED     8   0
  SLC7A13 WILD-TYPE 173  80
  SLC7A13 MUTATED SLC7A13 WILD-TYPE 
                8               253 
  SLC7A13 MUTATED SLC7A13 WILD-TYPE 
                0                80 
$`SLC7A13 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8368 TCGA-CD-A4MI TCGA-CD-A4MJ 
       26.70        34.68        12.26         4.31         0.10        12.62 
TCGA-HU-A4G8 TCGA-HU-A4H8 
       11.84         8.88 

$`SLC7A13 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        6.58        12.20        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        9.67        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  SLC7A13 MUTATED SLC7A13 WILD-TYPE 
              0.1               0.0 
  SLC7A13 MUTATED SLC7A13 WILD-TYPE 
            34.68            105.07 
  SLC7A13 MUTATED SLC7A13 WILD-TYPE 
            12.05             12.76 
[1] "0.1 - 34.7 (12.1)"  "0.0 - 105.1 (12.8)"
[1] "hr="     "2.6e+07"
D722V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC7A13 MUTATED         0        0        3        0         1         3
  SLC7A13 WILD-TYPE       1        9       24       26        30        41
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC7A13 MUTATED           0          0          1          0        0
  SLC7A13 WILD-TYPE         3         49         35         24       24
D722V3, multiclass
            clus
vv           SLC7A13 MUTATED SLC7A13 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 0                 9
  STAGE IB                 3                24
  STAGE II                 0                26
  STAGE IIA                1                30
  STAGE IIB                3                41
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               1                35
  STAGE IIIC               0                24
  STAGE IV                 0                24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC7A13 MUTATED     1   2   4   2
  SLC7A13 WILD-TYPE  10  70 118  73
D722V4, multiclass
    clus
vv   SLC7A13 MUTATED SLC7A13 WILD-TYPE
  T1               1                10
  T2               2                70
  T3               4               118
  T4               2                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  SLC7A13 MUTATED    5  3  0  0
  SLC7A13 WILD-TYPE 88 78 50 53
D722V5, multiclass
    clus
vv   SLC7A13 MUTATED SLC7A13 WILD-TYPE
  N0               5                88
  N1               3                78
  N2               0                50
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D722V6, binary
                   cls
clus                  0   1
  SLC7A13 MUTATED     8   0
  SLC7A13 WILD-TYPE 249  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A13 MUTATED      8    0
  SLC7A13 WILD-TYPE  249   18
   clus
vv  SLC7A13 MUTATED SLC7A13 WILD-TYPE
  0               8               249
  1               0                18
[1] 2 2
[1] FALSE
D722V7, binary
                   cls
clus                  0   1
  SLC7A13 MUTATED     6   3
  SLC7A13 WILD-TYPE 104 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A13 MUTATED      6    3
  SLC7A13 WILD-TYPE  104  176
        clus
vv       SLC7A13 MUTATED SLC7A13 WILD-TYPE
  FEMALE               6               104
  MALE                 3               176
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SLC7A13 MUTATED                                       2
  SLC7A13 WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC7A13 MUTATED                                                        6
  SLC7A13 WILD-TYPE                                                    129
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLC7A13 MUTATED                                                                   0
  SLC7A13 WILD-TYPE                                                                40
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SLC7A13 MUTATED                                                  1
  SLC7A13 WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SLC7A13 MUTATED                                                          0
  SLC7A13 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SLC7A13 MUTATED                                                           0
  SLC7A13 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SLC7A13 MUTATED                                          0
  SLC7A13 WILD-TYPE                                        3
D722V8, multiclass
                                                                   clus
vv                                                                  SLC7A13 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  SLC7A13 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D722V9, binary
                   cls
clus                  0   1
  SLC7A13 MUTATED     0   9
  SLC7A13 WILD-TYPE   5 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A13 MUTATED      0    9
  SLC7A13 WILD-TYPE    5  275
     clus
vv    SLC7A13 MUTATED SLC7A13 WILD-TYPE
  NO                0                 5
  YES               9               275
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC7A13 MUTATED     5   0   0   1
  SLC7A13 WILD-TYPE 222  10  10  23
D722V10, multiclass
    clus
vv   SLC7A13 MUTATED SLC7A13 WILD-TYPE
  R0               5               222
  R1               0                10
  R2               0                10
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D722V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC7A13 MUTATED       4                         0     5
  SLC7A13 WILD-TYPE    72                         4   163
D722V12, multiclass
                           clus
vv                          SLC7A13 MUTATED SLC7A13 WILD-TYPE
  ASIAN                                   4                72
  BLACK OR AFRICAN AMERICAN               0                 4
  WHITE                                   5               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(723) Variable = FANCA MUTATION ANALYSIS
D723V1, survival
                 sevent
clus2               0   1
  FANCA MUTATED     5   1
  FANCA WILD-TYPE 176  79
  FANCA MUTATED FANCA WILD-TYPE 
              6             255 
  FANCA MUTATED FANCA WILD-TYPE 
              1              79 
$`FANCA MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8372 TCGA-HU-A4GX 
       26.70         6.97        34.68        19.50        19.17        10.19 

$`FANCA WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  FANCA MUTATED FANCA WILD-TYPE 
           6.97            0.00 
  FANCA MUTATED FANCA WILD-TYPE 
          34.68          105.07 
  FANCA MUTATED FANCA WILD-TYPE 
         19.335          12.590 
[1] "7.0 - 34.7 (19.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.8"
D723V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FANCA MUTATED         0        0        1        0         1         1
  FANCA WILD-TYPE       1        9       26       26        30        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FANCA MUTATED           0          1          0          3        0
  FANCA WILD-TYPE         3         48         36         21       24
D723V3, multiclass
            clus
vv           FANCA MUTATED FANCA WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              1              30
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             1              48
  STAGE IIIB             0              36
  STAGE IIIC             3              21
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FANCA MUTATED     0   1   2   4
  FANCA WILD-TYPE  11  71 120  71
D723V4, multiclass
    clus
vv   FANCA MUTATED FANCA WILD-TYPE
  T1             0              11
  T2             1              71
  T3             2             120
  T4             4              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  FANCA MUTATED    3  1  2  1
  FANCA WILD-TYPE 90 80 48 52
D723V5, multiclass
    clus
vv   FANCA MUTATED FANCA WILD-TYPE
  N0             3              90
  N1             1              80
  N2             2              48
  N3             1              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D723V6, binary
                 cls
clus                0   1
  FANCA MUTATED     6   0
  FANCA WILD-TYPE 251  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANCA MUTATED      6    0
  FANCA WILD-TYPE  251   18
   clus
vv  FANCA MUTATED FANCA WILD-TYPE
  0             6             251
  1             0              18
[1] 2 2
[1] FALSE
D723V7, binary
                 cls
clus                0   1
  FANCA MUTATED     4   3
  FANCA WILD-TYPE 106 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANCA MUTATED      4    3
  FANCA WILD-TYPE  106  176
        clus
vv       FANCA MUTATED FANCA WILD-TYPE
  FEMALE             4             106
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FANCA MUTATED                                       2
  FANCA WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FANCA MUTATED                                                        4
  FANCA WILD-TYPE                                                    131
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FANCA MUTATED                                                                   1
  FANCA WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FANCA MUTATED                                                  0
  FANCA WILD-TYPE                                               38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FANCA MUTATED                                                          0
  FANCA WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FANCA MUTATED                                                           0
  FANCA WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FANCA MUTATED                                          0
  FANCA WILD-TYPE                                        3
D723V8, multiclass
                                                                   clus
vv                                                                  FANCA MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  FANCA WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D723V9, binary
                 cls
clus                0   1
  FANCA MUTATED     0   7
  FANCA WILD-TYPE   5 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANCA MUTATED      0    7
  FANCA WILD-TYPE    5  277
     clus
vv    FANCA MUTATED FANCA WILD-TYPE
  NO              0               5
  YES             7             277
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FANCA MUTATED     6   0   0   1
  FANCA WILD-TYPE 221  10  10  23
D723V10, multiclass
    clus
vv   FANCA MUTATED FANCA WILD-TYPE
  R0             6             221
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D723V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FANCA MUTATED       1                         0     5
  FANCA WILD-TYPE    75                         4   163
D723V12, multiclass
                           clus
vv                          FANCA MUTATED FANCA WILD-TYPE
  ASIAN                                 1              75
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(724) Variable = CLIP1 MUTATION ANALYSIS
D724V1, survival
                 sevent
clus2               0   1
  CLIP1 MUTATED    11   2
  CLIP1 WILD-TYPE 170  78
  CLIP1 MUTATED CLIP1 WILD-TYPE 
             13             248 
  CLIP1 MUTATED CLIP1 WILD-TYPE 
              2              78 
$`CLIP1 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7851 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8297 
        6.97        34.68        12.43        12.26        20.55         7.40 
TCGA-BR-8369 TCGA-BR-8680 TCGA-CD-5800 TCGA-F1-6875 TCGA-FP-A4BE TCGA-HU-A4GF 
       14.04        15.81        13.15        72.23        11.08        25.81 
TCGA-HU-A4GU 
        6.25 

$`CLIP1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        0.69         9.60         8.05        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20        15.58         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 
       13.64        11.57         5.13         2.83         3.25        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 
        0.62         7.99        16.24        14.47        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       11.77        29.98         8.98         0.10         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  CLIP1 MUTATED CLIP1 WILD-TYPE 
           6.25            0.00 
  CLIP1 MUTATED CLIP1 WILD-TYPE 
          72.23          105.07 
  CLIP1 MUTATED CLIP1 WILD-TYPE 
         13.150          12.605 
[1] "6.2 - 72.2 (13.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "3"  
D724V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CLIP1 MUTATED         1        1        0        1         3         4
  CLIP1 WILD-TYPE       0        8       27       25        28        40
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLIP1 MUTATED           0          2          1          1        1
  CLIP1 WILD-TYPE         3         47         35         23       23
D724V3, multiclass
            clus
vv           CLIP1 MUTATED CLIP1 WILD-TYPE
  STAGE I                1               0
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               1              25
  STAGE IIA              3              28
  STAGE IIB              4              40
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             1              35
  STAGE IIIC             1              23
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CLIP1 MUTATED     1   1   7   6
  CLIP1 WILD-TYPE  10  71 115  69
D724V4, multiclass
    clus
vv   CLIP1 MUTATED CLIP1 WILD-TYPE
  T1             1              10
  T2             1              71
  T3             7             115
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CLIP1 MUTATED    9  3  1  2
  CLIP1 WILD-TYPE 84 78 49 51
D724V5, multiclass
    clus
vv   CLIP1 MUTATED CLIP1 WILD-TYPE
  N0             9              84
  N1             3              78
  N2             1              49
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D724V6, binary
                 cls
clus                0   1
  CLIP1 MUTATED    12   1
  CLIP1 WILD-TYPE 245  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP1 MUTATED     12    1
  CLIP1 WILD-TYPE  245   17
   clus
vv  CLIP1 MUTATED CLIP1 WILD-TYPE
  0            12             245
  1             1              17
[1] 2 2
[1] FALSE
D724V7, binary
                 cls
clus                0   1
  CLIP1 MUTATED     6   9
  CLIP1 WILD-TYPE 104 170
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP1 MUTATED      6    9
  CLIP1 WILD-TYPE  104  170
        clus
vv       CLIP1 MUTATED CLIP1 WILD-TYPE
  FEMALE             6             104
  MALE               9             170
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CLIP1 MUTATED                                       2
  CLIP1 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CLIP1 MUTATED                                                        9
  CLIP1 WILD-TYPE                                                    126
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CLIP1 MUTATED                                                                   1
  CLIP1 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CLIP1 MUTATED                                                  2
  CLIP1 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CLIP1 MUTATED                                                          0
  CLIP1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CLIP1 MUTATED                                                           1
  CLIP1 WILD-TYPE                                                         5
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CLIP1 MUTATED                                          0
  CLIP1 WILD-TYPE                                        3
D724V8, multiclass
                                                                   clus
vv                                                                  CLIP1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  CLIP1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D724V9, binary
                 cls
clus                0   1
  CLIP1 MUTATED     0  15
  CLIP1 WILD-TYPE   5 269
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP1 MUTATED      0   15
  CLIP1 WILD-TYPE    5  269
     clus
vv    CLIP1 MUTATED CLIP1 WILD-TYPE
  NO              0               5
  YES            15             269
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CLIP1 MUTATED    13   0   0   2
  CLIP1 WILD-TYPE 214  10  10  22
D724V10, multiclass
    clus
vv   CLIP1 MUTATED CLIP1 WILD-TYPE
  R0            13             214
  R1             0              10
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D724V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CLIP1 MUTATED       4                         3     8
  CLIP1 WILD-TYPE    72                         1   160
D724V12, multiclass
                           clus
vv                          CLIP1 MUTATED CLIP1 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             3               1
  WHITE                                 8             160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(725) Variable = ZNF217 MUTATION ANALYSIS
D725V1, survival
                  sevent
clus2                0   1
  ZNF217 MUTATED     8   3
  ZNF217 WILD-TYPE 173  77
  ZNF217 MUTATED ZNF217 WILD-TYPE 
              11              250 
  ZNF217 MUTATED ZNF217 WILD-TYPE 
               3               77 
$`ZNF217 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8382 
        6.97        34.68        24.76        19.50        19.17        15.85 
TCGA-BR-8487 TCGA-CG-5726 TCGA-D7-6527 TCGA-HU-A4H5 TCGA-HU-A4H8 
        1.12        28.96        10.26        12.30         8.88 

$`ZNF217 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 
       30.90        31.20        32.94        12.82         9.21        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
       14.04         3.32        11.80        14.79         0.26         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 
        0.99         6.02         0.99       105.07        12.03        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
       12.95        19.36        23.84         9.67        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  ZNF217 MUTATED ZNF217 WILD-TYPE 
            1.12             0.00 
  ZNF217 MUTATED ZNF217 WILD-TYPE 
           34.68           105.07 
  ZNF217 MUTATED ZNF217 WILD-TYPE 
          15.850           12.605 
[1] "1.1 - 34.7 (15.8)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D725V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF217 MUTATED         0        2        2        1         2         0
  ZNF217 WILD-TYPE       1        7       25       25        29        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF217 MUTATED           0          1          0          3        0
  ZNF217 WILD-TYPE         3         48         36         21       24
D725V3, multiclass
            clus
vv           ZNF217 MUTATED ZNF217 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                2                7
  STAGE IB                2               25
  STAGE II                1               25
  STAGE IIA               2               29
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              3               21
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF217 MUTATED     4   2   3   3
  ZNF217 WILD-TYPE   7  70 119  72
D725V4, multiclass
    clus
vv   ZNF217 MUTATED ZNF217 WILD-TYPE
  T1              4                7
  T2              2               70
  T3              3              119
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZNF217 MUTATED    5  4  1  2
  ZNF217 WILD-TYPE 88 77 49 51
D725V5, multiclass
    clus
vv   ZNF217 MUTATED ZNF217 WILD-TYPE
  N0              5               88
  N1              4               77
  N2              1               49
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D725V6, binary
                  cls
clus                 0   1
  ZNF217 MUTATED    13   0
  ZNF217 WILD-TYPE 244  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF217 MUTATED     13    0
  ZNF217 WILD-TYPE  244   18
   clus
vv  ZNF217 MUTATED ZNF217 WILD-TYPE
  0             13              244
  1              0               18
[1] 2 2
[1] FALSE
D725V7, binary
                  cls
clus                 0   1
  ZNF217 MUTATED     7   7
  ZNF217 WILD-TYPE 103 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF217 MUTATED      7    7
  ZNF217 WILD-TYPE  103  172
        clus
vv       ZNF217 MUTATED ZNF217 WILD-TYPE
  FEMALE              7              103
  MALE                7              172
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZNF217 MUTATED                                       0
  ZNF217 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF217 MUTATED                                                        9
  ZNF217 WILD-TYPE                                                    126
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZNF217 MUTATED                                                                   1
  ZNF217 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZNF217 MUTATED                                                  1
  ZNF217 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZNF217 MUTATED                                                          0
  ZNF217 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZNF217 MUTATED                                                           3
  ZNF217 WILD-TYPE                                                         3
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZNF217 MUTATED                                          0
  ZNF217 WILD-TYPE                                        3
D725V8, multiclass
                                                                   clus
vv                                                                  ZNF217 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ZNF217 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D725V9, binary
                  cls
clus                 0   1
  ZNF217 MUTATED     0  14
  ZNF217 WILD-TYPE   5 270
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF217 MUTATED      0   14
  ZNF217 WILD-TYPE    5  270
     clus
vv    ZNF217 MUTATED ZNF217 WILD-TYPE
  NO               0                5
  YES             14              270
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF217 MUTATED    10   0   0   4
  ZNF217 WILD-TYPE 217  10  10  20
D725V10, multiclass
    clus
vv   ZNF217 MUTATED ZNF217 WILD-TYPE
  R0             10              217
  R1              0               10
  R2              0               10
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D725V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF217 MUTATED       2                         0    11
  ZNF217 WILD-TYPE    74                         4   157
D725V12, multiclass
                           clus
vv                          ZNF217 MUTATED ZNF217 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                 11              157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(726) Variable = SLA MUTATION ANALYSIS
D726V1, survival
               sevent
clus2             0   1
  SLA MUTATED     4   0
  SLA WILD-TYPE 177  80
  SLA MUTATED SLA WILD-TYPE 
            4           257 
  SLA MUTATED SLA WILD-TYPE 
            0            80 
$`SLA MUTATED`
TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8487 TCGA-HU-8602 
       34.68        23.93         1.12        11.41 

$`SLA WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  SLA MUTATED SLA WILD-TYPE 
         1.12          0.00 
  SLA MUTATED SLA WILD-TYPE 
        34.68        105.07 
  SLA MUTATED SLA WILD-TYPE 
        17.67         12.62 
[1] "1.1 - 34.7 (17.7)"  "0.0 - 105.1 (12.6)"
[1] "hr="     "9300000"
D726V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLA MUTATED         0        0        1        0         2         1
  SLA WILD-TYPE       1        9       26       26        29        43
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLA MUTATED           0          0          0          0        0
  SLA WILD-TYPE         3         49         36         24       24
D726V3, multiclass
            clus
vv           SLA MUTATED SLA WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             9
  STAGE IB             1            26
  STAGE II             0            26
  STAGE IIA            2            29
  STAGE IIB            1            43
  STAGE III            0             3
  STAGE IIIA           0            49
  STAGE IIIB           0            36
  STAGE IIIC           0            24
  STAGE IV             0            24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  SLA MUTATED     0   1   2   1
  SLA WILD-TYPE  11  71 120  74
D726V4, multiclass
    clus
vv   SLA MUTATED SLA WILD-TYPE
  T1           0            11
  T2           1            71
  T3           2           120
  T4           1            74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  SLA MUTATED    4  0  0  0
  SLA WILD-TYPE 89 81 50 53
D726V5, multiclass
    clus
vv   SLA MUTATED SLA WILD-TYPE
  N0           4            89
  N1           0            81
  N2           0            50
  N3           0            53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D726V6, binary
               cls
clus              0   1
  SLA MUTATED     4   0
  SLA WILD-TYPE 253  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  SLA MUTATED      4    0
  SLA WILD-TYPE  253   18
   clus
vv  SLA MUTATED SLA WILD-TYPE
  0           4           253
  1           0            18
[1] 2 2
[1] FALSE
D726V7, binary
               cls
clus              0   1
  SLA MUTATED     4   0
  SLA WILD-TYPE 106 179
[1] "tbl2"
               cls
clus            [,1] [,2]
  SLA MUTATED      4    0
  SLA WILD-TYPE  106  179
        clus
vv       SLA MUTATED SLA WILD-TYPE
  FEMALE           4           106
  MALE             0           179
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SLA MUTATED                                       1
  SLA WILD-TYPE                                    49
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLA MUTATED                                                        3
  SLA WILD-TYPE                                                    132
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SLA MUTATED                                                                   0
  SLA WILD-TYPE                                                                40
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SLA MUTATED                                                  0
  SLA WILD-TYPE                                               38
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SLA MUTATED                                                          0
  SLA WILD-TYPE                                                       16
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SLA MUTATED                                                           0
  SLA WILD-TYPE                                                         6
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SLA MUTATED                                          0
  SLA WILD-TYPE                                        3
D726V8, multiclass
                                                                   clus
vv                                                                  SLA MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  SLA WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D726V9, binary
               cls
clus              0   1
  SLA MUTATED     0   4
  SLA WILD-TYPE   5 280
[1] "tbl2"
               cls
clus            [,1] [,2]
  SLA MUTATED      0    4
  SLA WILD-TYPE    5  280
     clus
vv    SLA MUTATED SLA WILD-TYPE
  NO            0             5
  YES           4           280
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  SLA MUTATED     4   0   0   0
  SLA WILD-TYPE 223  10  10  24
D726V10, multiclass
    clus
vv   SLA MUTATED SLA WILD-TYPE
  R0           4           223
  R1           0            10
  R2           0            10
  RX           0            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D726V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLA MUTATED       1                         0     3
  SLA WILD-TYPE    75                         4   165
D726V12, multiclass
                           clus
vv                          SLA MUTATED SLA WILD-TYPE
  ASIAN                               1            75
  BLACK OR AFRICAN AMERICAN           0             4
  WHITE                               3           165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(727) Variable = HDAC4 MUTATION ANALYSIS
D727V1, survival
                 sevent
clus2               0   1
  HDAC4 MUTATED    14   4
  HDAC4 WILD-TYPE 167  76
  HDAC4 MUTATED HDAC4 WILD-TYPE 
             18             243 
  HDAC4 MUTATED HDAC4 WILD-TYPE 
              4              76 
$`HDAC4 MUTATED`
TCGA-B7-5816 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8591 
       26.70        19.50         4.31        19.17         1.12        13.45 
TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-5733 TCGA-D7-A4YY TCGA-F1-6874 TCGA-HJ-7597 
       11.57         6.58        21.07        13.78        14.47        26.47 
TCGA-HU-8602 TCGA-HU-A4G9 TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 
       11.41        24.20         0.10         6.51        10.19        19.36 

$`HDAC4 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
       26.33        14.04         3.32        11.80        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        15.81         9.34         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        13.64         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-EQ-5647 
       14.27        16.44         5.92        15.16        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.99        16.24        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56        11.08         5.52         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       11.84         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        8.98         6.25         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  HDAC4 MUTATED HDAC4 WILD-TYPE 
            0.1             0.0 
  HDAC4 MUTATED HDAC4 WILD-TYPE 
          26.70          105.07 
  HDAC4 MUTATED HDAC4 WILD-TYPE 
         13.615          12.590 
[1] "0.1 - 26.7 (13.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.4"
D727V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HDAC4 MUTATED         1        1        4        1         3         2
  HDAC4 WILD-TYPE       0        8       23       25        28        42
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HDAC4 MUTATED           0          2          2          6        0
  HDAC4 WILD-TYPE         3         47         34         18       24
D727V3, multiclass
            clus
vv           HDAC4 MUTATED HDAC4 WILD-TYPE
  STAGE I                1               0
  STAGE IA               1               8
  STAGE IB               4              23
  STAGE II               1              25
  STAGE IIA              3              28
  STAGE IIB              2              42
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             2              34
  STAGE IIIC             6              18
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HDAC4 MUTATED     2   6   5   9
  HDAC4 WILD-TYPE   9  66 117  66
D727V4, multiclass
    clus
vv   HDAC4 MUTATED HDAC4 WILD-TYPE
  T1             2               9
  T2             6              66
  T3             5             117
  T4             9              66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  HDAC4 MUTATED   11  2  4  5
  HDAC4 WILD-TYPE 82 79 46 48
D727V5, multiclass
    clus
vv   HDAC4 MUTATED HDAC4 WILD-TYPE
  N0            11              82
  N1             2              79
  N2             4              46
  N3             5              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D727V6, binary
                 cls
clus                0   1
  HDAC4 MUTATED    20   0
  HDAC4 WILD-TYPE 237  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC4 MUTATED     20    0
  HDAC4 WILD-TYPE  237   18
   clus
vv  HDAC4 MUTATED HDAC4 WILD-TYPE
  0            20             237
  1             0              18
[1] 2 2
[1] FALSE
D727V7, binary
                 cls
clus                0   1
  HDAC4 MUTATED    13   9
  HDAC4 WILD-TYPE  97 170
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC4 MUTATED     13    9
  HDAC4 WILD-TYPE   97  170
        clus
vv       HDAC4 MUTATED HDAC4 WILD-TYPE
  FEMALE            13              97
  MALE               9             170
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  HDAC4 MUTATED                                       5
  HDAC4 WILD-TYPE                                    45
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HDAC4 MUTATED                                                        9
  HDAC4 WILD-TYPE                                                    126
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HDAC4 MUTATED                                                                   3
  HDAC4 WILD-TYPE                                                                37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  HDAC4 MUTATED                                                  3
  HDAC4 WILD-TYPE                                               35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  HDAC4 MUTATED                                                          1
  HDAC4 WILD-TYPE                                                       15
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  HDAC4 MUTATED                                                           0
  HDAC4 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  HDAC4 MUTATED                                          1
  HDAC4 WILD-TYPE                                        2
D727V8, multiclass
                                                                   clus
vv                                                                  HDAC4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  HDAC4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D727V9, binary
                 cls
clus                0   1
  HDAC4 MUTATED     1  21
  HDAC4 WILD-TYPE   4 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC4 MUTATED      1   21
  HDAC4 WILD-TYPE    4  263
     clus
vv    HDAC4 MUTATED HDAC4 WILD-TYPE
  NO              1               4
  YES            21             263
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HDAC4 MUTATED    20   0   0   1
  HDAC4 WILD-TYPE 207  10  10  23
D727V10, multiclass
    clus
vv   HDAC4 MUTATED HDAC4 WILD-TYPE
  R0            20             207
  R1             0              10
  R2             0              10
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D727V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HDAC4 MUTATED       7                         1    11
  HDAC4 WILD-TYPE    69                         3   157
D727V12, multiclass
                           clus
vv                          HDAC4 MUTATED HDAC4 WILD-TYPE
  ASIAN                                 7              69
  BLACK OR AFRICAN AMERICAN             1               3
  WHITE                                11             157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(728) Variable = AHI1 MUTATION ANALYSIS
D728V1, survival
                sevent
clus2              0   1
  AHI1 MUTATED     6   2
  AHI1 WILD-TYPE 175  78
  AHI1 MUTATED AHI1 WILD-TYPE 
             8            253 
  AHI1 MUTATED AHI1 WILD-TYPE 
             2             78 
$`AHI1 MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8680 TCGA-CG-5721 TCGA-CG-5733 
       26.70        30.90        34.68        15.81         6.02        21.07 
TCGA-HU-A4GX TCGA-HU-A4H8 
       10.19         8.88 

$`AHI1 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        0.69        12.26         9.60        20.55         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       11.08         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        9.67        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  AHI1 MUTATED AHI1 WILD-TYPE 
          6.02           0.00 
  AHI1 MUTATED AHI1 WILD-TYPE 
         34.68         105.07 
  AHI1 MUTATED AHI1 WILD-TYPE 
         18.44          12.59 
[1] "6.0 - 34.7 (18.4)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.9"
D728V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AHI1 MUTATED         1        0        1        0         1         1
  AHI1 WILD-TYPE       0        9       26       26        30        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AHI1 MUTATED           0          1          0          1        2
  AHI1 WILD-TYPE         3         48         36         23       22
D728V3, multiclass
            clus
vv           AHI1 MUTATED AHI1 WILD-TYPE
  STAGE I               1              0
  STAGE IA              0              9
  STAGE IB              1             26
  STAGE II              0             26
  STAGE IIA             1             30
  STAGE IIB             1             43
  STAGE III             0              3
  STAGE IIIA            1             48
  STAGE IIIB            0             36
  STAGE IIIC            1             23
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AHI1 MUTATED     2   2   1   4
  AHI1 WILD-TYPE   9  70 121  71
D728V4, multiclass
    clus
vv   AHI1 MUTATED AHI1 WILD-TYPE
  T1            2              9
  T2            2             70
  T3            1            121
  T4            4             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  AHI1 MUTATED    2  3  3  0
  AHI1 WILD-TYPE 91 78 47 53
D728V5, multiclass
    clus
vv   AHI1 MUTATED AHI1 WILD-TYPE
  N0            2             91
  N1            3             78
  N2            3             47
  N3            0             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D728V6, binary
                cls
clus               0   1
  AHI1 MUTATED     7   1
  AHI1 WILD-TYPE 250  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  AHI1 MUTATED      7    1
  AHI1 WILD-TYPE  250   17
   clus
vv  AHI1 MUTATED AHI1 WILD-TYPE
  0            7            250
  1            1             17
[1] 2 2
[1] FALSE
D728V7, binary
                cls
clus               0   1
  AHI1 MUTATED     5   4
  AHI1 WILD-TYPE 105 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  AHI1 MUTATED      5    4
  AHI1 WILD-TYPE  105  175
        clus
vv       AHI1 MUTATED AHI1 WILD-TYPE
  FEMALE            5            105
  MALE              4            175
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AHI1 MUTATED                                       2
  AHI1 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AHI1 MUTATED                                                        3
  AHI1 WILD-TYPE                                                    132
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AHI1 MUTATED                                                                   2
  AHI1 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AHI1 MUTATED                                                  2
  AHI1 WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AHI1 MUTATED                                                          0
  AHI1 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AHI1 MUTATED                                                           0
  AHI1 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AHI1 MUTATED                                          0
  AHI1 WILD-TYPE                                        3
D728V8, multiclass
                                                                   clus
vv                                                                  AHI1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  AHI1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D728V9, binary
                cls
clus               0   1
  AHI1 MUTATED     0   9
  AHI1 WILD-TYPE   5 275
[1] "tbl2"
                cls
clus             [,1] [,2]
  AHI1 MUTATED      0    9
  AHI1 WILD-TYPE    5  275
     clus
vv    AHI1 MUTATED AHI1 WILD-TYPE
  NO             0              5
  YES            9            275
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  AHI1 MUTATED     8   0   0   1
  AHI1 WILD-TYPE 219  10  10  23
D728V10, multiclass
    clus
vv   AHI1 MUTATED AHI1 WILD-TYPE
  R0            8            219
  R1            0             10
  R2            0             10
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D728V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AHI1 MUTATED       3                         1     3
  AHI1 WILD-TYPE    73                         3   165
D728V12, multiclass
                           clus
vv                          AHI1 MUTATED AHI1 WILD-TYPE
  ASIAN                                3             73
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                                3            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(729) Variable = CLSTN1 MUTATION ANALYSIS
D729V1, survival
                  sevent
clus2                0   1
  CLSTN1 MUTATED     5   3
  CLSTN1 WILD-TYPE 176  77
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
               8              253 
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
               3               77 
$`CLSTN1 MUTATED`
TCGA-BR-6566 TCGA-BR-7723 TCGA-BR-8363 TCGA-CD-8536 TCGA-CG-5733 TCGA-D7-8570 
       32.78        28.73         0.26         0.10        21.07        24.72 
TCGA-FP-A4BE TCGA-HU-8602 
       11.08        11.41 

$`CLSTN1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        19.50        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.16        13.78        14.76         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        5.52        26.47         5.92        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
             0.1              0.0 
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
           32.78           105.07 
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
           16.24            12.62 
[1] "0.1 - 32.8 (16.2)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1"  
D729V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CLSTN1 MUTATED         0        0        1        2         2         1
  CLSTN1 WILD-TYPE       1        9       26       24        29        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLSTN1 MUTATED           0          2          2          0        1
  CLSTN1 WILD-TYPE         3         47         34         24       23
D729V3, multiclass
            clus
vv           CLSTN1 MUTATED CLSTN1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                1               26
  STAGE II                2               24
  STAGE IIA               2               29
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              2               34
  STAGE IIIC              0               24
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CLSTN1 MUTATED     0   3   5   3
  CLSTN1 WILD-TYPE  11  69 117  72
D729V4, multiclass
    clus
vv   CLSTN1 MUTATED CLSTN1 WILD-TYPE
  T1              0               11
  T2              3               69
  T3              5              117
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CLSTN1 MUTATED    6  1  2  2
  CLSTN1 WILD-TYPE 87 80 48 51
D729V5, multiclass
    clus
vv   CLSTN1 MUTATED CLSTN1 WILD-TYPE
  N0              6               87
  N1              1               80
  N2              2               48
  N3              2               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D729V6, binary
                  cls
clus                 0   1
  CLSTN1 MUTATED    11   0
  CLSTN1 WILD-TYPE 246  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLSTN1 MUTATED     11    0
  CLSTN1 WILD-TYPE  246   18
   clus
vv  CLSTN1 MUTATED CLSTN1 WILD-TYPE
  0             11              246
  1              0               18
[1] 2 2
[1] FALSE
D729V7, binary
                  cls
clus                 0   1
  CLSTN1 MUTATED     6   5
  CLSTN1 WILD-TYPE 104 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLSTN1 MUTATED      6    5
  CLSTN1 WILD-TYPE  104  174
        clus
vv       CLSTN1 MUTATED CLSTN1 WILD-TYPE
  FEMALE              6              104
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CLSTN1 MUTATED                                       1
  CLSTN1 WILD-TYPE                                    49
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CLSTN1 MUTATED                                                        7
  CLSTN1 WILD-TYPE                                                    128
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CLSTN1 MUTATED                                                                   1
  CLSTN1 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CLSTN1 MUTATED                                                  1
  CLSTN1 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CLSTN1 MUTATED                                                          1
  CLSTN1 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CLSTN1 MUTATED                                                           0
  CLSTN1 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CLSTN1 MUTATED                                          0
  CLSTN1 WILD-TYPE                                        3
D729V8, multiclass
                                                                   clus
vv                                                                  CLSTN1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  CLSTN1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D729V9, binary
                  cls
clus                 0   1
  CLSTN1 MUTATED     1  10
  CLSTN1 WILD-TYPE   4 274
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLSTN1 MUTATED      1   10
  CLSTN1 WILD-TYPE    4  274
     clus
vv    CLSTN1 MUTATED CLSTN1 WILD-TYPE
  NO               1                4
  YES             10              274
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CLSTN1 MUTATED     9   0   0   2
  CLSTN1 WILD-TYPE 218  10  10  22
D729V10, multiclass
    clus
vv   CLSTN1 MUTATED CLSTN1 WILD-TYPE
  R0              9              218
  R1              0               10
  R2              0               10
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D729V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CLSTN1 MUTATED       2                         1     6
  CLSTN1 WILD-TYPE    74                         3   162
D729V12, multiclass
                           clus
vv                          CLSTN1 MUTATED CLSTN1 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              1                3
  WHITE                                  6              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(730) Variable = PPM1H MUTATION ANALYSIS
D730V1, survival
                 sevent
clus2               0   1
  PPM1H MUTATED     5   1
  PPM1H WILD-TYPE 176  79
  PPM1H MUTATED PPM1H WILD-TYPE 
              6             255 
  PPM1H MUTATED PPM1H WILD-TYPE 
              1              79 
$`PPM1H MUTATED`
TCGA-BR-4184 TCGA-BR-8361 TCGA-BR-8589 TCGA-BR-8680 TCGA-HU-8602 TCGA-HU-A4GX 
        6.97        19.50        15.81        15.81        11.41        10.19 

$`PPM1H WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22         1.12        12.79         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  PPM1H MUTATED PPM1H WILD-TYPE 
           6.97            0.00 
  PPM1H MUTATED PPM1H WILD-TYPE 
          19.50          105.07 
  PPM1H MUTATED PPM1H WILD-TYPE 
          13.61           12.62 
[1] "7.0 - 19.5 (13.6)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.7"
D730V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPM1H MUTATED         0        0        0        0         0         1
  PPM1H WILD-TYPE       1        9       27       26        31        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPM1H MUTATED           0          2          1          2        1
  PPM1H WILD-TYPE         3         47         35         22       23
D730V3, multiclass
            clus
vv           PPM1H MUTATED PPM1H WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               9
  STAGE IB               0              27
  STAGE II               0              26
  STAGE IIA              0              31
  STAGE IIB              1              43
  STAGE III              0               3
  STAGE IIIA             2              47
  STAGE IIIB             1              35
  STAGE IIIC             2              22
  STAGE IV               1              23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PPM1H MUTATED     0   0   2   6
  PPM1H WILD-TYPE  11  72 120  69
D730V4, multiclass
    clus
vv   PPM1H MUTATED PPM1H WILD-TYPE
  T1             0              11
  T2             0              72
  T3             2             120
  T4             6              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PPM1H MUTATED    2  2  3  0
  PPM1H WILD-TYPE 91 79 47 53
D730V5, multiclass
    clus
vv   PPM1H MUTATED PPM1H WILD-TYPE
  N0             2              91
  N1             2              79
  N2             3              47
  N3             0              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D730V6, binary
                 cls
clus                0   1
  PPM1H MUTATED     5   1
  PPM1H WILD-TYPE 252  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1H MUTATED      5    1
  PPM1H WILD-TYPE  252   17
   clus
vv  PPM1H MUTATED PPM1H WILD-TYPE
  0             5             252
  1             1              17
[1] 2 2
[1] FALSE
D730V7, binary
                 cls
clus                0   1
  PPM1H MUTATED     5   3
  PPM1H WILD-TYPE 105 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1H MUTATED      5    3
  PPM1H WILD-TYPE  105  176
        clus
vv       PPM1H MUTATED PPM1H WILD-TYPE
  FEMALE             5             105
  MALE               3             176
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PPM1H MUTATED                                       2
  PPM1H WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PPM1H MUTATED                                                        5
  PPM1H WILD-TYPE                                                    130
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PPM1H MUTATED                                                                   0
  PPM1H WILD-TYPE                                                                40
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PPM1H MUTATED                                                  1
  PPM1H WILD-TYPE                                               37
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PPM1H MUTATED                                                          0
  PPM1H WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PPM1H MUTATED                                                           0
  PPM1H WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PPM1H MUTATED                                          0
  PPM1H WILD-TYPE                                        3
D730V8, multiclass
                                                                   clus
vv                                                                  PPM1H MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  PPM1H WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D730V9, binary
                 cls
clus                0   1
  PPM1H MUTATED     0   8
  PPM1H WILD-TYPE   5 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1H MUTATED      0    8
  PPM1H WILD-TYPE    5  276
     clus
vv    PPM1H MUTATED PPM1H WILD-TYPE
  NO              0               5
  YES             8             276
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PPM1H MUTATED     5   0   0   3
  PPM1H WILD-TYPE 222  10  10  21
D730V10, multiclass
    clus
vv   PPM1H MUTATED PPM1H WILD-TYPE
  R0             5             222
  R1             0              10
  R2             0              10
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D730V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPM1H MUTATED       3                         0     5
  PPM1H WILD-TYPE    73                         4   163
D730V12, multiclass
                           clus
vv                          PPM1H MUTATED PPM1H WILD-TYPE
  ASIAN                                 3              73
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 5             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(731) Variable = KYNU MUTATION ANALYSIS
D731V1, survival
                sevent
clus2              0   1
  KYNU MUTATED     7   1
  KYNU WILD-TYPE 174  79
  KYNU MUTATED KYNU WILD-TYPE 
             8            253 
  KYNU MUTATED KYNU WILD-TYPE 
             1             79 
$`KYNU MUTATED`
TCGA-BR-6852 TCGA-BR-7958 TCGA-BR-8368 TCGA-BR-8680 TCGA-CG-4465 TCGA-CG-5721 
       32.94        12.76         4.31        15.81         9.01         6.02 
TCGA-CG-5723 TCGA-HU-A4HD 
      105.07        27.42 

$`KYNU WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        30.90        31.20        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 
       28.73        12.43         3.45         9.07        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
       36.00         1.02         0.99         0.99        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       13.78        14.76         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        26.47         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        9.67         8.88        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  KYNU MUTATED KYNU WILD-TYPE 
          4.31           0.00 
  KYNU MUTATED KYNU WILD-TYPE 
        105.07          79.07 
  KYNU MUTATED KYNU WILD-TYPE 
        14.285         12.590 
[1] "4.3 - 105.1 (14.3)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "4.5"
D731V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KYNU MUTATED         0        0        2        1         1         0
  KYNU WILD-TYPE       1        9       25       25        30        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KYNU MUTATED           0          2          1          0        3
  KYNU WILD-TYPE         3         47         35         24       21
D731V3, multiclass
            clus
vv           KYNU MUTATED KYNU WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              9
  STAGE IB              2             25
  STAGE II              1             25
  STAGE IIA             1             30
  STAGE IIB             0             44
  STAGE III             0              3
  STAGE IIIA            2             47
  STAGE IIIB            1             35
  STAGE IIIC            0             24
  STAGE IV              3             21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KYNU MUTATED     0   3   2   5
  KYNU WILD-TYPE  11  69 120  70
D731V4, multiclass
    clus
vv   KYNU MUTATED KYNU WILD-TYPE
  T1            0             11
  T2            3             69
  T3            2            120
  T4            5             70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  KYNU MUTATED    5  2  2  1
  KYNU WILD-TYPE 88 79 48 52
D731V5, multiclass
    clus
vv   KYNU MUTATED KYNU WILD-TYPE
  N0            5             88
  N1            2             79
  N2            2             48
  N3            1             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D731V6, binary
                cls
clus               0   1
  KYNU MUTATED     8   2
  KYNU WILD-TYPE 249  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  KYNU MUTATED      8    2
  KYNU WILD-TYPE  249   16
   clus
vv  KYNU MUTATED KYNU WILD-TYPE
  0            8            249
  1            2             16
[1] 2 2
[1] FALSE
D731V7, binary
                cls
clus               0   1
  KYNU MUTATED     4   6
  KYNU WILD-TYPE 106 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  KYNU MUTATED      4    6
  KYNU WILD-TYPE  106  173
        clus
vv       KYNU MUTATED KYNU WILD-TYPE
  FEMALE            4            106
  MALE              6            173
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KYNU MUTATED                                       1
  KYNU WILD-TYPE                                    49
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KYNU MUTATED                                                        5
  KYNU WILD-TYPE                                                    130
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KYNU MUTATED                                                                   2
  KYNU WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KYNU MUTATED                                                  2
  KYNU WILD-TYPE                                               36
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KYNU MUTATED                                                          0
  KYNU WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KYNU MUTATED                                                           0
  KYNU WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KYNU MUTATED                                          0
  KYNU WILD-TYPE                                        3
D731V8, multiclass
                                                                   clus
vv                                                                  KYNU MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  KYNU WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D731V9, binary
                cls
clus               0   1
  KYNU MUTATED     0  10
  KYNU WILD-TYPE   5 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  KYNU MUTATED      0   10
  KYNU WILD-TYPE    5  274
     clus
vv    KYNU MUTATED KYNU WILD-TYPE
  NO             0              5
  YES           10            274
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  KYNU MUTATED     8   0   1   1
  KYNU WILD-TYPE 219  10   9  23
D731V10, multiclass
    clus
vv   KYNU MUTATED KYNU WILD-TYPE
  R0            8            219
  R1            0             10
  R2            1              9
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D731V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KYNU MUTATED       2                         0     4
  KYNU WILD-TYPE    74                         4   164
D731V12, multiclass
                           clus
vv                          KYNU MUTATED KYNU WILD-TYPE
  ASIAN                                2             74
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                4            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(732) Variable = MLL4 MUTATION ANALYSIS
D732V1, survival
                sevent
clus2              0   1
  MLL4 MUTATED    12   8
  MLL4 WILD-TYPE 169  72
  MLL4 MUTATED MLL4 WILD-TYPE 
            20            241 
  MLL4 MUTATED MLL4 WILD-TYPE 
             8             72 
$`MLL4 MUTATED`
TCGA-BR-4188 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6852 
        7.43         6.61        34.68        17.29        19.33        32.94 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8381 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-8536 
       12.26        20.55         0.26        13.45        11.57         0.10 
TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-5720 TCGA-CG-5726 TCGA-FP-A4BE 
        6.58        12.62         1.02         0.99        28.96        11.08 
TCGA-HU-A4H3 TCGA-HU-A4H8 
       19.36         8.88 

$`MLL4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 
       26.70        11.70         6.61         6.97         4.64        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
       30.90         6.18         9.57        15.95        13.87        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       19.89         8.98        21.11        30.90        31.20        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 
       18.71        17.49        14.43         0.69         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        15.81         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        13.64         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.39         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 
        0.13         0.16         0.10         0.10         0.13         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        9.67        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  MLL4 MUTATED MLL4 WILD-TYPE 
           0.1            0.0 
  MLL4 MUTATED MLL4 WILD-TYPE 
         34.68         105.07 
  MLL4 MUTATED MLL4 WILD-TYPE 
        11.915         12.760 
[1] "0.1 - 34.7 (11.9)"  "0.0 - 105.1 (12.8)"
[1] "hr=" "1.4"
D732V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MLL4 MUTATED         0        1        4        1         4         5
  MLL4 WILD-TYPE       1        8       23       25        27        39
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MLL4 MUTATED           1          1          1          2        2
  MLL4 WILD-TYPE         2         48         35         22       22
D732V3, multiclass
            clus
vv           MLL4 MUTATED MLL4 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              8
  STAGE IB              4             23
  STAGE II              1             25
  STAGE IIA             4             27
  STAGE IIB             5             39
  STAGE III             1              2
  STAGE IIIA            1             48
  STAGE IIIB            1             35
  STAGE IIIC            2             22
  STAGE IV              2             22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MLL4 MUTATED     2   4  10   6
  MLL4 WILD-TYPE   9  68 112  69
D732V4, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  T1            2              9
  T2            4             68
  T3           10            112
  T4            6             69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  MLL4 MUTATED   12  6  2  3
  MLL4 WILD-TYPE 81 75 48 50
D732V5, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  N0           12             81
  N1            6             75
  N2            2             48
  N3            3             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D732V6, binary
                cls
clus               0   1
  MLL4 MUTATED    22   1
  MLL4 WILD-TYPE 235  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     22    1
  MLL4 WILD-TYPE  235   17
   clus
vv  MLL4 MUTATED MLL4 WILD-TYPE
  0           22            235
  1            1             17
[1] 2 2
[1] FALSE
D732V7, binary
                cls
clus               0   1
  MLL4 MUTATED    12  11
  MLL4 WILD-TYPE  98 168
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     12   11
  MLL4 WILD-TYPE   98  168
        clus
vv       MLL4 MUTATED MLL4 WILD-TYPE
  FEMALE           12             98
  MALE             11            168
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MLL4 MUTATED                                       2
  MLL4 WILD-TYPE                                    48
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MLL4 MUTATED                                                       18
  MLL4 WILD-TYPE                                                    117
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MLL4 MUTATED                                                                   2
  MLL4 WILD-TYPE                                                                38
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MLL4 MUTATED                                                  1
  MLL4 WILD-TYPE                                               37
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MLL4 MUTATED                                                          0
  MLL4 WILD-TYPE                                                       16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MLL4 MUTATED                                                           0
  MLL4 WILD-TYPE                                                         6
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MLL4 MUTATED                                          0
  MLL4 WILD-TYPE                                        3
D732V8, multiclass
                                                                   clus
vv                                                                  MLL4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      18
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  MLL4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       117
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D732V9, binary
                cls
clus               0   1
  MLL4 MUTATED     0  23
  MLL4 WILD-TYPE   5 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED      0   23
  MLL4 WILD-TYPE    5  261
     clus
vv    MLL4 MUTATED MLL4 WILD-TYPE
  NO             0              5
  YES           23            261
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MLL4 MUTATED    16   0   1   4
  MLL4 WILD-TYPE 211  10   9  20
D732V10, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  R0           16            211
  R1            0             10
  R2            1              9
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D732V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL4 MUTATED       5                         1    13
  MLL4 WILD-TYPE    71                         3   155
D732V12, multiclass
                           clus
vv                          MLL4 MUTATED MLL4 WILD-TYPE
  ASIAN                                5             71
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                               13            155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(733) Variable = PHKG2 MUTATION ANALYSIS
D733V1, survival
                 sevent
clus2               0   1
  PHKG2 MUTATED    10   2
  PHKG2 WILD-TYPE 171  78
  PHKG2 MUTATED PHKG2 WILD-TYPE 
             12             249 
  PHKG2 MUTATED PHKG2 WILD-TYPE 
              2              78 
$`PHKG2 MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8487 TCGA-BR-A4QL 
        6.97         6.61        34.68        32.78         1.12        11.57 
TCGA-CD-A4MI TCGA-D7-6518 TCGA-F1-6874 TCGA-HU-8602 TCGA-HU-A4G9 TCGA-HU-A4GN 
        0.10        19.13        14.47        11.41        24.20        29.98 

$`PHKG2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       30.90         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       13.68        19.33        39.12        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       12.26         9.60        20.55         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.36        12.66        11.93        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 
       14.76         0.62         7.99        16.24        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        11.84         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  PHKG2 MUTATED PHKG2 WILD-TYPE 
            0.1             0.0 
  PHKG2 MUTATED PHKG2 WILD-TYPE 
          34.68          105.07 
  PHKG2 MUTATED PHKG2 WILD-TYPE 
          13.02           12.62 
[1] "0.1 - 34.7 (13.0)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "2.3"
D733V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PHKG2 MUTATED         0        1        1        0         4         1
  PHKG2 WILD-TYPE       1        8       26       26        27        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PHKG2 MUTATED           1          2          2          0        0
  PHKG2 WILD-TYPE         2         47         34         24       24
D733V3, multiclass
            clus
vv           PHKG2 MUTATED PHKG2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               1              26
  STAGE II               0              26
  STAGE IIA              4              27
  STAGE IIB              1              43
  STAGE III              1               2
  STAGE IIIA             2              47
  STAGE IIIB             2              34
  STAGE IIIC             0              24
  STAGE IV               0              24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PHKG2 MUTATED     1   4   6   1
  PHKG2 WILD-TYPE  10  68 116  74
D733V4, multiclass
    clus
vv   PHKG2 MUTATED PHKG2 WILD-TYPE
  T1             1              10
  T2             4              68
  T3             6             116
  T4             1              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PHKG2 MUTATED    6  4  0  2
  PHKG2 WILD-TYPE 87 77 50 51
D733V5, multiclass
    clus
vv   PHKG2 MUTATED PHKG2 WILD-TYPE
  N0             6              87
  N1             4              77
  N2             0              50
  N3             2              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D733V6, binary
                 cls
clus                0   1
  PHKG2 MUTATED    11   0
  PHKG2 WILD-TYPE 246  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHKG2 MUTATED     11    0
  PHKG2 WILD-TYPE  246   18
   clus
vv  PHKG2 MUTATED PHKG2 WILD-TYPE
  0            11             246
  1             0              18
[1] 2 2
[1] FALSE
D733V7, binary
                 cls
clus                0   1
  PHKG2 MUTATED     7   5
  PHKG2 WILD-TYPE 103 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHKG2 MUTATED      7    5
  PHKG2 WILD-TYPE  103  174
        clus
vv       PHKG2 MUTATED PHKG2 WILD-TYPE
  FEMALE             7             103
  MALE               5             174
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PHKG2 MUTATED                                       2
  PHKG2 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PHKG2 MUTATED                                                        7
  PHKG2 WILD-TYPE                                                    128
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PHKG2 MUTATED                                                                   1
  PHKG2 WILD-TYPE                                                                39
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PHKG2 MUTATED                                                  2
  PHKG2 WILD-TYPE                                               36
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PHKG2 MUTATED                                                          0
  PHKG2 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PHKG2 MUTATED                                                           0
  PHKG2 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PHKG2 MUTATED                                          0
  PHKG2 WILD-TYPE                                        3
D733V8, multiclass
                                                                   clus
vv                                                                  PHKG2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  PHKG2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D733V9, binary
                 cls
clus                0   1
  PHKG2 MUTATED     0  12
  PHKG2 WILD-TYPE   5 272
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHKG2 MUTATED      0   12
  PHKG2 WILD-TYPE    5  272
     clus
vv    PHKG2 MUTATED PHKG2 WILD-TYPE
  NO              0               5
  YES            12             272
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PHKG2 MUTATED     8   1   0   2
  PHKG2 WILD-TYPE 219   9  10  22
D733V10, multiclass
    clus
vv   PHKG2 MUTATED PHKG2 WILD-TYPE
  R0             8             219
  R1             1               9
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D733V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHKG2 MUTATED       4                         0     8
  PHKG2 WILD-TYPE    72                         4   160
D733V12, multiclass
                           clus
vv                          PHKG2 MUTATED PHKG2 WILD-TYPE
  ASIAN                                 4              72
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 8             160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(734) Variable = OR4C16 MUTATION ANALYSIS
D734V1, survival
                  sevent
clus2                0   1
  OR4C16 MUTATED    11   2
  OR4C16 WILD-TYPE 170  78
  OR4C16 MUTATED OR4C16 WILD-TYPE 
              13              248 
  OR4C16 MUTATED OR4C16 WILD-TYPE 
               2               78 
$`OR4C16 MUTATED`
TCGA-BR-6452 TCGA-BR-A4QL TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4469 TCGA-CG-4477 
       34.68        11.57        29.98        47.05         7.07        30.97 
TCGA-CG-5721 TCGA-CG-5724 TCGA-CG-5728 TCGA-D7-5578 TCGA-F1-A448 TCGA-HU-8604 
        6.02        12.03        65.10        12.66        21.27        12.10 
TCGA-HU-A4GN 
       29.98 

$`OR4C16 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         0.66        19.36        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        13.64         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 
        8.05        54.08         4.01        14.01        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 
        0.00         9.01        18.97        22.98         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 
        1.02         0.99         0.99       105.07        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 
        4.01        69.04        21.07         7.99        12.36        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 
       16.44         5.92        15.16        13.78        14.76         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        7.99        16.24        14.47        72.23         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        11.41        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  OR4C16 MUTATED OR4C16 WILD-TYPE 
            6.02             0.00 
  OR4C16 MUTATED OR4C16 WILD-TYPE 
           65.10           105.07 
  OR4C16 MUTATED OR4C16 WILD-TYPE 
          21.270           12.575 
[1] "6.0 - 65.1 (21.3)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "3.9"
D734V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OR4C16 MUTATED         0        1        2        0         3         0
  OR4C16 WILD-TYPE       1        8       25       26        28        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR4C16 MUTATED           0          2          2          0        3
  OR4C16 WILD-TYPE         3         47         34         24       21
D734V3, multiclass
            clus
vv           OR4C16 MUTATED OR4C16 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                2               25
  STAGE II                0               26
  STAGE IIA               3               28
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              2               47
  STAGE IIIB              2               34
  STAGE IIIC              0               24
  STAGE IV                3               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR4C16 MUTATED     1   4   7   1
  OR4C16 WILD-TYPE  10  68 115  74
D734V4, multiclass
    clus
vv   OR4C16 MUTATED OR4C16 WILD-TYPE
  T1              1               10
  T2              4               68
  T3              7              115
  T4              1               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  OR4C16 MUTATED    5  2  2  4
  OR4C16 WILD-TYPE 88 79 48 49
D734V5, multiclass
    clus
vv   OR4C16 MUTATED OR4C16 WILD-TYPE
  N0              5               88
  N1              2               79
  N2              2               48
  N3              4               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D734V6, binary
                  cls
clus                 0   1
  OR4C16 MUTATED    12   1
  OR4C16 WILD-TYPE 245  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4C16 MUTATED     12    1
  OR4C16 WILD-TYPE  245   17
   clus
vv  OR4C16 MUTATED OR4C16 WILD-TYPE
  0             12              245
  1              1               17
[1] 2 2
[1] FALSE
D734V7, binary
                  cls
clus                 0   1
  OR4C16 MUTATED     5   8
  OR4C16 WILD-TYPE 105 171
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4C16 MUTATED      5    8
  OR4C16 WILD-TYPE  105  171
        clus
vv       OR4C16 MUTATED OR4C16 WILD-TYPE
  FEMALE              5              105
  MALE                8              171
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  OR4C16 MUTATED                                       2
  OR4C16 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OR4C16 MUTATED                                                        2
  OR4C16 WILD-TYPE                                                    133
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  OR4C16 MUTATED                                                                   5
  OR4C16 WILD-TYPE                                                                35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  OR4C16 MUTATED                                                  3
  OR4C16 WILD-TYPE                                               35
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  OR4C16 MUTATED                                                          1
  OR4C16 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  OR4C16 MUTATED                                                           0
  OR4C16 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  OR4C16 MUTATED                                          0
  OR4C16 WILD-TYPE                                        3
D734V8, multiclass
                                                                   clus
vv                                                                  OR4C16 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  OR4C16 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D734V9, binary
                  cls
clus                 0   1
  OR4C16 MUTATED     0  13
  OR4C16 WILD-TYPE   5 271
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4C16 MUTATED      0   13
  OR4C16 WILD-TYPE    5  271
     clus
vv    OR4C16 MUTATED OR4C16 WILD-TYPE
  NO               0                5
  YES             13              271
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR4C16 MUTATED    11   1   1   0
  OR4C16 WILD-TYPE 216   9   9  24
D734V10, multiclass
    clus
vv   OR4C16 MUTATED OR4C16 WILD-TYPE
  R0             11              216
  R1              1                9
  R2              1                9
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D734V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR4C16 MUTATED       2                         0     4
  OR4C16 WILD-TYPE    74                         4   164
D734V12, multiclass
                           clus
vv                          OR4C16 MUTATED OR4C16 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(735) Variable = NUAK1 MUTATION ANALYSIS
D735V1, survival
                 sevent
clus2               0   1
  NUAK1 MUTATED    11   3
  NUAK1 WILD-TYPE 170  77
  NUAK1 MUTATED NUAK1 WILD-TYPE 
             14             247 
  NUAK1 MUTATED NUAK1 WILD-TYPE 
              3              77 
$`NUAK1 MUTATED`
TCGA-BR-6566 TCGA-BR-7901 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8680 TCGA-BR-A4QL 
       32.78         3.45        12.26        20.55        15.81        11.57 
TCGA-CD-8536 TCGA-CG-4469 TCGA-CG-5723 TCGA-CG-5726 TCGA-D7-A4YU TCGA-HU-8602 
        0.10         7.07       105.07        28.96        16.44        11.41 
TCGA-HU-A4H0 TCGA-HU-A4H4 
        2.10        23.84 

$`NUAK1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73        12.43         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       14.43         0.69         9.60         8.05        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
        0.16         0.10         0.10         0.13         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        6.02         0.99        12.03        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-EQ-8122 
        5.92        15.16        13.78        14.76         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56        11.08         5.52        26.47         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
       10.19         0.26        12.95        19.36        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88        27.42        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  NUAK1 MUTATED NUAK1 WILD-TYPE 
            0.1             0.0 
  NUAK1 MUTATED NUAK1 WILD-TYPE 
         105.07           79.07 
  NUAK1 MUTATED NUAK1 WILD-TYPE 
         14.035          12.620 
[1] "0.1 - 105.1 (14.0)" "0.0 - 79.1 (12.6)" 
[1] "hr=" "2.1"
D735V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NUAK1 MUTATED         0        1        0        2         1         5
  NUAK1 WILD-TYPE       1        8       27       24        30        39
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUAK1 MUTATED           0          0          2          1        2
  NUAK1 WILD-TYPE         3         49         34         23       22
D735V3, multiclass
            clus
vv           NUAK1 MUTATED NUAK1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               8
  STAGE IB               0              27
  STAGE II               2              24
  STAGE IIA              1              30
  STAGE IIB              5              39
  STAGE III              0               3
  STAGE IIIA             0              49
  STAGE IIIB             2              34
  STAGE IIIC             1              23
  STAGE IV               2              22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NUAK1 MUTATED     1   2   7   5
  NUAK1 WILD-TYPE  10  70 115  70
D735V4, multiclass
    clus
vv   NUAK1 MUTATED NUAK1 WILD-TYPE
  T1             1              10
  T2             2              70
  T3             7             115
  T4             5              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  NUAK1 MUTATED    6  3  2  4
  NUAK1 WILD-TYPE 87 78 48 49
D735V5, multiclass
    clus
vv   NUAK1 MUTATED NUAK1 WILD-TYPE
  N0             6              87
  N1             3              78
  N2             2              48
  N3             4              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D735V6, binary
                 cls
clus                0   1
  NUAK1 MUTATED    14   1
  NUAK1 WILD-TYPE 243  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUAK1 MUTATED     14    1
  NUAK1 WILD-TYPE  243   17
   clus
vv  NUAK1 MUTATED NUAK1 WILD-TYPE
  0            14             243
  1             1              17
[1] 2 2
[1] FALSE
D735V7, binary
                 cls
clus                0   1
  NUAK1 MUTATED     7   9
  NUAK1 WILD-TYPE 103 170
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUAK1 MUTATED      7    9
  NUAK1 WILD-TYPE  103  170
        clus
vv       NUAK1 MUTATED NUAK1 WILD-TYPE
  FEMALE             7             103
  MALE               9             170
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NUAK1 MUTATED                                       2
  NUAK1 WILD-TYPE                                    48
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NUAK1 MUTATED                                                        9
  NUAK1 WILD-TYPE                                                    126
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NUAK1 MUTATED                                                                   2
  NUAK1 WILD-TYPE                                                                38
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NUAK1 MUTATED                                                  3
  NUAK1 WILD-TYPE                                               35
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NUAK1 MUTATED                                                          0
  NUAK1 WILD-TYPE                                                       16
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NUAK1 MUTATED                                                           0
  NUAK1 WILD-TYPE                                                         6
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NUAK1 MUTATED                                          0
  NUAK1 WILD-TYPE                                        3
D735V8, multiclass
                                                                   clus
vv                                                                  NUAK1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  NUAK1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D735V9, binary
                 cls
clus                0   1
  NUAK1 MUTATED     0  16
  NUAK1 WILD-TYPE   5 268
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUAK1 MUTATED      0   16
  NUAK1 WILD-TYPE    5  268
     clus
vv    NUAK1 MUTATED NUAK1 WILD-TYPE
  NO              0               5
  YES            16             268
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NUAK1 MUTATED    13   1   0   2
  NUAK1 WILD-TYPE 214   9  10  22
D735V10, multiclass
    clus
vv   NUAK1 MUTATED NUAK1 WILD-TYPE
  R0            13             214
  R1             1               9
  R2             0              10
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D735V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NUAK1 MUTATED       5                         0     8
  NUAK1 WILD-TYPE    71                         4   160
D735V12, multiclass
                           clus
vv                          NUAK1 MUTATED NUAK1 WILD-TYPE
  ASIAN                                 5              71
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 8             160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(736) Variable = FAM82A1 MUTATION ANALYSIS
D736V1, survival
                   sevent
clus2                 0   1
  FAM82A1 MUTATED     1   2
  FAM82A1 WILD-TYPE 180  78
  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
                3               258 
  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
                2                78 
$`FAM82A1 MUTATED`
TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5726 
        1.02         6.02        28.96 

$`FAM82A1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 
        0.99         0.99       105.07        12.03        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       27.42        21.21         3.45        18.81         3.39         2.53 

  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
             1.02              0.00 
  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
            28.96            105.07 
  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
             6.02             12.64 
[1] "1.0 - 29.0 (6.0)"   "0.0 - 105.1 (12.6)"
[1] "hr=" "2.3"
D736V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM82A1 MUTATED         0        1        0        0         0         0
  FAM82A1 WILD-TYPE       1        8       27       26        31        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM82A1 MUTATED           0          0          0          0        2
  FAM82A1 WILD-TYPE         3         49         36         24       22
D736V3, multiclass
            clus
vv           FAM82A1 MUTATED FAM82A1 WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 1                 8
  STAGE IB                 0                27
  STAGE II                 0                26
  STAGE IIA                0                31
  STAGE IIB                0                44
  STAGE III                0                 3
  STAGE IIIA               0                49
  STAGE IIIB               0                36
  STAGE IIIC               0                24
  STAGE IV                 2                22
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM82A1 MUTATED     1   0   1   1
  FAM82A1 WILD-TYPE  10  72 121  74
D736V4, multiclass
    clus
vv   FAM82A1 MUTATED FAM82A1 WILD-TYPE
  T1               1                10
  T2               0                72
  T3               1               121
  T4               1                74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  FAM82A1 MUTATED    1  2  1  0
  FAM82A1 WILD-TYPE 92 79 49 53
D736V5, multiclass
    clus
vv   FAM82A1 MUTATED FAM82A1 WILD-TYPE
  N0               1                92
  N1               2                79
  N2               1                49
  N3               0                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D736V6, binary
                   cls
clus                  0   1
  FAM82A1 MUTATED     3   1
  FAM82A1 WILD-TYPE 254  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM82A1 MUTATED      3    1
  FAM82A1 WILD-TYPE  254   17
   clus
vv  FAM82A1 MUTATED FAM82A1 WILD-TYPE
  0               3               254
  1               1                17
[1] 2 2
[1] FALSE
D736V7, binary
                   cls
clus                  0   1
  FAM82A1 MUTATED     1   3
  FAM82A1 WILD-TYPE 109 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM82A1 MUTATED      1    3
  FAM82A1 WILD-TYPE  109  176
        clus
vv       FAM82A1 MUTATED FAM82A1 WILD-TYPE
  FEMALE               1               109
  MALE                 3               176
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FAM82A1 MUTATED                                       0
  FAM82A1 WILD-TYPE                                    50
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAM82A1 MUTATED                                                        2
  FAM82A1 WILD-TYPE                                                    133
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FAM82A1 MUTATED                                                                   2
  FAM82A1 WILD-TYPE                                                                38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FAM82A1 MUTATED                                                  0
  FAM82A1 WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FAM82A1 MUTATED                                                          0
  FAM82A1 WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FAM82A1 MUTATED                                                           0
  FAM82A1 WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FAM82A1 MUTATED                                          0
  FAM82A1 WILD-TYPE                                        3
D736V8, multiclass
                                                                   clus
vv                                                                  FAM82A1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  FAM82A1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D736V9, binary
                   cls
clus                  0   1
  FAM82A1 MUTATED     0   4
  FAM82A1 WILD-TYPE   5 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM82A1 MUTATED      0    4
  FAM82A1 WILD-TYPE    5  280
     clus
vv    FAM82A1 MUTATED FAM82A1 WILD-TYPE
  NO                0                 5
  YES               4               280
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM82A1 MUTATED     2   0   1   1
  FAM82A1 WILD-TYPE 225  10   9  23
D736V10, multiclass
    clus
vv   FAM82A1 MUTATED FAM82A1 WILD-TYPE
  R0               2               225
  R1               0                10
  R2               1                 9
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D736V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM82A1 MUTATED       0                         0     1
  FAM82A1 WILD-TYPE    76                         4   167
D736V12, multiclass
[1] "Remove cluster labels:" "FAM82A1 MUTATED"       
clus
  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
                1               247 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-4187        TCGA-BR-4188        TCGA-BR-4191        TCGA-BR-4201 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-4294        TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4363 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-4366        TCGA-BR-4368        TCGA-BR-4369        TCGA-BR-4370 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-4371        TCGA-BR-6452        TCGA-BR-6453        TCGA-BR-6454 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457        TCGA-BR-6458 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565        TCGA-BR-6566 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707        TCGA-BR-6710 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-7196        TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7707 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8058        TCGA-BR-8059 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297        TCGA-BR-8360 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8361        TCGA-BR-8363        TCGA-BR-8364        TCGA-BR-8365 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8366        TCGA-BR-8367        TCGA-BR-8368        TCGA-BR-8369 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8370        TCGA-BR-8371        TCGA-BR-8372        TCGA-BR-8373 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8380        TCGA-BR-8381        TCGA-BR-8382        TCGA-BR-8384 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8483        TCGA-BR-8484        TCGA-BR-8485        TCGA-BR-8486 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8487        TCGA-BR-8588        TCGA-BR-8589        TCGA-BR-8590 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8591        TCGA-BR-8592        TCGA-BR-8676        TCGA-BR-8677 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8678        TCGA-BR-8679        TCGA-BR-8680        TCGA-BR-8682 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8683        TCGA-BR-8686        TCGA-BR-8687        TCGA-BR-8690 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-A44T        TCGA-BR-A44U        TCGA-BR-A452        TCGA-BR-A453 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-A4CQ        TCGA-BR-A4CR        TCGA-BR-A4CS        TCGA-BR-A4IU 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-A4IV        TCGA-BR-A4IY        TCGA-BR-A4IZ        TCGA-BR-A4J1 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-A4J2        TCGA-BR-A4J4        TCGA-BR-A4J6        TCGA-BR-A4J7 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-A4J8        TCGA-BR-A4PD        TCGA-BR-A4PE        TCGA-BR-A4PF 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-BR-A4QM        TCGA-CD-5798 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-CD-5803        TCGA-CD-5804        TCGA-CD-5813        TCGA-CD-8524 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-CD-8525        TCGA-CD-8526        TCGA-CD-8527        TCGA-CD-8528 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-CD-8529        TCGA-CD-8530        TCGA-CD-8531        TCGA-CD-8532 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-CD-8534        TCGA-CD-8535        TCGA-CD-8536        TCGA-CD-A486 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-CD-A487        TCGA-CD-A489        TCGA-CD-A48A        TCGA-CD-A48C 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-CD-A4MG        TCGA-CD-A4MH        TCGA-CD-A4MI        TCGA-CD-A4MJ 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-D7-8570        TCGA-D7-8572 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-D7-8573        TCGA-D7-8574        TCGA-D7-8575        TCGA-D7-8576 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-D7-8578        TCGA-D7-8579        TCGA-D7-A4YT        TCGA-D7-A4YU 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-D7-A4YV        TCGA-D7-A4YX        TCGA-D7-A4YY        TCGA-D7-A4Z0 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-EQ-A4SO        TCGA-F1-6177 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-F1-A448        TCGA-FP-7735 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8211        TCGA-FP-8631 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-FP-A4BE        TCGA-FP-A4BF        TCGA-HJ-7597        TCGA-HU-8243 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-HU-8245        TCGA-HU-8249        TCGA-HU-8602        TCGA-HU-8604 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-HU-8608        TCGA-HU-8610        TCGA-HU-A4G2        TCGA-HU-A4G3 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-HU-A4G6        TCGA-HU-A4G8        TCGA-HU-A4G9        TCGA-HU-A4GC 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-HU-A4GD        TCGA-HU-A4GF        TCGA-HU-A4GH        TCGA-HU-A4GN 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-HU-A4GP        TCGA-HU-A4GQ        TCGA-HU-A4GT        TCGA-HU-A4GU 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-HU-A4GX        TCGA-HU-A4GY        TCGA-HU-A4H0        TCGA-HU-A4H2 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-HU-A4H3        TCGA-HU-A4H4        TCGA-HU-A4H5        TCGA-HU-A4H6 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-HU-A4H8        TCGA-HU-A4HD        TCGA-IN-7806        TCGA-IN-7808 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-IN-8462        TCGA-IN-8663        TCGA-IP-7968 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 

Clustering(737) Variable = RASSF5 MUTATION ANALYSIS
D737V1, survival
                  sevent
clus2                0   1
  RASSF5 MUTATED     2   2
  RASSF5 WILD-TYPE 179  78
  RASSF5 MUTATED RASSF5 WILD-TYPE 
               4              257 
  RASSF5 MUTATED RASSF5 WILD-TYPE 
               2               78 
$`RASSF5 MUTATED`
TCGA-B7-5816 TCGA-BR-8372 TCGA-CD-A4MG TCGA-HU-A4GQ 
       26.70        19.17         6.58         0.10 

$`RASSF5 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  RASSF5 MUTATED RASSF5 WILD-TYPE 
             0.1              0.0 
  RASSF5 MUTATED RASSF5 WILD-TYPE 
           26.70           105.07 
  RASSF5 MUTATED RASSF5 WILD-TYPE 
          12.875           12.620 
[1] "0.1 - 26.7 (12.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.7"
D737V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RASSF5 MUTATED         0        0        0        0         1         1
  RASSF5 WILD-TYPE       1        9       27       26        30        43
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RASSF5 MUTATED           0          0          0          2        0
  RASSF5 WILD-TYPE         3         49         36         22       24
D737V3, multiclass
            clus
vv           RASSF5 MUTATED RASSF5 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                9
  STAGE IB                0               27
  STAGE II                0               26
  STAGE IIA               1               30
  STAGE IIB               1               43
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              2               22
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RASSF5 MUTATED     0   0   1   3
  RASSF5 WILD-TYPE  11  72 121  72
D737V4, multiclass
    clus
vv   RASSF5 MUTATED RASSF5 WILD-TYPE
  T1              0               11
  T2              0               72
  T3              1              121
  T4              3               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  RASSF5 MUTATED    2  0  1  1
  RASSF5 WILD-TYPE 91 81 49 52
D737V5, multiclass
    clus
vv   RASSF5 MUTATED RASSF5 WILD-TYPE
  N0              2               91
  N1              0               81
  N2              1               49
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D737V6, binary
                  cls
clus                 0   1
  RASSF5 MUTATED     4   0
  RASSF5 WILD-TYPE 253  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASSF5 MUTATED      4    0
  RASSF5 WILD-TYPE  253   18
   clus
vv  RASSF5 MUTATED RASSF5 WILD-TYPE
  0              4              253
  1              0               18
[1] 2 2
[1] FALSE
D737V7, binary
                  cls
clus                 0   1
  RASSF5 MUTATED     1   3
  RASSF5 WILD-TYPE 109 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASSF5 MUTATED      1    3
  RASSF5 WILD-TYPE  109  176
        clus
vv       RASSF5 MUTATED RASSF5 WILD-TYPE
  FEMALE              1              109
  MALE                3              176
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RASSF5 MUTATED                                       2
  RASSF5 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RASSF5 MUTATED                                                        1
  RASSF5 WILD-TYPE                                                    134
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RASSF5 MUTATED                                                                   0
  RASSF5 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RASSF5 MUTATED                                                  1
  RASSF5 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RASSF5 MUTATED                                                          0
  RASSF5 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RASSF5 MUTATED                                                           0
  RASSF5 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RASSF5 MUTATED                                          0
  RASSF5 WILD-TYPE                                        3
D737V8, multiclass
                                                                   clus
vv                                                                  RASSF5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         1
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  RASSF5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D737V9, binary
                  cls
clus                 0   1
  RASSF5 MUTATED     0   4
  RASSF5 WILD-TYPE   5 280
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASSF5 MUTATED      0    4
  RASSF5 WILD-TYPE    5  280
     clus
vv    RASSF5 MUTATED RASSF5 WILD-TYPE
  NO               0                5
  YES              4              280
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RASSF5 MUTATED     3   0   0   0
  RASSF5 WILD-TYPE 224  10  10  24
D737V10, multiclass
    clus
vv   RASSF5 MUTATED RASSF5 WILD-TYPE
  R0              3              224
  R1              0               10
  R2              0               10
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D737V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RASSF5 MUTATED       2                         0     2
  RASSF5 WILD-TYPE    74                         4   166
D737V12, multiclass
                           clus
vv                          RASSF5 MUTATED RASSF5 WILD-TYPE
  ASIAN                                  2               74
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  2              166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(738) Variable = MTMR11 MUTATION ANALYSIS
D738V1, survival
                  sevent
clus2                0   1
  MTMR11 MUTATED     6   0
  MTMR11 WILD-TYPE 175  80
  MTMR11 MUTATED MTMR11 WILD-TYPE 
               6              255 
  MTMR11 MUTATED MTMR11 WILD-TYPE 
               0               80 
$`MTMR11 MUTATED`
TCGA-BR-6452 TCGA-BR-8487 TCGA-CD-A487 TCGA-F1-6874 TCGA-HU-A4G3 TCGA-HU-A4GH 
       34.68         1.12         9.34        14.47         5.59        11.77 

$`MTMR11 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         0.10         3.42        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        0.62         7.99        16.24        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56        11.08         5.52        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  MTMR11 MUTATED MTMR11 WILD-TYPE 
            1.12             0.00 
  MTMR11 MUTATED MTMR11 WILD-TYPE 
           34.68           105.07 
  MTMR11 MUTATED MTMR11 WILD-TYPE 
          10.555           12.660 
[1] "1.1 - 34.7 (10.6)"  "0.0 - 105.1 (12.7)"
[1] "hr="     "9300000"
D738V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MTMR11 MUTATED         0        1        1        0         2         2
  MTMR11 WILD-TYPE       1        8       26       26        29        42
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MTMR11 MUTATED           0          0          0          1        1
  MTMR11 WILD-TYPE         3         49         36         23       23
D738V3, multiclass
            clus
vv           MTMR11 MUTATED MTMR11 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                1               26
  STAGE II                0               26
  STAGE IIA               2               29
  STAGE IIB               2               42
  STAGE III               0                3
  STAGE IIIA              0               49
  STAGE IIIB              0               36
  STAGE IIIC              1               23
  STAGE IV                1               23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MTMR11 MUTATED     1   2   3   2
  MTMR11 WILD-TYPE  10  70 119  73
D738V4, multiclass
    clus
vv   MTMR11 MUTATED MTMR11 WILD-TYPE
  T1              1               10
  T2              2               70
  T3              3              119
  T4              2               73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  MTMR11 MUTATED    4  1  2  1
  MTMR11 WILD-TYPE 89 80 48 52
D738V5, multiclass
    clus
vv   MTMR11 MUTATED MTMR11 WILD-TYPE
  N0              4               89
  N1              1               80
  N2              2               48
  N3              1               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D738V6, binary
                  cls
clus                 0   1
  MTMR11 MUTATED     8   0
  MTMR11 WILD-TYPE 249  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MTMR11 MUTATED      8    0
  MTMR11 WILD-TYPE  249   18
   clus
vv  MTMR11 MUTATED MTMR11 WILD-TYPE
  0              8              249
  1              0               18
[1] 2 2
[1] FALSE
D738V7, binary
                  cls
clus                 0   1
  MTMR11 MUTATED     3   5
  MTMR11 WILD-TYPE 107 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MTMR11 MUTATED      3    5
  MTMR11 WILD-TYPE  107  174
        clus
vv       MTMR11 MUTATED MTMR11 WILD-TYPE
  FEMALE              3              107
  MALE                5              174
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MTMR11 MUTATED                                       2
  MTMR11 WILD-TYPE                                    48
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MTMR11 MUTATED                                                        3
  MTMR11 WILD-TYPE                                                    132
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MTMR11 MUTATED                                                                   1
  MTMR11 WILD-TYPE                                                                39
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MTMR11 MUTATED                                                  2
  MTMR11 WILD-TYPE                                               36
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MTMR11 MUTATED                                                          0
  MTMR11 WILD-TYPE                                                       16
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MTMR11 MUTATED                                                           0
  MTMR11 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MTMR11 MUTATED                                          0
  MTMR11 WILD-TYPE                                        3
D738V8, multiclass
                                                                   clus
vv                                                                  MTMR11 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  MTMR11 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D738V9, binary
                  cls
clus                 0   1
  MTMR11 MUTATED     0   8
  MTMR11 WILD-TYPE   5 276
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MTMR11 MUTATED      0    8
  MTMR11 WILD-TYPE    5  276
     clus
vv    MTMR11 MUTATED MTMR11 WILD-TYPE
  NO               0                5
  YES              8              276
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MTMR11 MUTATED     7   0   0   1
  MTMR11 WILD-TYPE 220  10  10  23
D738V10, multiclass
    clus
vv   MTMR11 MUTATED MTMR11 WILD-TYPE
  R0              7              220
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D738V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MTMR11 MUTATED       3                         0     4
  MTMR11 WILD-TYPE    73                         4   164
D738V12, multiclass
                           clus
vv                          MTMR11 MUTATED MTMR11 WILD-TYPE
  ASIAN                                  3               73
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  4              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(739) Variable = KRT222 MUTATION ANALYSIS
D739V1, survival
                  sevent
clus2                0   1
  KRT222 MUTATED     3   1
  KRT222 WILD-TYPE 178  79
  KRT222 MUTATED KRT222 WILD-TYPE 
               4              257 
  KRT222 MUTATED KRT222 WILD-TYPE 
               1               79 
$`KRT222 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-CG-4305 TCGA-HU-A4GH 
        6.97        34.68        15.95        11.77 

$`KRT222 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       12.03         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HJ-7597 
        5.03        13.58         0.56        11.08         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
       19.36        23.84        12.30         9.67         8.88        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  KRT222 MUTATED KRT222 WILD-TYPE 
            6.97             0.00 
  KRT222 MUTATED KRT222 WILD-TYPE 
           34.68           105.07 
  KRT222 MUTATED KRT222 WILD-TYPE 
           13.86            12.62 
[1] "7.0 - 34.7 (13.9)"  "0.0 - 105.1 (12.6)"
[1] "hr=" "1.6"
D739V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KRT222 MUTATED         0        1        0        2         1         0
  KRT222 WILD-TYPE       1        8       27       24        30        44
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KRT222 MUTATED           0          1          0          0        0
  KRT222 WILD-TYPE         3         48         36         24       24
D739V3, multiclass
            clus
vv           KRT222 MUTATED KRT222 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                8
  STAGE IB                0               27
  STAGE II                2               24
  STAGE IIA               1               30
  STAGE IIB               0               44
  STAGE III               0                3
  STAGE IIIA              1               48
  STAGE IIIB              0               36
  STAGE IIIC              0               24
  STAGE IV                0               24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KRT222 MUTATED     1   2   2   0
  KRT222 WILD-TYPE  10  70 120  75
D739V4, multiclass
    clus
vv   KRT222 MUTATED KRT222 WILD-TYPE
  T1              1               10
  T2              2               70
  T3              2              120
  T4              0               75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  KRT222 MUTATED    2  3  0  0
  KRT222 WILD-TYPE 91 78 50 53
D739V5, multiclass
    clus
vv   KRT222 MUTATED KRT222 WILD-TYPE
  N0              2               91
  N1              3               78
  N2              0               50
  N3              0               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D739V6, binary
                  cls
clus                 0   1
  KRT222 MUTATED     4   0
  KRT222 WILD-TYPE 253  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KRT222 MUTATED      4    0
  KRT222 WILD-TYPE  253   18
   clus
vv  KRT222 MUTATED KRT222 WILD-TYPE
  0              4              253
  1              0               18
[1] 2 2
[1] FALSE
D739V7, binary
                  cls
clus                 0   1
  KRT222 MUTATED     1   4
  KRT222 WILD-TYPE 109 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KRT222 MUTATED      1    4
  KRT222 WILD-TYPE  109  175
        clus
vv       KRT222 MUTATED KRT222 WILD-TYPE
  FEMALE              1              109
  MALE                4              175
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KRT222 MUTATED                                       0
  KRT222 WILD-TYPE                                    50
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KRT222 MUTATED                                                        3
  KRT222 WILD-TYPE                                                    132
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KRT222 MUTATED                                                                   0
  KRT222 WILD-TYPE                                                                40
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KRT222 MUTATED                                                  1
  KRT222 WILD-TYPE                                               37
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KRT222 MUTATED                                                          1
  KRT222 WILD-TYPE                                                       15
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KRT222 MUTATED                                                           0
  KRT222 WILD-TYPE                                                         6
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KRT222 MUTATED                                          0
  KRT222 WILD-TYPE                                        3
D739V8, multiclass
                                                                   clus
vv                                                                  KRT222 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  KRT222 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D739V9, binary
                  cls
clus                 0   1
  KRT222 MUTATED     1   4
  KRT222 WILD-TYPE   4 280
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KRT222 MUTATED      1    4
  KRT222 WILD-TYPE    4  280
     clus
vv    KRT222 MUTATED KRT222 WILD-TYPE
  NO               1                4
  YES              4              280
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  KRT222 MUTATED     4   0   0   1
  KRT222 WILD-TYPE 223  10  10  23
D739V10, multiclass
    clus
vv   KRT222 MUTATED KRT222 WILD-TYPE
  R0              4              223
  R1              0               10
  R2              0               10
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D739V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRT222 MUTATED       1                         0     2
  KRT222 WILD-TYPE    75                         4   166
D739V12, multiclass
                           clus
vv                          KRT222 MUTATED KRT222 WILD-TYPE
  ASIAN                                  1               75
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  2              166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
